U.S. patent application number 16/736493 was filed with the patent office on 2020-10-29 for nucleotide cleavable linkers and uses thereof.
The applicant listed for this patent is Singular Genomics Systems, Inc.. Invention is credited to Olga Adelfinskaya, Megha Cila, Ronald Graham, Rodrigo Rodriguez.
Application Number | 20200340051 16/736493 |
Document ID | / |
Family ID | 1000004623179 |
Filed Date | 2020-10-29 |
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United States Patent
Application |
20200340051 |
Kind Code |
A1 |
Graham; Ronald ; et
al. |
October 29, 2020 |
NUCLEOTIDE CLEAVABLE LINKERS AND USES THEREOF
Abstract
Disclosed herein, inter alia, are compounds, compositions, and
methods of use thereof for sequencing a nucleic acid.
Inventors: |
Graham; Ronald; (Carlsbad,
CA) ; Adelfinskaya; Olga; (San Marcos, CA) ;
Cila; Megha; (San Diego, CA) ; Rodriguez;
Rodrigo; (San Diego, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Singular Genomics Systems, Inc. |
La Jolla |
CA |
US |
|
|
Family ID: |
1000004623179 |
Appl. No.: |
16/736493 |
Filed: |
January 7, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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62789879 |
Jan 8, 2019 |
|
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|
62841168 |
Apr 30, 2019 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2525/101 20130101;
C07H 19/14 20130101; C12Q 1/6806 20130101; C12Q 2521/101 20130101;
C07F 9/65515 20130101; C07H 19/16 20130101; C12Q 1/6869 20130101;
C07H 19/06 20130101; C12Q 2334/40 20130101; C12Q 2535/00 20130101;
C07H 19/10 20130101; C07H 19/20 20130101 |
International
Class: |
C12Q 1/6869 20060101
C12Q001/6869; C12Q 1/6806 20060101 C12Q001/6806; C07F 9/655
20060101 C07F009/655 |
Claims
1. A compound having the formula: ##STR00717## wherein, B is a
divalent nucleobase; R.sup.1 is independently a 5'-nucleoside
protecting group, monophosphate moiety, polyphosphate moiety, or
nucleic acid moiety; and R.sup.2 and R.sup.3 are independently
hydrogen, halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3,
--CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2,
--CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3,
--OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2,
--OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I,
--OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; L.sup.101,
L.sup.103, L.sup.104, and L.sup.105 are independently a bond,
--NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--,
--C(O)O--, --OC(O)--, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; R.sup.100 is
--SR.sup.102, or --CN; R.sup.102 and R.sup.102a are independently
hydrogen, halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3,
--CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2,
--CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3,
--OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2,
--OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I,
--OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; and R.sup.4 is a detectable
moiety.
2. The compound of claim 1, wherein R.sup.3 is an
--O-polymerase-compatible cleavable moiety.
3. The compound of claim 1, wherein the polymerase-compatible
cleavable moiety is independently (substituted or unsubstituted
alkylene)-SS-(unsubstituted alkyl).
4. The compound of claim 1, wherein the polymerase-compatible
cleavable moiety is independently (halo-substituted or
unsubstituted C.sub.1-C.sub.3 alkylene)-SS-(unsubstituted
C.sub.1-C.sub.4 alkyl).
5. The compound of claim 1, wherein the polymerase-compatible
cleavable moiety is independently: ##STR00718## ##STR00719##
##STR00720## ##STR00721##
6. The compound of claim 1, wherein the polymerase-compatible
cleavable moiety is independently: ##STR00722##
7. The compound of claim 1, wherein R.sup.2 is hydrogen or
--OH.
8. The compound of claim 1, wherein R.sup.1 is a monophosphate
moiety or a polyphosphate moiety.
9. The compound of claim 1, wherein R.sup.1 is a nucleic acid
moiety.
10. The compound of claim 1, wherein B is a divalent cytosine or a
derivative thereof, divalent guanine or a derivative thereof,
divalent adenine or a derivative thereof, divalent thymine or a
derivative thereof, divalent uracil or a derivative thereof,
divalent hypoxanthine or a derivative thereof, divalent xanthine or
a derivative thereof, divalent 7-methylguanine or a derivative
thereof, divalent 5,6-dihydrouracil or a derivative thereof,
divalent 5-methylcytosine or a derivative thereof, or divalent
5-hydroxymethylcytosine or a derivative thereof.
11. The compound of claim 1, wherein; L.sup.101, L.sup.103,
L.sup.104, and L.sup.105 are independently a bond, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; and R.sup.102 and R.sup.102a are independently
hydrogen or unsubstituted alkyl.
12. The compound of claim 1, wherein L.sup.101 is independently a
substituted or unsubstituted C.sub.1-C.sub.4 alkylene or
substituted or unsubstituted 8 to 20 membered heteroalkylene;
L.sup.103 is independently a bond or substituted or unsubstituted 2
to 10 membered heteroalkylene; L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; L.sup.105 is independently
bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and R.sup.102 is unsubstituted C.sub.1-C.sub.4
alkyl; and R.sup.102a is hydrogen or unsubstituted methyl.
13. The compound of claim 1, wherein L.sup.101, L.sup.103, and
L.sup.105 are independently a bond, --NH--, --O--, --C(O)--,
--C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--,
substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; L.sup.104 is unsubstituted phenylene; and R.sup.102
and R.sup.102a are independently hydrogen or unsubstituted
alkyl.
14. The compound of claim 1, wherein L.sup.101 is independently a
substituted or unsubstituted C.sub.1-C.sub.4 alkylene or
substituted or unsubstituted 8 to 20 membered heteroalkylene;
L.sup.103 is independently a bond or substituted or unsubstituted 2
to 10 membered heteroalkylene; L.sup.104 is independently an
unsubstituted phenylene; L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
R.sup.102 is unsubstituted C.sub.1-C.sub.4 alkyl; and R.sup.102a is
hydrogen or unsubstituted methyl.
15. The compound of claim 1, wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is ##STR00723## ##STR00724##
16. The compound of claim 1, wherein R.sup.4 is a fluorescent dye
moiety.
17. The compound of claim 1, having the formula: ##STR00725##
wherein R.sup.3 is an --O-polymerase-compatible cleavable
moiety.
18. A method for sequencing a nucleic acid, comprising: (i)
incorporating in series with a nucleic acid polymerase, within a
reaction vessel, one of four different compounds into a primer to
create an extension strand, wherein said primer is hybridized to
said nucleic acid and wherein each of the four different compounds
comprises a unique detectable label; (ii) detecting said unique
detectable label of each incorporated compound, so as to thereby
identify each incorporated compound in said extension strand,
thereby sequencing the nucleic acid; wherein each of said four
different compounds is independently a compound of claim 1.
19. A method of incorporating a compound into a primer, the method
comprising combining a polymerase, a primer hybridized to nucleic
acid template and the compound within a reaction vessel and
allowing said polymerase to incorporate said compound into said
primer thereby forming an extended primer, wherein said compound is
a compound of claim 1.
20. A nucleic acid polymerase complex comprising a nucleic acid
polymerase, wherein said nucleic acid polymerase is bound to a
compound of claim 1.
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application No. 62/789,879, filed Jan. 8, 2019; and U.S.
Provisional Application No. 62/841,168, filed Apr. 30, 2019; which
are incorporated herein by reference in their entirety and for all
purposes.
BACKGROUND
[0002] DNA sequencing is a fundamental tool in biological and
medical research; it is an essential technology for the paradigm of
personalized precision medicine. Among various new DNA sequencing
methods, sequencing by synthesis (SBS) is the leading method for
realizing the goal of the $1,000 genome. Accordingly, there is a
need for modified nucleotides and nucleosides that are effectively
recognized as substrates by DNA polymerases, that are efficiently
and accurately incorporated into growing DNA chains during SBS.
Disclosed herein, inter alia, are solutions to these and other
problems in the art.
BRIEF SUMMARY
[0003] In an aspect is provided a compound having the formula:
##STR00001##
[0004] B is a divalent nucleobase.
[0005] R.sup.1 is independently hydrogen, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, substituted or unsubstituted heteroaryl, a 5'-nucleoside
protecting group, monophosphate moiety or derivative thereof (e.g.,
phosphoramidate moiety, phosphorothioate moiety, phosphorodithioate
moiety, or O-methylphosphoroamidite moiety), polyphosphate moiety
or derivative thereof (e.g., including a phosphoramidate,
phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite),
or nucleic acid moiety or derivative thereof (e.g., including a
phosphoramidate, phosphorothioate, phosphorodithioate, or
O-methylphosphoroamidite).
[0006] R.sup.2 and R.sup.3 are independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety.
[0007] L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are
independently a bond, --NH--, --S--, --O--, --C(O)--, --C(O)O--,
--OC(O)--, --NHC(O)--, --C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--,
--C(S)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene; a bioconjugate linker; a cleavable
linker, a self-immolative linker, a linker capable of dendritic
amplification of signal (e.g., capable of increasing fluorescence
by releasing fluorophores from the remainder of the linker), a
trivalent linker, or a self-immolative dendrimer linker (e.g.,
capable of increasing fluorescence by releasing fluorophores from
the remainder of the linker).
[0008] R.sup.100 is --SR.sup.102 or --CN.
[0009] R.sup.102 and R.sup.102a are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0010] R.sup.4 is a detectable moiety.
[0011] In an aspect is provided a nucleic acid polymerase complex,
wherein the nucleic acid polymerase is bound (e.g., non-covalently
bound) to a compound described herein, including embodiments.
[0012] In an aspect is provided a method for sequencing a nucleic
acid, including:
[0013] incorporating in series with a nucleic acid polymerase,
within a reaction vessel, one of four different compounds into a
primer to create an extension strand, wherein the primer is
hybridized to the nucleic acid and wherein each of the four
different compounds includes a unique detectable label; detecting
the unique detectable label of each incorporated compound, so as to
thereby identify each incorporated compound in the extension
strand, thereby sequencing the nucleic acid; wherein each of the
four different compounds is independently a compound described
herein.
[0014] In an aspect is provided a method for sequencing a nucleic
acid, including: incorporating in series with a nucleic acid
polymerase, within a reaction vessel, a compound into a primer to
create an extension strand, wherein the primer is hybridized to the
nucleic acid and wherein the compound includes a detectable label;
detecting the detectable label of the incorporated compound, so as
to thereby identify the incorporated compound in the extension
strand, thereby sequencing the nucleic acid; wherein the compound
is independently a compound described herein.
[0015] In an aspect is provided a method of incorporating a
compound into a primer, the method including combining a
polymerase, a primer hybridized to nucleic acid template and the
compound within a reaction vessel and allowing the polymerase to
incorporate the compound into the primer thereby forming an
extended primer, wherein the compound is a compound described
herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIG. 1. Structures and LCMS data for compounds containing a
thio-trigger containing linker.
[0017] FIG. 2. An illustration of a cleavable fluorescent
nucleotide reversible terminator (NRT) that contains a reversible
terminator moiety on the 3' oxygen and a dye attached to the base
via a linker, wherein the linker includes a trigger moiety (e.g., a
thio-trigger moiety, as described herein). In the presence of an
appropriate reducing agent (e.g., di-mercaptopropanesulfonate,
di-mercaptopropanephosphonate, di-mercaptopropanol, cysteine,
cysteamine, dithio-succinic acid, dithiothreitol (DTT),
dithiobutylamine,
meso-2,5-dimercapto-N,N,N',N'-tetramethyladipamide (DTA),
Bis(2-mercaptoethyl)sulfone (BMS), and N,N'-dimethyl, or
N,N'-bis(mercaptoacetyl)-hydrazine (DMH)) and suitable reaction
conditions (e.g., elevated pH and/or elevated temperature) the
trigger moiety breaks the linker (represented as the crack
illustration in FIG. 2), thus separating the dye from the
nucleotide. Though not shown in FIG. 2, the reducing agent may also
remove the reversible terminator simultaneously.
DETAILED DESCRIPTION
I. Definitions
[0018] The abbreviations used herein have their conventional
meaning within the chemical and biological arts. The chemical
structures and formulae set forth herein are constructed according
to the standard rules of chemical valency known in the chemical
arts.
[0019] Where substituent groups are specified by their conventional
chemical formulae, written from left to right, they equally
encompass the chemically identical substituents that would result
from writing the structure from right to left, e.g., --CH.sub.2O--
is equivalent to --OCH.sub.2--.
[0020] The term "alkyl," by itself or as part of another
substituent, means, unless otherwise stated, a straight (i.e.,
unbranched) or branched carbon chain (or carbon), or combination
thereof, which may be fully saturated, mono- or polyunsaturated and
can include mono-, di- and multivalent radicals. The alkyl may
include a designated number of carbons (e.g., C.sub.1-C.sub.10
means one to ten carbons). Alkyl is an uncyclized chain. Examples
of saturated hydrocarbon radicals include, but are not limited to,
groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl,
t-butyl, isobutyl, sec-butyl, methyl, homologs and isomers of, for
example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. An
unsaturated alkyl group is one having one or more double bonds or
triple bonds. Examples of unsaturated alkyl groups include, but are
not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl,
2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1-
and 3-propynyl, 3-butynyl, and the higher homologs and isomers. An
alkoxy is an alkyl attached to the remainder of the molecule via an
oxygen linker (--O--). An alkyl moiety may be an alkenyl moiety. An
alkyl moiety may be an alkynyl moiety. An alkyl moiety may be fully
saturated. An alkenyl may include more than one double bond and/or
one or more triple bonds in addition to the one or more double
bonds. An alkynyl may include more than one triple bond and/or one
or more double bonds in addition to the one or more triple
bonds.
[0021] The term "alkylene," by itself or as part of another
substituent, means, unless otherwise stated, a divalent radical
derived from an alkyl, as exemplified, but not limited by,
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2--. Typically, an alkyl (or
alkylene) group will have from 1 to 24 carbon atoms, with those
groups having 10 or fewer carbon atoms being preferred herein. A
"lower alkyl" or "lower alkylene" is a shorter chain alkyl or
alkylene group, generally having eight or fewer carbon atoms. The
term "alkenylene," by itself or as part of another substituent,
means, unless otherwise stated, a divalent radical derived from an
alkene.
[0022] The term "heteroalkyl," by itself or in combination with
another term, means, unless otherwise stated, a stable straight or
branched chain, or combinations thereof, including at least one
carbon atom and at least one heteroatom (e.g., O, N, P, Si, and S),
and wherein the nitrogen and sulfur atoms may optionally be
oxidized, and the nitrogen heteroatom may optionally be
quaternized. The heteroatom(s) (e.g., N, S, Si, or P) may be placed
at any interior position of the heteroalkyl group or at the
position at which the alkyl group is attached to the remainder of
the molecule. Heteroalkyl is an uncyclized chain. Examples include,
but are not limited to: --CH.sub.2--CH.sub.2--O--CH.sub.3,
--CH.sub.2--CH.sub.2--NH--CH.sub.3,
--CH.sub.2--CH.sub.2--N(CH.sub.3)--CH.sub.3,
--CH.sub.2--S--CH.sub.2--CH.sub.3, --CH.sub.2--S--CH.sub.2,
--S(O)--CH.sub.3, --CH.sub.2--CH.sub.2--S(O).sub.2--CH.sub.3,
--CH.dbd.CH--O--CH.sub.3, --Si(CH.sub.3).sub.3,
--CH.sub.2--CH.dbd.N--OCH.sub.3,
--CH.dbd.CH--N(CH.sub.3)--CH.sub.3, --O--CH.sub.3,
--O--CH.sub.2--CH.sub.3, and --CN. Up to two or three heteroatoms
may be consecutive, such as, for example, --CH.sub.2--NH--OCH.sub.3
and --CH.sub.2--O--Si(CH.sub.3).sub.3. A heteroalkyl moiety may
include one heteroatom (e.g., O, N, S, Si, or P). A heteroalkyl
moiety may include two optionally different heteroatoms (e.g., O,
N, S, Si, or P). A heteroalkyl moiety may include three optionally
different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl
moiety may include four optionally different heteroatoms (e.g., O,
N, S, Si, or P). A heteroalkyl moiety may include five optionally
different heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl
moiety may include up to 8 optionally different heteroatoms (e.g.,
O, N, S, Si, or P). The term "heteroalkenyl," by itself or in
combination with another term, means, unless otherwise stated, a
heteroalkyl including at least one double bond. A heteroalkenyl may
optionally include more than one double bond and/or one or more
triple bonds in additional to the one or more double bonds. The
term "heteroalkynyl," by itself or in combination with another
term, means, unless otherwise stated, a heteroalkyl including at
least one triple bond. A heteroalkynyl may optionally include more
than one triple bond and/or one or more double bonds in additional
to the one or more triple bonds.
[0023] Similarly, the term "heteroalkylene," by itself or as part
of another substituent, means, unless otherwise stated, a divalent
radical derived from heteroalkyl, as exemplified, but not limited
by, --CH.sub.2--CH.sub.2--S--CH.sub.2--CH.sub.2-- and
--CH.sub.2--S--CH.sub.2--CH.sub.2--NH--CH.sub.2--. For
heteroalkylene groups, heteroatoms can also occupy either or both
of the chain termini (e.g., alkyleneoxy, alkylenedioxy,
alkyleneamino, alkylenediamino, and the like). Still further, for
alkylene and heteroalkylene linking groups, no orientation of the
linking group is implied by the direction in which the formula of
the linking group is written. For example, the formula
--C(O).sub.2R'-- represents both --C(O).sub.2R'-- and
--R'C(O).sub.2--. As described above, heteroalkyl groups, as used
herein, include those groups that are attached to the remainder of
the molecule through a heteroatom, such as --C(O)R', --C(O)NR',
--NR'R'', --OR', --SR', and/or --SO.sub.2R'. Where "heteroalkyl" is
recited, followed by recitations of specific heteroalkyl groups,
such as --NR'R'' or the like, it will be understood that the terms
heteroalkyl and --NR'R'' are not redundant or mutually exclusive.
Rather, the specific heteroalkyl groups are recited to add clarity.
Thus, the term "heteroalkyl" should not be interpreted herein as
excluding specific heteroalkyl groups, such as --NR'R'' or the
like.
[0024] The terms "cycloalkyl" and "heterocycloalkyl," by themselves
or in combination with other terms, mean, unless otherwise stated,
cyclic versions of "alkyl" and "heteroalkyl," respectively.
Cycloalkyl and heterocycloalkyl are not aromatic. Additionally, for
heterocycloalkyl, a heteroatom can occupy the position at which the
heterocycle is attached to the remainder of the molecule. Examples
of cycloalkyl include, but are not limited to, cyclopropyl,
cyclobutyl, cyclopentyl, cyclohexyl, 1-cyclohexenyl,
3-cyclohexenyl, cycloheptyl, and the like. Examples of
heterocycloalkyl include, but are not limited to,
1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl,
3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,
tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl,
1-piperazinyl, 2-piperazinyl, and the like. A "cycloalkylene" and a
"heterocycloalkylene," alone or as part of another substituent,
means a divalent radical derived from a cycloalkyl and
heterocycloalkyl, respectively.
[0025] In embodiments, the term "cycloalkyl" means a monocyclic,
bicyclic, or a multicyclic cycloalkyl ring system. In embodiments,
monocyclic ring systems are cyclic hydrocarbon groups containing
from 3 to 8 carbon atoms, where such groups can be saturated or
unsaturated, but not aromatic. In embodiments, cycloalkyl groups
are fully saturated. Examples of monocyclic cycloalkyls include
cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl,
cyclohexenyl, cycloheptyl, and cyclooctyl. Bicyclic cycloalkyl ring
systems are bridged monocyclic rings or fused bicyclic rings. In
embodiments, bridged monocyclic rings contain a monocyclic
cycloalkyl ring where two non adjacent carbon atoms of the
monocyclic ring are linked by an alkylene bridge of between one and
three additional carbon atoms (i.e., a bridging group of the form
(CH.sub.2).sub.w, where w is 1, 2, or 3). Representative examples
of bicyclic ring systems include, but are not limited to,
bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane,
bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and
bicyclo[4.2.1]nonane. In embodiments, fused bicyclic cycloalkyl
ring systems contain a monocyclic cycloalkyl ring fused to either a
phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a
monocyclic heterocyclyl, or a monocyclic heteroaryl. In
embodiments, the bridged or fused bicyclic cycloalkyl is attached
to the parent molecular moiety through any carbon atom contained
within the monocyclic cycloalkyl ring. In embodiments, cycloalkyl
groups are optionally substituted with one or two groups which are
independently oxo or thia. In embodiments, the fused bicyclic
cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to
either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5
or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic
heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein
the fused bicyclic cycloalkyl is optionally substituted by one or
two groups which are independently oxo or thia. In embodiments,
multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl
ring (base ring) fused to either (i) one ring system selected from
the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a
bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic
heterocyclyl; or (ii) two other ring systems independently selected
from the group consisting of a phenyl, a bicyclic aryl, a
monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic
cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic
or bicyclic heterocyclyl. In embodiments, the multicyclic
cycloalkyl is attached to the parent molecular moiety through any
carbon atom contained within the base ring. In embodiments,
multicyclic cycloalkyl ring systems are a monocyclic cycloalkyl
ring (base ring) fused to either (i) one ring system selected from
the group consisting of a bicyclic aryl, a bicyclic heteroaryl, a
bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic
heterocyclyl; or (ii) two other ring systems independently selected
from the group consisting of a phenyl, a monocyclic heteroaryl, a
monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic
heterocyclyl. Examples of multicyclic cycloalkyl groups include,
but are not limited to tetradecahydrophenanthrenyl,
perhydrophenothiazin-1-yl, and perhydrophenoxazin-1-yl.
[0026] In embodiments, a cycloalkyl is a cycloalkenyl. The term
"cycloalkenyl" is used in accordance with its plain ordinary
meaning. In embodiments, a cycloalkenyl is a monocyclic, bicyclic,
or a multicyclic cycloalkenyl ring system. In embodiments,
monocyclic cycloalkenyl ring systems are cyclic hydrocarbon groups
containing from 3 to 8 carbon atoms, where such groups are
unsaturated (i.e., containing at least one annular carbon carbon
double bond), but not aromatic. Examples of monocyclic cycloalkenyl
ring systems include cyclopentenyl and cyclohexenyl. In
embodiments, bicyclic cycloalkenyl rings are bridged monocyclic
rings or a fused bicyclic rings. In embodiments, bridged monocyclic
rings contain a monocyclic cycloalkenyl ring where two non adjacent
carbon atoms of the monocyclic ring are linked by an alkylene
bridge of between one and three additional carbon atoms (i.e., a
bridging group of the form (CH.sub.2).sub.w, where w is 1, 2, or
3). Representative examples of bicyclic cycloalkenyls include, but
are not limited to, norbornenyl and bicyclo[2.2.2]oct 2 enyl. In
embodiments, fused bicyclic cycloalkenyl ring systems contain a
monocyclic cycloalkenyl ring fused to either a phenyl, a monocyclic
cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl,
or a monocyclic heteroaryl. In embodiments, the bridged or fused
bicyclic cycloalkenyl is attached to the parent molecular moiety
through any carbon atom contained within the monocyclic
cycloalkenyl ring. In embodiments, cycloalkenyl groups are
optionally substituted with one or two groups which are
independently oxo or thia. In embodiments, multicyclic cycloalkenyl
rings contain a monocyclic cycloalkenyl ring (base ring) fused to
either (i) one ring system selected from the group consisting of a
bicyclic aryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a
bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two
ring systems independently selected from the group consisting of a
phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, a
monocyclic or bicyclic cycloalkyl, a monocyclic or bicyclic
cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. In
embodiments, the multicyclic cycloalkenyl is attached to the parent
molecular moiety through any carbon atom contained within the base
ring. In embodiments, multicyclic cycloalkenyl rings contain a
monocyclic cycloalkenyl ring (base ring) fused to either (i) one
ring system selected from the group consisting of a bicyclic aryl,
a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicyclic
cycloalkenyl, and a bicyclic heterocyclyl; or (ii) two ring systems
independently selected from the group consisting of a phenyl, a
monocyclic heteroaryl, a monocyclic cycloalkyl, a monocyclic
cycloalkenyl, and a monocyclic heterocyclyl.
[0027] In embodiments, a heterocycloalkyl is a heterocyclyl. The
term "heterocyclyl" as used herein, means a monocyclic, bicyclic,
or multicyclic heterocycle. The heterocyclyl monocyclic heterocycle
is a 3, 4, 5, 6 or 7 membered ring containing at least one
heteroatom independently selected from the group consisting of O,
N, and S where the ring is saturated or unsaturated, but not
aromatic. The 3 or 4 membered ring contains 1 heteroatom selected
from the group consisting of O, N and S. The 5 membered ring can
contain zero or one double bond and one, two or three heteroatoms
selected from the group consisting of O, N and S. The 6 or 7
membered ring contains zero, one or two double bonds and one, two
or three heteroatoms selected from the group consisting of O, N and
S. The heterocyclyl monocyclic heterocycle is connected to the
parent molecular moiety through any carbon atom or any nitrogen
atom contained within the heterocyclyl monocyclic heterocycle.
Representative examples of heterocyclyl monocyclic heterocycles
include, but are not limited to, azetidinyl, azepanyl, aziridinyl,
diazepanyl, 1,3-dioxanyl, 1,3-dioxolanyl, 1,3-dithiolanyl,
1,3-dithianyl, imidazolinyl, imidazolidinyl, isothiazolinyl,
isothiazolidinyl, isoxazolinyl, isoxazolidinyl, morpholinyl,
oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl,
piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl,
pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl,
thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl,
thiomorpholinyl, 1,1-dioxidothiomorpholinyl (thiomorpholine
sulfone), thiopyranyl, and trithianyl. The heterocyclyl bicyclic
heterocycle is a monocyclic heterocycle fused to either a phenyl, a
monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic
heterocycle, or a monocyclic heteroaryl. The heterocyclyl bicyclic
heterocycle is connected to the parent molecular moiety through any
carbon atom or any nitrogen atom contained within the monocyclic
heterocycle portion of the bicyclic ring system. Representative
examples of bicyclic heterocyclyls include, but are not limited to,
2,3-dihydrobenzofuran-2-yl, 2,3-dihydrobenzofuran-3-yl,
indolin-1-yl, indolin-2-yl, indolin-3-yl,
2,3-dihydrobenzothien-2-yl, decahydroquinolinyl,
decahydroisoquinolinyl, octahydro-1H-indolyl, and
octahydrobenzofuranyl. In embodiments, heterocyclyl groups are
optionally substituted with one or two groups which are
independently oxo or thia. In certain embodiments, the bicyclic
heterocyclyl is a 5 or 6 membered monocyclic heterocyclyl ring
fused to a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a
5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered
monocyclic heterocyclyl, or a 5 or 6 membered monocyclic
heteroaryl, wherein the bicyclic heterocyclyl is optionally
substituted by one or two groups which are independently oxo or
thia. Multicyclic heterocyclyl ring systems are a monocyclic
heterocyclyl ring (base ring) fused to either (i) one ring system
selected from the group consisting of a bicyclic aryl, a bicyclic
heteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a
bicyclic heterocyclyl; or (ii) two other ring systems independently
selected from the group consisting of a phenyl, a bicyclic aryl, a
monocyclic or bicyclic heteroaryl, a monocyclic or bicyclic
cycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic
or bicyclic heterocyclyl. The multicyclic heterocyclyl is attached
to the parent molecular moiety through any carbon atom or nitrogen
atom contained within the base ring. In embodiments, multicyclic
heterocyclyl ring systems are a monocyclic heterocyclyl ring (base
ring) fused to either (i) one ring system selected from the group
consisting of a bicyclic aryl, a bicyclic heteroaryl, a bicyclic
cycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl;
or (ii) two other ring systems independently selected from the
group consisting of a phenyl, a monocyclic heteroaryl, a monocyclic
cycloalkyl, a monocyclic cycloalkenyl, and a monocyclic
heterocyclyl. Examples of multicyclic heterocyclyl groups include,
but are not limited to 10H-phenothiazin-10-yl,
9,10-dihydroacridin-9-yl, 9,10-dihydroacridin-10-yl,
10H-phenoxazin-10-yl, 10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl,
1,2,3,4-tetrahydropyrido[4,3-g]isoquinolin-2-yl,
12H-benzo[b]phenoxazin-12-yl, and dodecahydro-1H-carbazol-9-yl.
[0028] The terms "halo" or "halogen," by themselves or as part of
another substituent, mean, unless otherwise stated, a fluorine,
chlorine, bromine, or iodine atom. Additionally, terms such as
"haloalkyl" are meant to include monohaloalkyl and polyhaloalkyl.
For example, the term "halo(C.sub.1-C.sub.4)alkyl" includes, but is
not limited to, fluoromethyl, difluoromethyl, trifluoromethyl,
2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the
like.
[0029] The term "acyl" means, unless otherwise stated, --C(O)R
where R is a substituted or unsubstituted alkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0030] The term "aryl" means, unless otherwise stated, a
polyunsaturated, aromatic, hydrocarbon substituent, which can be a
single ring or multiple rings (preferably from 1 to 3 rings) that
are fused together (i.e., a fused ring aryl) or linked covalently.
A fused ring aryl refers to multiple rings fused together wherein
at least one of the fused rings is an aryl ring. The term
"heteroaryl" refers to aryl groups (or rings) that contain at least
one heteroatom such as N, O, or S, wherein the nitrogen and sulfur
atoms are optionally oxidized, and the nitrogen atom(s) are
optionally quaternized. Thus, the term "heteroaryl" includes fused
ring heteroaryl groups (i.e., multiple rings fused together wherein
at least one of the fused rings is a heteroaromatic ring). A
5,6-fused ring heteroarylene refers to two rings fused together,
wherein one ring has 5 members and the other ring has 6 members,
and wherein at least one ring is a heteroaryl ring. Likewise, a
6,6-fused ring heteroarylene refers to two rings fused together,
wherein one ring has 6 members and the other ring has 6 members,
and wherein at least one ring is a heteroaryl ring. And a 6,5-fused
ring heteroarylene refers to two rings fused together, wherein one
ring has 6 members and the other ring has 5 members, and wherein at
least one ring is a heteroaryl ring. A heteroaryl group can be
attached to the remainder of the molecule through a carbon or
heteroatom. Non-limiting examples of aryl and heteroaryl groups
include phenyl, naphthyl, pyrrolyl, pyrazolyl, pyridazinyl,
triazinyl, pyrimidinyl, imidazolyl, pyrazinyl, purinyl, oxazolyl,
isoxazolyl, thiazolyl, furyl, thienyl, pyridyl, pyrimidyl,
benzothiazolyl, benzoxazoyl benzimidazolyl, benzofuran,
isobenzofuranyl, indolyl, isoindolyl, benzothiophenyl, isoquinolyl,
quinoxalinyl, quinolyl, 1-naphthyl, 2-naphthyl, 4-biphenyl,
1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl,
4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl,
2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl,
5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl,
3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl,
2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl,
2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl,
2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl.
Substituents for each of the above noted aryl and heteroaryl ring
systems are selected from the group of acceptable substituents
described below. An "arylene" and a "heteroarylene," alone or as
part of another substituent, mean a divalent radical derived from
an aryl and heteroaryl, respectively. A heteroaryl group
substituent may be --O-- bonded to a ring heteroatom nitrogen.
[0031] Spirocyclic rings are two or more rings wherein adjacent
rings are attached through a single atom. The individual rings
within spirocyclic rings may be identical or different. Individual
rings in spirocyclic rings may be substituted or unsubstituted and
may have different substituents from other individual rings within
a set of spirocyclic rings. Possible substituents for individual
rings within spirocyclic rings are the possible substituents for
the same ring when not part of spirocyclic rings (e.g.,
substituents for cycloalkyl or heterocycloalkyl rings). Spirocylic
rings may be substituted or unsubstituted cycloalkyl, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted
heterocycloalkylene and individual rings within a spirocyclic ring
group may be any of the immediately previous list, including having
all rings of one type (e.g., all rings being substituted
heterocycloalkylene wherein each ring may be the same or different
substituted heterocycloalkylene). When referring to a spirocyclic
ring system, heterocyclic spirocyclic rings means a spirocyclic
rings wherein at least one ring is a heterocyclic ring and wherein
each ring may be a different ring. When referring to a spirocyclic
ring system, substituted spirocyclic rings means that at least one
ring is substituted and each substituent may optionally be
different.
[0032] The symbol "" denotes the point of attachment of a chemical
moiety to the remainder of a molecule or chemical formula.
[0033] The term "oxo," as used herein, means an oxygen that is
double bonded to a carbon atom.
[0034] The term "alkylarylene" as an arylene moiety covalently
bonded to an alkylene moiety (also referred to herein as an
alkylene linker). In embodiments, the alkylarylene group has the
formula:
##STR00002##
[0035] An alkylarylene moiety may be substituted (e.g., with a
substituent group) on the alkylene moiety or the arylene linker
(e.g., at carbons 2, 3, 4, or 6) with halogen, oxo, --N.sub.3,
--CF.sub.3, --CCl.sub.3, --CBr.sub.3, --CI.sub.3, --CN, --CHO,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2CH.sub.3, --SO.sub.3H, --OSO.sub.3H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, substituted or
unsubstituted C.sub.1-C.sub.5 alkyl or substituted or unsubstituted
2 to 5 membered heteroalkyl). In embodiments, the alkylarylene is
unsubstituted.
[0036] Each of the above terms (e.g., "alkyl," "heteroalkyl,"
"cycloalkyl," "heterocycloalkyl," "aryl," and "heteroaryl")
includes both substituted and unsubstituted forms of the indicated
radical. Preferred substituents for each type of radical are
provided below.
[0037] Substituents for the alkyl and heteroalkyl radicals
(including those groups often referred to as alkylene, alkenyl,
heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl,
heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one
or more of a variety of groups selected from, but not limited to,
--OR', .dbd.O, .dbd.NR', .dbd.N--OR', --NR'R'', --SR', halogen,
--SiR'R''R''', --OC(O)R', --C(O)R', --CO.sub.2R', --CONR'R'',
--OC(O)NR'R'', --NR''C(O)R', --NR'--OC(O)NR''R''',
--NR''C(O).sub.2R', --NR--C(NR'R''R''').dbd.NR'''',
--NR--C(NR'R'').dbd.NR''', --S(O)R', --S(O).sub.2R',
--S(O).sub.2NR'R'', --NRSO.sub.2R', --NR'NR''R''', --ONR'R'',
--NR'C(O)NR''NR'''R'''', --CN, --NO.sub.2, --NR'SO.sub.2R'',
--NR'C(O)R'', --NR'C(O)--OR'', --NR'OR'', in a number ranging from
zero to (2m'+1), where m' is the total number of carbon atoms in
such radical. R, R', R'', R''', and R'''' each preferably
independently refer to hydrogen, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl (e.g., aryl substituted with 1-3 halogens), substituted or
unsubstituted heteroaryl, substituted or unsubstituted alkyl,
alkoxy, or thioalkoxy groups, or arylalkyl groups. When a compound
described herein includes more than one R group, for example, each
of the R groups is independently selected as are each R', R'',
R''', and R'''' group when more than one of these groups is
present. When R' and R'' are attached to the same nitrogen atom,
they can be combined with the nitrogen atom to form a 4-, 5-, 6-,
or 7-membered ring. For example, --NR'R'' includes, but is not
limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above
discussion of substituents, one of skill in the art will understand
that the term "alkyl" is meant to include groups including carbon
atoms bound to groups other than hydrogen groups, such as haloalkyl
(e.g., --CF.sub.3 and --CH.sub.2CF.sub.3) and acyl (e.g.,
--C(O)CH.sub.3, --C(O)CF.sub.3, --C(O)CH.sub.2OCH.sub.3, and the
like).
[0038] Similar to the substituents described for the alkyl radical,
substituents for the aryl and heteroaryl groups are varied and are
selected from, for example: --OR', --NR'R'', --SR', halogen,
--SiR'R''R''', --OC(O)R', --C(O)R', --CO.sub.2R', --CONR'R'',
--OC(O)NR'R'', --NR''C(O)R', --NR'--C(O)NR''R''',
--NR''C(O).sub.2R', --NR--C(NR'R''R''').dbd.NR'''',
--NR--C(NR'R'').dbd.NR''', --S(O)R', --S(O).sub.2R',
--S(O).sub.2NR'R'', --NRSO.sub.2R', --NR'NR''R''', --ONR'R'',
--NR'C(O)NR''NR'''R'''', --CN, --NO.sub.2, --R', --N.sub.3,
--CH(Ph).sub.2, fluoro(C.sub.1-C.sub.4)alkoxy, and
fluoro(C.sub.1-C.sub.4)alkyl, --NR'SO.sub.2R'', --NR'C(O)R'',
--NR'C(O)--OR'', --NR'OR'', in a number ranging from zero to the
total number of open valences on the aromatic ring system; and
where R', R'', R''', and R'''' are preferably independently
selected from hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, and
substituted or unsubstituted heteroaryl. When a compound described
herein includes more than one R group, for example, each of the R
groups is independently selected as are each R', R'', R''', and
R'''' groups when more than one of these groups is present.
[0039] Substituents for rings (e.g., cycloalkyl, heterocycloalkyl,
aryl, heteroaryl, cycloalkylene, heterocycloalkylene, arylene, or
heteroarylene) may be depicted as substituents on the ring rather
than on a specific atom of a ring (commonly referred to as a
floating substituent). In such a case, the substituent may be
attached to any of the ring atoms (obeying the rules of chemical
valency) and in the case of fused rings or spirocyclic rings, a
substituent depicted as associated with one member of the fused
rings or spirocyclic rings (a floating substituent on a single
ring), may be a substituent on any of the fused rings or
spirocyclic rings (a floating substituent on multiple rings). When
a substituent is attached to a ring, but not a specific atom (a
floating substituent), and a subscript for the substituent is an
integer greater than one, the multiple substituents may be on the
same atom, same ring, different atoms, different fused rings,
different spirocyclic rings, and each substituent may optionally be
different. Where a point of attachment of a ring to the remainder
of a molecule is not limited to a single atom (a floating
substituent), the attachment point may be any atom of the ring and
in the case of a fused ring or spirocyclic ring, any atom of any of
the fused rings or spirocyclic rings while obeying the rules of
chemical valency. Where a ring, fused rings, or spirocyclic rings
contain one or more ring heteroatoms and the ring, fused rings, or
spirocyclic rings are shown with one more floating substituents
(including, but not limited to, points of attachment to the
remainder of the molecule), the floating substituents may be bonded
to the heteroatoms. Where the ring heteroatoms are shown bound to
one or more hydrogens (e.g., a ring nitrogen with two bonds to ring
atoms and a third bond to a hydrogen) in the structure or formula
with the floating substituent, when the heteroatom is bonded to the
floating substituent, the substituent will be understood to replace
the hydrogen, while obeying the rules of chemical valency.
[0040] Two or more substituents may optionally be joined to form
aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such
so-called ring-forming substituents are typically, though not
necessarily, found attached to a cyclic base structure. In one
embodiment, the ring-forming substituents are attached to adjacent
members of the base structure. For example, two ring-forming
substituents attached to adjacent members of a cyclic base
structure create a fused ring structure. In another embodiment, the
ring-forming substituents are attached to a single member of the
base structure. For example, two ring-forming substituents attached
to a single member of a cyclic base structure create a spirocyclic
structure. In yet another embodiment, the ring-forming substituents
are attached to non-adjacent members of the base structure.
[0041] Two of the substituents on adjacent atoms of the aryl or
heteroaryl ring may optionally form a ring of the formula
-T-C(O)--(CRR').sub.q--U--, wherein T and U are independently
--NR--, --O--, --CRR'--, or a single bond, and q is an integer of
from 0 to 3. Alternatively, two of the substituents on adjacent
atoms of the aryl or heteroaryl ring may optionally be replaced
with a substituent of the formula -A-(CH.sub.2).sub.r--B--, wherein
A and B are independently --CRR'--, --O--, --NR--, --S--, --S(O)--,
--S(O).sub.2--, --S(O).sub.2NR'--, or a single bond, and r is an
integer of from 1 to 4. One of the single bonds of the new ring so
formed may optionally be replaced with a double bond.
Alternatively, two of the substituents on adjacent atoms of the
aryl or heteroaryl ring may optionally be replaced with a
substituent of the formula --(CRR').sub.s--X'--(C''R''R''').sub.d,
where s and d are independently integers of from 0 to 3, and X' is
--O--, --NR'--, --S--, --S(O)--, --S(O).sub.2--, or
--S(O).sub.2NR'--. The substituents R, R', R'', and R''' are
preferably independently selected from hydrogen, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
and substituted or unsubstituted heteroaryl.
[0042] As used herein, the terms "heteroatom" or "ring heteroatom"
are meant to include oxygen (O), nitrogen (N), sulfur (S),
phosphorus (P), and silicon (Si).
[0043] A "substituent group," as used herein, means a group
selected from the following moieties: [0044] (A) oxo, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4 alkyl), unsubstituted
heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered
heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted
cycloalkyl (e.g., C.sub.3-C.sub.8 cycloalkyl, C.sub.3-C.sub.6
cycloalkyl, or C.sub.5-C.sub.6 cycloalkyl), unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6
membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl),
unsubstituted aryl (e.g., C.sub.6-C.sub.10 aryl, C.sub.10 aryl, or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered
heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered
heteroaryl), and [0045] (B) alkyl (e.g., C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4 alkyl), heteroalkyl
(e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or
2 to 4 membered heteroalkyl), cycloalkyl (e.g., C.sub.3-C.sub.8
cycloalkyl, C.sub.3-C.sub.6 cycloalkyl, or C.sub.5-C.sub.6
cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered
heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6
membered heterocycloalkyl), aryl (e.g., C.sub.6-C.sub.10 aryl,
C.sub.10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered
heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered
heteroaryl), substituted with at least one substituent selected
from: [0046] (i) oxo, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2 , --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, unsubstituted alkyl (e.g.,
C.sub.1-C.sub.8 alkyl, C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4
alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered
heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered
heteroalkyl), unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8
cycloalkyl, C.sub.3-C.sub.6 cycloalkyl, or C.sub.5-C.sub.6
cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered
heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6
membered heterocycloalkyl), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10 aryl, C.sub.10 aryl, or phenyl), or unsubstituted
heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered
heteroaryl, or 5 to 6 membered heteroaryl), and [0047] (ii) alkyl
(e.g., C.sub.1-C.sub.8 alkyl, C.sub.1-C.sub.6 alkyl, or
C.sub.1-C.sub.4 alkyl), heteroalkyl (e.g., 2 to 8 membered
heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered
heteroalkyl), cycloalkyl (e.g., C.sub.3-C.sub.8 cycloalkyl,
C.sub.3-C.sub.6 cycloalkyl, or C.sub.5-C.sub.6 cycloalkyl),
heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6
membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl),
aryl (e.g., C.sub.6-C.sub.10 aryl, C.sub.10 aryl, or phenyl),
heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered
heteroaryl, or 5 to 6 membered heteroaryl), substituted with at
least one substituent selected from: [0048] (a) oxo, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4 alkyl), unsubstituted
heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered
heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted
cycloalkyl (e.g., C.sub.3-C.sub.8 cycloalkyl, C.sub.3-C.sub.6
cycloalkyl, or C.sub.5-C.sub.6 cycloalkyl), unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6
membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl),
unsubstituted aryl (e.g., C.sub.6-C.sub.10 aryl, C.sub.10 aryl, or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered
heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered
heteroaryl), and [0049] (b) alkyl (e.g., C.sub.1-C.sub.8 alkyl,
C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4 alkyl), heteroalkyl
(e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or
2 to 4 membered heteroalkyl), cycloalkyl (e.g., C.sub.3-C.sub.8
cycloalkyl, C.sub.3-C.sub.6 cycloalkyl, or C.sub.5-C.sub.6
cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered
heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6
membered heterocycloalkyl), aryl (e.g., C.sub.6-C.sub.10 aryl,
C.sub.10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered
heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered
heteroaryl), substituted with at least one substituent selected
from: oxo, halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3,
--CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, CHF.sub.2, --CHI.sub.2,
--CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3,
--OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2,
--OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I,
--OCH.sub.2F, --N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.8
alkyl, C.sub.1-C.sub.6 alkyl, or C.sub.1-C.sub.4 alkyl),
unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to
6 membered heteroalkyl, or 2 to 4 membered heteroalkyl),
unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8 cycloalkyl,
C.sub.3-C.sub.6 cycloalkyl, or C.sub.5-C.sub.6 cycloalkyl),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered
heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6
membered heterocycloalkyl), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10 aryl, C.sub.10 aryl, or phenyl), or unsubstituted
heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered
heteroaryl, or 5 to 6 membered heteroaryl).
[0050] A "size-limited substituent" or " size-limited substituent
group," as used herein, means a group selected from all of the
substituents described above for a "substituent group," wherein
each substituted or unsubstituted alkyl is a substituted or
unsubstituted C.sub.1-C.sub.20 alkyl, each substituted or
unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20
membered heteroalkyl, each substituted or unsubstituted cycloalkyl
is a substituted or unsubstituted C.sub.3-C.sub.8 cycloalkyl, each
substituted or unsubstituted heterocycloalkyl is a substituted or
unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or
unsubstituted aryl is a substituted or unsubstituted
C.sub.6-C.sub.10 aryl, and each substituted or unsubstituted
heteroaryl is a substituted or unsubstituted 5 to 10 membered
heteroaryl.
[0051] A "lower substituent" or "lower substituent group," as used
herein, means a group selected from all of the substituents
described above for a "substituent group," wherein each substituted
or unsubstituted alkyl is a substituted or unsubstituted
C.sub.1-C.sub.8 alkyl, each substituted or unsubstituted
heteroalkyl is a substituted or unsubstituted 2 to 8 membered
heteroalkyl, each substituted or unsubstituted cycloalkyl is a
substituted or unsubstituted C.sub.3-C.sub.7 cycloalkyl, each
substituted or unsubstituted heterocycloalkyl is a substituted or
unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or
unsubstituted aryl is a substituted or unsubstituted phenyl, and
each substituted or unsubstituted heteroaryl is a substituted or
unsubstituted 5 to 6 membered heteroaryl.
[0052] In some embodiments, each substituted group described in the
compounds herein is substituted with at least one substituent
group. More specifically, in some embodiments, each substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene described in the
compounds herein are substituted with at least one substituent
group. In other embodiments, at least one or all of these groups
are substituted with at least one size-limited substituent group.
In other embodiments, at least one or all of these groups are
substituted with at least one lower substituent group.
[0053] In other embodiments of the compounds herein, each
substituted or unsubstituted alkyl may be a substituted or
unsubstituted C.sub.1-C.sub.20 alkyl, each substituted or
unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20
membered heteroalkyl, each substituted or unsubstituted cycloalkyl
is a substituted or unsubstituted C.sub.3-C.sub.8 cycloalkyl, each
substituted or unsubstituted heterocycloalkyl is a substituted or
unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or
unsubstituted aryl is a substituted or unsubstituted
C.sub.6-C.sub.10 aryl, and/or each substituted or unsubstituted
heteroaryl is a substituted or unsubstituted 5 to 10 membered
heteroaryl. In some embodiments of the compounds herein, each
substituted or unsubstituted alkylene is a substituted or
unsubstituted C.sub.1-C.sub.20 alkylene, each substituted or
unsubstituted heteroalkylene is a substituted or unsubstituted 2 to
20 membered heteroalkylene, each substituted or unsubstituted
cycloalkylene is a substituted or unsubstituted C.sub.3-C.sub.8
cycloalkylene, each substituted or unsubstituted
heterocycloalkylene is a substituted or unsubstituted 3 to 8
membered heterocycloalkylene, each substituted or unsubstituted
arylene is a substituted or unsubstituted C.sub.6-C.sub.10 arylene,
and/or each substituted or unsubstituted heteroarylene is a
substituted or unsubstituted 5 to 10 membered heteroarylene.
[0054] In some embodiments, each substituted or unsubstituted alkyl
is a substituted or unsubstituted C.sub.1-C.sub.8 alkyl, each
substituted or unsubstituted heteroalkyl is a substituted or
unsubstituted 2 to 8 membered heteroalkyl, each substituted or
unsubstituted cycloalkyl is a substituted or unsubstituted
C.sub.3-C.sub.7 cycloalkyl, each substituted or unsubstituted
heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered
heterocycloalkyl, each substituted or unsubstituted aryl is a
substituted or unsubstituted phenyl, and/or each substituted or
unsubstituted heteroaryl is a substituted or unsubstituted 5 to 6
membered heteroaryl. In some embodiments, each substituted or
unsubstituted alkylene is a substituted or unsubstituted
C.sub.1-C.sub.8 alkylene, each substituted or unsubstituted
heteroalkylene is a substituted or unsubstituted 2 to 8 membered
heteroalkylene, each substituted or unsubstituted cycloalkylene is
a substituted or unsubstituted C.sub.3-C.sub.7 cycloalkylene, each
substituted or unsubstituted heterocycloalkylene is a substituted
or unsubstituted 3 to 7 membered heterocycloalkylene, each
substituted or unsubstituted arylene is a substituted or
unsubstituted phenylene, and/or each substituted or unsubstituted
heteroarylene is a substituted or unsubstituted 5 to 6 membered
heteroarylene. In some embodiments, the compound (e.g., nucleotide
analogue) is a chemical species set forth in the Examples section,
claims, embodiments, figures, or tables below.
[0055] In embodiments, a substituted or unsubstituted moiety (e.g.,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, substituted or unsubstituted heteroaryl, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, and/or substituted or unsubstituted
heteroarylene) is unsubstituted (e.g., is an unsubstituted alkyl,
unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted
heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl,
unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted
cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted
arylene, and/or unsubstituted heteroarylene, respectively). In
embodiments, a substituted or unsubstituted moiety (e.g.,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, substituted or unsubstituted heteroaryl, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, and/or substituted or unsubstituted
heteroarylene) is substituted (e.g., is a substituted alkyl,
substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene, respectively).
[0056] In embodiments, a substituted moiety (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene) is substituted with at
least one substituent group, wherein if the substituted moiety is
substituted with a plurality of substituent groups, each
substituent group may optionally be different. In embodiments, if
the substituted moiety is substituted with a plurality of
substituent groups, each substituent group is different.
[0057] In embodiments, a substituted moiety (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene) is substituted with at
least one size-limited substituent group, wherein if the
substituted moiety is substituted with a plurality of size-limited
substituent groups, each size-limited substituent group may
optionally be different. In embodiments, if the substituted moiety
is substituted with a plurality of size-limited substituent groups,
each size-limited substituent group is different.
[0058] In embodiments, a substituted moiety (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene) is substituted with at
least one lower substituent group, wherein if the substituted
moiety is substituted with a plurality of lower substituent groups,
each lower substituent group may optionally be different. In
embodiments, if the substituted moiety is substituted with a
plurality of lower substituent groups, each lower substituent group
is different.
[0059] In embodiments, a substituted moiety (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene) is substituted with at
least one substituent group, size-limited substituent group, or
lower substituent group; wherein if the substituted moiety is
substituted with a plurality of groups selected from substituent
groups, size-limited substituent groups, and lower substituent
groups; each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, if the substituted moiety is substituted with a
plurality of groups selected from substituent groups, size-limited
substituent groups, and lower substituent groups; each substituent
group, size-limited substituent group, and/or lower substituent
group is different.
[0060] Certain compounds of the present disclosure possess
asymmetric carbon atoms (optical or chiral centers) or double
bonds; the enantiomers, racemates, diastereomers, tautomers,
geometric isomers, stereoisometric forms that may be defined, in
terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or
(L)- for amino acids, and individual isomers are encompassed within
the scope of the present disclosure. The compounds of the present
disclosure do not include those that are known in art to be too
unstable to synthesize and/or isolate. The present disclosure is
meant to include compounds in racemic and optically pure forms.
Optically active (R)- and (S)-, or (D)- and (L)-isomers may be
prepared using chiral synthons or chiral reagents, or resolved
using conventional techniques. When the compounds described herein
contain olefinic bonds or other centers of geometric asymmetry, and
unless specified otherwise, it is intended that the compounds
include both E and Z geometric isomers.
[0061] As used herein, the term "isomers" refers to compounds
having the same number and kind of atoms, and hence the same
molecular weight, but differing in respect to the structural
arrangement or configuration of the atoms.
[0062] The term "tautomer," as used herein, refers to one of two or
more structural isomers which exist in equilibrium and which are
readily converted from one isomeric form to another.
[0063] It will be apparent to one skilled in the art that certain
compounds of this disclosure may exist in tautomeric forms, all
such tautomeric forms of the compounds being within the scope of
the disclosure.
[0064] Unless otherwise stated, structures depicted herein are also
meant to include all stereochemical forms of the structure; i.e.,
the R and S configurations for each asymmetric center. Therefore,
single stereochemical isomers as well as enantiomeric and
diastereomeric mixtures of the present compounds are within the
scope of the disclosure.
[0065] Unless otherwise stated, structures depicted herein are also
meant to include compounds which differ only in the presence of one
or more isotopically enriched atoms. For example, compounds having
the present structures except for the replacement of a hydrogen by
a deuterium or tritium, or the replacement of a carbon by .sup.13C-
or .sup.14C-enriched carbon are within the scope of this
disclosure.
[0066] The compounds of the present disclosure may also contain
unnatural proportions of atomic isotopes at one or more of the
atoms that constitute such compounds. For example, the compounds
may be radiolabeled with radioactive isotopes, such as for example
tritium (.sup.3H), iodine-125 (.sup.125I) or carbon-14 (.sup.14C).
All isotopic variations of the compounds of the present disclosure,
whether radioactive or not, are encompassed within the scope of the
present disclosure.
[0067] It should be noted that throughout the application that
alternatives are written in Markush groups, for example, each amino
acid position that contains more than one possible amino acid. It
is specifically contemplated that each member of the Markush group
should be considered separately, thereby comprising another
embodiment, and the Markush group is not to be read as a single
unit.
[0068] "Analog," "analogue" or "derivative" is used in accordance
with its plain ordinary meaning within Chemistry and Biology and
refers to a chemical compound that is structurally similar to
another compound (i.e., a so-called "reference" compound) but
differs in composition, e.g., in the replacement of one atom by an
atom of a different element, or in the presence of a particular
functional group, or the replacement of one functional group by
another functional group, or the absolute stereochemistry of one or
more chiral centers of the reference compound. Accordingly, an
analog is a compound that is similar or comparable in function and
appearance but not in structure or origin to a reference
compound.
[0069] The terms "a" or "an," as used in herein means one or more.
In addition, the phrase "substituted with a[n]," as used herein,
means the specified group may be substituted with one or more of
any or all of the named substituents. For example, where a group,
such as an alkyl or heteroaryl group, is "substituted with an
unsubstituted C.sub.1-C.sub.20 alkyl, or unsubstituted 2 to 20
membered heteroalkyl," the group may contain one or more
unsubstituted C.sub.1-C.sub.20 alkyls, and/or one or more
unsubstituted 2 to 20 membered heteroalkyls.
[0070] As used herein, the term "about" means a range of values
including the specified value, which a person of ordinary skill in
the art would consider reasonably similar to the specified value.
In embodiments, about means within a standard deviation using
measurements generally acceptable in the art. In embodiments, about
means a range extending to +/-10% of the specified value. In
embodiments, about includes the specified value.
[0071] Moreover, where a moiety is substituted with an R
substituent, the group may be referred to as "R-substituted." Where
a moiety is R-substituted, the moiety is substituted with at least
one R substituent and each R substituent is optionally different.
Where a particular R group is present in the description of a
chemical genus (such as Formula (I)), a Roman alphabetic symbol may
be used to distinguish each appearance of that particular R group.
For example, where multiple R.sup.13 substituents are present, each
R.sup.13 substituent may be distinguished as R.sup.13A, R.sup.13B,
R.sup.13C, R.sup.13D, etc., wherein each of R.sup.13A, R.sup.13B,
R.sup.13C, R.sup.13D, etc. is defined within the scope of the
definition of 10.sup.3 and optionally differently.
[0072] A "detectable agent," "detectable compound," "detectable
label," or "detectable moiety" is a substance, molecule, or
composition detectable by spectroscopic, photochemical,
biochemical, immunochemical, chemical, magnetic resonance imaging,
or other physical means. For example, detectable agents include
.sup.18F, .sup.32P, .sup.33P, .sup.45Ti, .sup.47Sc, .sup.52Fe,
.sup.59Fe, .sup.62Cu, .sup.64Cu, .sup.67Cu, .sup.67Ga, .sup.68 Ga,
.sup.77As, .sup.86Y, .sup.90Y, .sup.89Sr, .sup.89Zr, .sup.94Tc,
.sup.94Tc, .sup.99mTc, .sup.99Mo, .sup.105Pd, .sup.105Rh,
.sup.111Ag, .sup.111In, .sup.123I, .sup.124I, .sup.125I ,
.sup.131I, .sup.142Pr, .sup.143Pr, .sup.149Pm, .sup.153Sm,
.sup.154-1581Gd, .sup.161Tb, .sup.166Dy, .sup.166Ho, .sup.169Er,
.sup.175Lu, .sup.177Lu, .sup.186Re, .sup.188Re, .sup.189Re,
.sup.194Ir, .sup.198Au, .sup.199Au, .sup.211At, .sup.211Pb,
.sup.212Bi, .sup.212Pb, .sup.213Bi, .sup.223Ra, .sup.225Ac, Cr, V,
Mn, Fe, Co, Ni, Cu, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er,
Tm, Yb, Lu, .sup.32P, fluorophore (e.g., fluorescent dyes),
modified oligonucleotides (e.g., moieties described in
PCT/US2015/022063, which is incorporated herein by reference),
electron-dense reagents, enzymes (e.g., as commonly used in an
ELISA), biotin, digoxigenin, paramagnetic molecules, paramagnetic
nanoparticles, ultrasmall superparamagnetic iron oxide ("USPIO")
nanoparticles, USPIO nanoparticle aggregates, superparamagnetic
iron oxide ("SPIO") nanoparticles, SPIO nanoparticle aggregates,
monochrystalline iron oxide nanoparticles, monochrystalline iron
oxide, nanoparticle contrast agents, liposomes or other delivery
vehicles containing Gadolinium chelate ("Gd-chelate") molecules,
Gadolinium, radioisotopes, radionuclides (e.g., carbon-11,
nitrogen-13, oxygen-15, fluorine-18, rubidium-82),
fluorodeoxyglucose (e.g., fluorine-18 labeled), any gamma ray
emitting radionuclides, positron-emitting radionuclide,
radiolabeled glucose, radiolabeled water, radiolabeled ammonia,
biocolloids, microbubbles (e.g., including microbubble shells
including albumin, galactose, lipid, and/or polymers; microbubble
gas core including air, heavy gas(es), perfluorcarbon, nitrogen,
octafluoropropane, perflexane lipid microsphere, perflutren, etc.),
iodinated contrast agents (e.g., iohexol, iodixanol, ioversol,
iopamidol, ioxilan, iopromide, diatrizoate, metrizoate, ioxaglate),
barium sulfate, thorium dioxide, gold, gold nanoparticles, gold
nanoparticle aggregates, fluorophores, two-photon fluorophores, or
haptens and proteins or other entities which can be made
detectable, e.g., by incorporating a radiolabel into a peptide or
antibody specifically reactive with a target peptide.
[0073] Radioactive substances (e.g., radioisotopes) that may be
used as imaging and/or labeling agents in accordance with the
embodiments of the disclosure include, but are not limited to
.sup.18F, .sup.32P, .sup.33P, .sup.45Ti, .sup.47Sc, .sup.52Fe,
.sup.59Fe, .sup.62Cu, .sup.64Cu, .sup.67Cu, .sup.67Ga, .sup.68 Ga,
.sup.77As, .sup.86Y, .sup.90Y, .sup.89Sr, .sup.89Zr, .sup.94Tc,
.sup.94Tc, .sup.99mTc, .sup.99Mo, .sup.105Pd, .sup.105Rh,
.sup.111Ag, .sup.111In, .sup.123I, .sup.124I, .sup.125I, .sup.131I,
.sup.142Pr, .sup.143Pr, .sup.149Pm, .sup.153Sm, .sup.154-1581Gd,
.sup.161Tb, .sup.166Dy, .sup.166Ho, .sup.169Er, .sup.175Lu,
.sup.177Lu, .sup.186Re, .sup.188Re, .sup.189Re, .sup.194Ir,
.sup.198Au, .sup.199Au, .sup.211At, .sup.211Pb, .sup.212Bi,
.sup.212Pb, .sup.213Bi, .sup.223Ra and .sup.225Ac. Paramagnetic
ions that may be used as additional imaging agents in accordance
with the embodiments of the disclosure include, but are not limited
to, ions of transition and lanthanide metals (e.g., metals having
atomic numbers of 21-29, 42, 43, 44, or 57-71). These metals
include ions of Cr, V, Mn, Fe, Co, Ni, Cu, La, Ce, Pr, Nd, Pm, Sm,
Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu.
[0074] Examples of detectable agents include imaging agents,
including fluorescent and luminescent substances, molecules, or
compositions, including, but not limited to, a variety of organic
or inorganic small molecules commonly referred to as "dyes,"
"labels," or "indicators." Examples include fluorescein, rhodamine,
acridine dyes, Alexa dyes, and cyanine dyes. In embodiments, the
detectable moiety is a fluorescent molecule (e.g., acridine dye,
cyanine, dye, fluorine dye, oxazine dye, phenanthridine dye, or
rhodamine dye). In embodiments, the detectable moiety is a
fluorescent molecule (e.g., acridine dye, cyanine, dye, fluorine
dye, oxazine dye, phenanthridine dye, or rhodamine dye). In
embodiments, the detectable moiety is a fluorescein isothiocyanate
moiety, tetramethylrhodamine-5-(and 6)-isothiocyanate moiety, Cy2
moiety, Cy3 moiety, Cy5 moiety, Cy7 moiety,
4',6-diamidino-2-phenylindole moiety, Hoechst 33258 moiety, Hoechst
33342 moiety, Hoechst 34580 moiety, propidium-iodide moiety, or
acridine orange moiety. In embodiments, the detectable moiety is a
Indo-1, Ca saturated moiety, Indo-1 Ca2+ moiety, Cascade Blue BSA
pH 7.0 moiety, Cascade Blue moiety, LysoTracker Blue moiety, Alexa
405 moiety, LysoSensor Blue pH 5.0 moiety, LysoSensor Blue moiety,
DyLight 405 moiety, DyLight 350 moiety, BFP (Blue Fluorescent
Protein) moiety, Alexa 350 moiety, 7-Amino-4-methylcoumarin pH 7.0
moiety, Amino Coumarin moiety, AMCA conjugate moiety, Coumarin
moiety, 7-Hydroxy-4-methylcoumarin moiety,
7-Hydroxy-4-methylcoumarin pH 9.0 moiety,
6,8-Difluoro-7-hydroxy-4-methylcoumarin pH 9.0 moiety, Hoechst
33342 moiety, Pacific Blue moiety, Hoechst 33258 moiety, Hoechst
33258-DNA moiety, Pacific Blue antibody conjugate pH 8.0 moiety,
PO-PRO-1 moiety, PO-PRO-1-DNA moiety, POPO-1 moiety, POPO-1-DNA
moiety, DAPI-DNA moiety, DAPI moiety, Marina Blue moiety, SYTOX
Blue-DNA moiety, CFP (Cyan Fluorescent Protein) moiety, eCFP
(Enhanced Cyan Fluorescent Protein) moiety,
1-Anilinonaphthalene-8-sulfonic acid (1,8-ANS) moiety, Indo-1, Ca
free moiety, 1,8-ANS (1-Anilinonaphthalene-8-sulfonic acid) moiety,
BO-PRO-1-DNA moiety, BOPRO-1 moiety, BOBO-1-DNA moiety, SYTO 45-DNA
moiety, evoglow-Pp1 moiety, evoglow-Bs1 moiety, evoglow-Bs2 moiety,
Auramine O moiety, DiO moiety, LysoSensor Green pH 5.0 moiety, Cy 2
moiety, LysoSensor Green moiety, Fura-2, high Ca moiety, Fura-2
Ca2+sup> moiety, SYTO 13-DNA moiety, YO-PRO-1-DNA moiety,
YOYO-1-DNA moiety, eGFP (Enhanced Green Fluorescent Protein)
moiety, LysoTracker Green moiety, GFP (S65T) moiety, BODIPY FL,
MeOH moiety, Sapphire moiety, BODIPY FL conjugate moiety,
MitoTracker Green moiety, MitoTracker Green FM, MeOH moiety,
Fluorescein 0.1 M NaOH moiety, Calcein pH 9.0 moiety, Fluorescein
pH 9.0 moiety, Calcein moiety, Fura-2, no Ca moiety, Fluo-4 moiety,
FDA moiety, DTAF moiety, Fluorescein moiety, CFDA moiety, FITC
moiety, Alexa Fluor 488 hydrazide-water moiety, DyLight 488 moiety,
5-FAM pH 9.0 moiety, Alexa 488 moiety, Rhodamine 110 moiety,
Rhodamine 110 pH 7.0 moiety, Acridine Orange moiety, BCECF pH 5.5
moiety, PicoGreendsDNA quantitation reagent moiety, SYBR Green I
moiety, Rhodaminen Green pH 7.0 moiety, CyQUANT GR-DNA moiety,
NeuroTrace 500/525, green fluorescent Nissl stain-RNA moiety,
DansylCadaverine moiety, Fluoro-Emerald moiety, Nissl moiety,
Fluorescein dextran pH 8.0 moiety, Rhodamine Green moiety,
5-(and-6)-Carboxy-2',7'-dichlorofluorescein pH 9.0 moiety,
DansylCadaverine, MeOH moiety, eYFP (Enhanced Yellow Fluorescent
Protein) moiety, Oregon Green 488 moiety, Fluo-3 moiety, BCECF pH
9.0 moiety, SBFI-Na+ moiety, Fluo-3 Ca2+ moiety, Rhodamine 123 MeOH
moiety, FlAsH moiety, Calcium Green-1 Ca2+ moiety, Magnesium Green
moiety, DM-NERF pH 4.0 moiety, Calcium Green moiety, Citrine
moiety, LysoSensor Yellow pH 9.0 moiety, TO-PRO-1-DNA moiety,
Magnesium Green Mg2+moiety, Sodium Green Na+moiety, TOTO-1-DNA
moiety, Oregon Green 514 moiety, Oregon Green 514 antibody
conjugate pH 8.0 moiety, NBD-X moiety, DM-NERF pH 7.0 moiety,
NBD-X, MeOH moiety, CI-NERF pH 6.0 moiety, Alexa 430 moiety,
CI-NERF pH 2.5 moiety, Lucifer Yellow, CH moiety, LysoSensor Yellow
pH 3.0 moiety, 6-TET, SE pH 9.0 moiety, Eosin antibody conjugate pH
8.0 moiety, Eosin moiety, 6-Carboxyrhodamine 6G pH 7.0 moiety,
6-Carboxyrhodamine 6G, hydrochloride moiety, Bodipy R6G SE moiety,
BODIPY R6G MeOH moiety, 6 JOE moiety, Cascade Yellow moiety,
mBanana moiety, Alexa 532 moiety, Erythrosin-5-isothiocyanate pH
9.0 moiety, 6-HEX, SE pH 9.0 moiety, mOrange moiety, mHoneydew
moiety, Cy 3 moiety, Rhodamine B moiety, DiI moiety, 5-TAMRA-MeOH
moiety, Alexa 555 moiety, DyLight 549 moiety, BODIPY TMR-X, SE
moiety, BODIPY TMR-X MeOH moiety, PO-PRO-3-DNA moiety, PO-PRO-3
moiety, Rhodamine moiety, POPO-3 moiety, Alexa 546 moiety, Calcium
Orange Ca2+ moiety, TRITC moiety, Calcium Orange moiety,
Rhodaminephalloidin pH 7.0 moiety, MitoTracker Orange moiety,
MitoTracker Orange MeOH moiety, Phycoerythrin moiety, Magnesium
Orange moiety, R-Phycoerythrin pH 7.5 moiety, 5-TAMRA pH 7.0
moiety, 5-TAMRA moiety, Rhod-2 moiety, FM 1-43 moiety, Rhod-2 Ca2+
moiety, FM 1-43 lipid moiety, LOLO-1-DNA moiety, dTomato moiety,
DsRed moiety, Dapoxyl (2-aminoethyl) sulfonamide moiety,
Tetramethylrhodamine dextran pH 7.0 moiety, Fluor-Ruby moiety,
Resorufin moiety, Resorufin pH 9.0 moiety, mTangerine moiety,
LysoTracker Red moiety, Lissaminerhodamine moiety, Cy 3.5 moiety,
Rhodamine Red-X antibody conjugate pH 8.0 moiety, Sulforhodamine
101 EtOH moiety, JC-1 pH 8.2 moiety, JC-1 moiety, mStrawberry
moiety, MitoTracker Red moiety, MitoTracker Red, MeOH moiety,
X-Rhod-1 Ca2+ moiety, Alexa 568 moiety, 5-ROX pH 7.0 moiety, 5-ROX
(5-Carboxy-X-rhodamine, triethylammonium salt) moiety, BO-PRO-3-DNA
moiety, BOPRO-3 moiety, BOBO-3-DNA moiety, Ethidium Bromide moiety,
ReAsH moiety, Calcium Crimson moiety, Calcium Crimson Ca2+ moiety,
mRFP moiety, mCherry moiety, HcRed moiety, DyLight 594 moiety,
Ethidium homodimer-1-DNA moiety, Ethidiumhomodimer moiety,
Propidium Iodide moiety, SYPRO Ruby moiety, Propidium Iodide-DNA
moiety, Alexa 594 moiety, BODIPY TR-X, SE moiety, BODIPY TR-X, MeOH
moiety, BODIPY TR-X phallacidin pH 7.0 moiety, Alexa Fluor 610
R-phycoerythrin streptavidin pH 7.2 moiety, YO-PRO-3-DNA moiety,
Di-8 ANEPPS moiety, Di-8-ANEPPS-lipid moiety, YOYO-3-DNA moiety,
Nile Red-lipid moiety, Nile Red moiety, DyLight 633 moiety, mPlum
moiety, TO-PRO-3-DNA moiety, DDAO pH 9.0 moiety, Fura Red high Ca
moiety, Allophycocyanin pH 7.5 moiety, APC (allophycocyanin)
moiety, Nile Blue, EtOH moiety, TOTO-3-DNA moiety, Cy 5 moiety,
BODIPY 650/665-X, MeOH moiety, Alexa Fluor 647 R-phycoerythrin
streptavidin pH 7.2 moiety, DyLight 649 moiety, Alexa 647 moiety,
Fura Red Ca2+ moiety, Atto 647 moiety, Fura Red, low Ca moiety,
Carboxynaphthofluorescein pH 10.0 moiety, Alexa 660 moiety, Cy 5.5
moiety, Alexa 680 moiety, DyLight 680 moiety, Alexa 700 moiety, FM
4-64, 2% CHAPS moiety, or FM 4-64 moiety. In embodiments, the
detectable moiety is a moiety of 1,1-Diethyl-4,4-carbocyanine
iodide, 1,2-Diphenyl acetylene, 1,4-Diphenylbutadiene,
1,4-Diphenylbutadiyne, 1,6-Diphenylhexatriene,
1,6-Diphenylhexatriene, 1-anilinonaphthalene-8-sulfonic acid ,
2,7-Dichlorofluorescein, 2,5-DIPHENYLOXAZOLE, 2-Di-1-ASP,
2-dodecylresorufin, 2-Methylbenzoxazole,
3,3-Diethylthiadicarbocyanine iodide, 4-Dimethyl
amino-4-Nitrostilbene, 5(6)-Carboxyfluorescein,
5(6)-Carboxynaphtofluorescein, 5(6)-Carboxytetramethylrhodamine B,
5-(and-6)-carboxy-2',7'-dichlorofluorescein,
5-(and-6)-carboxy-2,7-dichlorofluorescein,
5-(N-hexadecanoyl)aminoeosin, 5-(N-hexadecanoyl)aminoeosin,
5-chloromethylfluorescein, 5-FAM, 5-ROX, 5-TAMRA, 5-TAMRA,
6,8-difluoro-7-hydroxy-4-methylcoumarin,
6,8-difluoro-7-hydroxy-4-methylcoumarin, 6-carboxyrhodamine 6G,
6-HEX, 6-JOE, 6-JOE, 6-TET, 7-aminoactinomycin D,
7-Benzylamino-4-Nitrobenz-2-Oxa-1,3-Diazole,
7-Methoxycoumarin-4-Acetic Acid, 8-Benzyloxy-5,7-diphenylquinoline,
8-Benzyloxy-5,7-diphenylquinoline,
9,10-Bis(Phenylethynyl)Anthracene, 9,10-Diphenylanthracene,
9-METHYLCARBAZOLE, (CS)2Ir(.mu.-Cl)2Ir(CS)2, AAA, Acridine Orange,
Acridine Orange, Acridine Yellow, Acridine Yellow, Adams Apple Red
680, Adirondack Green 520, Alexa Fluor 350, Alexa Fluor 405, Alexa
Fluor 430, Alexa Fluor 430, Alexa Fluor 480, Alexa Fluor 488, Alexa
Fluor 488, Alexa Fluor 488 hydrazide, Alexa Fluor 500, Alexa Fluor
514, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 546, Alexa Fluor
555, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor
594, Alexa Fluor 594, Alexa Fluor 610, Alexa Fluor 610-R-PE, Alexa
Fluor 633, Alexa Fluor 635, Alexa Fluor 647, Alexa Fluor 647, Alexa
Fluor 647-R-PE, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor
680-APC, Alexa Fluor 680-R-PE, Alexa Fluor 700, Alexa Fluor 750,
Alexa Fluor 790, Allophycocyanin, AmCyan1, Aminomethylcoumarin,
Amplex Gold (product), Amplex Red Reagent, Amplex UltraRed,
Anthracene, APC, APC-Seta-750, AsRed2, ATTO 390, ATTO 425, ATTO
430LS, ATTO 465, ATTO 488, ATTO 490LS, ATTO 495, ATTO 514, ATTO
520, ATTO 532, ATTO 550, ATTO 565, ATTO 590, ATTO 594, ATTO 610,
ATTO 620, ATTO 633, ATTO 635, ATTO 647, ATTO 647N, ATTO 655, ATTO
665, ATTO 680, ATTO 700, ATTO 725, ATTO 740, ATTO Oxa12, ATTO
Rho3B, ATTO Rho6G, ATTO Rho11, ATTO Rho12, ATTO Rho13, ATTO Rho14,
ATTO Rho101, ATTO Thio12, Auramine O, Azami Green, Azami Green
monomeric, B-phycoerythrin, BCECF, BCECF, Bex1, Biphenyl, Birch
Yellow 580, Blue-green algae, BO-PRO-1, BO-PRO-3, BOBO-1, BOBO-3,
BODIPY 630 650-X, BODIPY 650/665-X, BODIPY FL, BODIPY FL, BODIPY
R6G, BODIPY TMR-X, BODIPY TR-X, BODIPY TR-X Ph 7.0, BODIPY TR-X
phallacidin, BODIPY-DiMe, BODIPY-Phenyl, BODIPY-TMSCC,
C3-Indocyanine, C3-Indocyanine, C3-Oxacyanine, C3-Thiacyanine Dye
(EtOH), C3-Thiacyanine Dye (PrOH), C5-Indocyanine, C5-Oxacyanine,
C5-Thiacyanine, C7-Indocyanine, C7-Oxacyanine, C545T,
C-Phycocyanin, Calcein, Calcein red-orange, Calcium Crimson,
Calcium Green-1, Calcium Orange, Calcofluor white 2MR, Carboxy
SNARF-1 pH 6.0, Carboxy SNARF-1 pH 9.0, Carboxynaphthofluorescein,
Cascade Blue, Cascade Yellow, Catskill Green 540, CBQCA, CellMask
Orange, CellTrace BODIPY TR methyl ester, CellTrace calcein violet,
CellTrace.TM. Far Red, CellTracker Blue, CellTracker Red CMTPX,
CellTracker Violet BMQC, CF405M, CF405S, CF488A, CF543, CF555, CFP
, CFSE, CF.TM. 350, CF.TM. 485, Chlorophyll A, Chlorophyll B,
Chromeo 488, Chromeo 494, Chromeo 505, Chromeo 546, Chromeo 642,
Citrine, Citrine, ClOH butoxy aza-BODIPY, ClOH C12 aza-BODIPY,
CM-H2DCFDA, Coumarin 1, Coumarin 6, Coumarin 6, Coumarin 30,
Coumarin 314, Coumarin 334, Coumarin 343, Coumarine 545T, Cresyl
Violet Perchlorate, CryptoLight CF1, CryptoLight CF2, CryptoLight
CF3, CryptoLight CF4, CryptoLight CF5, CryptoLight CF6, Crystal
Violet, Cumarin153, Cy2, Cy3, Cy3, Cy3.5, Cy3B, Cy3B, Cy3Cy5 ET,
Cy5, Cy5, Cy5.5, Cy7, Cyanine3 NHS ester, Cyanine5 carboxylic acid,
Cyanine5 NHS ester, Cyclotella meneghiniana Kutzing, CypHer5 ,
CypHer5 pH 9.15, CyQUANT GR, CyTrak Orange, Dabcyl SE, DAF-FM, DAMC
(Weiss), dansyl cadaverine, Dansyl Glycine (Dioxane), DAPI, DAPI,
DAPI, DAPI, DAPI (DMSO), DAPI (H2O), Dapoxyl
(2-aminoethyl)sulfonamide, DCI, DCM, DCM, DCM (acetonitrile), DCM
(MeOH), DDAO, Deep Purple, di-8-ANEPPS, DiA,
Dichlorotris(1,10-phenanthroline) ruthenium(II), DiClOH C12
aza-BODIPY, DiClOHbutoxy aza-BODIPY, DiD, DiI, DiIC18(3), DiO, DiR,
Diversa Cyan-FP, Diversa Green-FP, DM-NERF pH 4.0, DOCI,
Doxorubicin, DPP pH-Probe 590-7.5, DPP pH-Probe 590-9.0, DPP
pH-Probe 590-11.0, DPP pH-Probe 590-11.0, Dragon Green, DRAQ5,
DsRed, DsRed, DsRed, DsRed-Express, DsRed-Express2, DsRed-Express
T1, dTomato, DY-350XL, DY-480, DY-480XL MegaStokes, DY-485,
DY-485XL MegaStokes, DY-490, DY-490XL MegaStokes, DY-500, DY-500XL
MegaStokes, DY-520, DY-520XL MegaStokes, DY-547, DY-549P1,
DY-549P1, DY-554, DY-555, DY-557, DY-557, DY-590, DY-590, DY-615,
DY-630, DY-631, DY-633, DY-635, DY-636, DY-647, DY-649P1, DY-649P1,
DY-650, DY-651, DY-656, DY-673, DY-675, DY-676, DY-680, DY-681,
DY-700, DY-701, DY-730, DY-731, DY-750, DY-751, DY-776, DY-782,
Dye-28, Dye-33, Dye-45, Dye-304, Dye-1041, DyLight 488, DyLight
549, DyLight 594, DyLight 633, DyLight 649, DyLight 680,
E2-Crimson, E2-Orange, E2-Red/Green, EBFP, ECF, ECFP, ECL Plus,
eGFP, ELF 97, Emerald, Envy Green, Eosin, Eosin Y, epicocconone,
EqFP611, Erythrosin-5-isothiocyanate, Ethidium bromide, ethidium
homodimer-1, Ethyl Eosin, Ethyl Eosin, Ethyl Nile Blue A,
Ethyl-p-Dimethylaminobenzoate, Ethyl-p-Dimethylaminobenzoate, Eu2O3
nanoparticles, Eu (Soini), Eu(tta)3DEADIT, EvaGreen, EVOblue-30,
EYFP, FAD, FITC, FITC, FlAsH (Adams), Flash Red EX, FlAsH-CCPGCC,
FlAsH-CCXXCC, Fluo-3, Fluo-4, Fluo-5F, Fluorescein, Fluorescein 0.1
NaOH, Fluorescein-Dibase, fluoro-emerald, Fluorol 5G, FluoSpheres
blue, FluoSpheres crimson, FluoSpheres dark red, FluoSpheres
orange, FluoSpheres red, FluoSpheres yellow-green, FM4-64 in CTC,
FM4-64 in SDS, FM 1-43, FM 4-64, Fort Orange 600, Fura Red, Fura
Red Ca free, fura-2, Fura-2 Ca free, Gadodiamide, Gd-Dtpa-Bma,
Gadodiamide, Gd-Dtpa-Bma, GelGreen.TM., GelRed.TM., H9-40, HcRed1,
Hemo Red 720, HiLyte Fluor 488, HiLyte Fluor 555, HiLyte Fluor 647,
HiLyte Fluor 680, HiLyte Fluor 750, HiLyte Plus 555, HiLyte Plus
647, HiLyte Plus 750, HmGFP, Hoechst 33258, Hoechst 33342,
Hoechst-33258, Hoechst-33258, Hops Yellow 560, HPTS, HPTS, HPTS,
HPTS, HPTS, indo-1, Indo-1 Ca free, Ir(Cn)2(acac), Ir(Cs)2(acac),
IR-775 chloride, IR-806, Ir-OEP--CO-Cl, IRDye.RTM. 650 Alkyne,
IRDye.RTM. 650 Azide, IRDye.RTM. 650 Carboxylate, IRDye.RTM. 650
DBCO, IRDye.RTM. 650 Maleimide, IRDye.RTM. 650 NHS Ester,
IRDye.RTM. 680LT Carboxylate, IRDye.RTM. 680LT Maleimide,
IRDye.RTM. 680LT NHS Ester, IRDye.RTM. 680RD Alkyne, IRDye.RTM.
680RD Azide, IRDye.RTM. 680RD Carboxylate, IRDye.RTM. 680RD DBCO,
IRDye.RTM. 680RD Maleimide, IRDye.RTM. 680RD NHS Ester, IRDye.RTM.
700 phosphoramidite, IRDye.RTM. 700DX, IRDye.RTM. 700DX, IRDye.RTM.
700DX Carboxylate, IRDye.RTM. 700DX NHS Ester, IRDye.RTM. 750
Carboxylate, IRDye.RTM. 750 Maleimide, IRDye.RTM. 750 NHS Ester,
IRDye.RTM. 800 phosphoramidite, IRDye.RTM. 800CW , IRDye.RTM. 800CW
Alkyne, IRDye.RTM. 800CW Azide, IRDye.RTM. 800CW Carboxylate,
IRDye.RTM. 800CW DBCO, IRDye.RTM. 800CW Maleimide, IRDye.RTM. 800CW
NHS Ester, IRDye.RTM. 800RS, IRDye.RTM. 800RS Carboxylate,
IRDye.RTM. 800RS NHS Ester, IRDye.RTM. QC-1 Carboxylate, IRDye.RTM.
QC-1 NHS Ester, Isochrysis galbana--Parke, JC-1, JC-1, JOJO-1,
Jonamac Red Evitag T2, Kaede Green, Kaede Red, kusabira orange,
Lake Placid 490, LDS 751, Lissamine Rhodamine (Weiss), LOLO-1,
lucifer yellow CH, Lucifer Yellow CH, lucifer yellow CH, Lucifer
Yellow CH Dilitium salt, Lumio Green, Lumio Red, Lumogen F Orange,
Lumogen Red F300, Lumogen Red F300, LysoSensor Blue DND-192,
LysoSensor Green DND-153, LysoSensor Green DND-153, LysoSensor
Yellow/Blue DND-160 pH 3, LysoSensor YellowBlue DND-160,
LysoTracker Blue DND-22, LysoTracker Blue DND-22, LysoTracker Green
DND-26, LysoTracker Red DND-99, LysoTracker Yellow HCK-123, Macoun
Red Evitag T2, Macrolex Fluorescence Red G, Macrolex Fluorescence
Yellow 10GN, Macrolex Fluorescence Yellow 10GN, Magnesium Green,
Magnesium Octaethylporphyrin, Magnesium Orange, Magnesium
Phthalocyanine, Magnesium Phthalocyanine, Magnesium
Tetramesitylporphyrin, Magnesium Tetraphenylporphyrin, malachite
green isothiocyanate, Maple Red-Orange 620, Marina Blue, mBanana,
mBBr, mCherry , Merocyanine 540, Methyl green, Methyl green, Methyl
green, Methylene Blue, Methylene Blue, mHoneyDew, MitoTracker Deep
Red 633, MitoTracker Green FM, MitoTracker Orange CMTMRos,
MitoTracker Red CMXRos, monobromobimane, Monochlorobimane,
Monoraphidium, mOrange, mOrange2, mPlum, mRaspberry, mRFP, mRFP1,
mRFP1.2 (Wang), mStrawberry (Shaner), mTangerine (Shaner),
N,N-Bis(2,4,6-trimethylphenyl)-3,4:9,10-perylenebis(dicarboximide),
NADH, Naphthalene, Naphthalene, Naphthofluorescein,
Naphthofluorescein, NBD-X, NeuroTrace 500525, Nilblau perchlorate,
nile blue, Nile Blue, Nile Blue (EtOH), nile red, Nile Red, Nile
Red, Nile red, Nileblue A, NIR1, NIR2, NIR3, NIR4, NIR820,
Octaethylporphyrin, OH butoxy aza-BODIPY, OHCl2 aza-BODIPY, Orange
Fluorescent Protein, Oregon Green 488, Oregon Green 488 DHPE,
Oregon Green 514, Oxazin1, Oxazin 750, Oxazine 1, Oxazine 170,
P4-3, P-Quaterphenyl, P-Terphenyl, PA-GFP (post-activation), PA-GFP
(pre-activation), Pacific Orange, Palladium(II)
meso-tetraphenyl-tetrabenzoporphyrin, PdOEPK, PdTFPP, PerCP-Cy5.5,
Perylene, Perylene, Perylene bisimide pH-Probe 550-5.0, Perylene
bisimide pH-Probe 550-5.5, Perylene bisimide pH-Probe 550-6.5,
Perylene Green pH-Probe 720-5.5, Perylene Green Tag pH-Probe
720-6.0, Perylene Orange pH-Probe 550-2.0, Perylene Orange Tag 550,
Perylene Red pH-Probe 600-5.5, Perylenediimid, Perylne Green
pH-Probe 740-5.5, Phenol, Phenylalanine, pHrodo, succinimidyl
ester, Phthalocyanine, PicoGreen dsDNA quantitation reagent,
Pinacyanol-Iodide, Piroxicam, Platinum(II)
tetraphenyltetrabenzoporphyrin, Plum Purple, PO-PRO-1, PO-PRO-3,
POPO-1, POPO-3, POPOP, Porphin, PPO, Proflavin, PromoFluor-350,
PromoFluor-405, PromoFluor-415, PromoFluor-488, PromoFluor-488
Premium, PromoFluor-488LSS, PromoFluor-500LSS, PromoFluor-505,
PromoFluor-510LSS, PromoFluor-514LSS, PromoFluor-520LSS,
PromoFluor-532, PromoFluor-546, PromoFluor-555, PromoFluor-590,
PromoFluor-610, PromoFluor-633, PromoFluor-647, PromoFluor-670,
PromoFluor-680, PromoFluor-700,
PromoFluor-750, PromoFluor-770, PromoFluor-780, PromoFluor-840,
propidium iodide, Protoporphyrin IX, PTIR475/UF, PTIR545/UF, PtOEP,
PtOEPK, PtTFPP, Pyrene, QD525, QD565, QD585, QD605, QD655, QD705,
QD800, QD903, QD PbS 950, QDot 525, QDot 545, QDot 565, Qdot 585,
Qdot 605, Qdot 625, Qdot 655, Qdot 705, Qdot 800, QpyMe2, QSY 7,
QSY 7, QSY 9, QSY 21, QSY 35, quinine, Quinine Sulfate, Quinine
sulfate, R-phycoerythrin, R-phycoerythrin, ReAsH-CCPGCC,
ReAsH-CCXXCC, Red Beads (Weiss), Redmond Red, Resorufin, resorufin,
rhod-2, Rhodamin 700 perchlorate, rhodamine, Rhodamine 6G,
Rhodamine 6G, Rhodamine 101, rhodamine 110, Rhodamine 123,
rhodamine 123, Rhodamine B, Rhodamine B, Rhodamine Green, Rhodamine
pH-Probe 585-7.0, Rhodamine pH-Probe 585-7.5, Rhodamine phalloidin,
Rhodamine Red-X, Rhodamine Red-X, Rhodamine Tag pH-Probe 585-7.0,
Rhodol Green, Riboflavin, Rose Bengal, Sapphire, SBFI, SBFI Zero
Na,
Scenedesmus sp., SensiLight PBXL-1, SensiLight PBXL-3, Seta
633-NHS, Seta-633-NHS, SeTau-380-NHS, SeTau-647-NHS, Snake-Eye Red
900, SNIR1, SNIR2, SNIR3, SNIR4, Sodium Green, Solophenyl flavine
7GFE 500, Spectrum Aqua, Spectrum Blue, Spectrum FRed, Spectrum
Gold, Spectrum Green, Spectrum Orange, Spectrum Red, Squarylium dye
III, Stains All, Stilben derivate, Stilbene, Styryl8 perchlorate,
Sulfo-Cyanine3 carboxylic acid, Sulfo-Cyanine3 carboxylic acid,
Sulfo-Cyanine3 NHS ester, Sulfo-Cyanine5 carboxylic acid,
Sulforhodamine 101, sulforhodamine 101, Sulforhodamine B,
Sulforhodamine G, Suncoast Yellow, SuperGlo BFP, SuperGlo GFP, Surf
Green EX, SYBR Gold nucleic acid gel stain, SYBR Green I, SYPRO
Ruby, SYTO 9, SYTO 11, SYTO 13, SYTO 16, SYTO 17, SYTO 45, SYTO 59,
SYTO 60, SYTO 61, SYTO 62, SYTO 82, SYTO RNASelect, SYTO RNASelect,
SYTOX Blue, SYTOX Green, SYTOX Orange, SYTOX Red, T-Sapphire, Tb
(Soini), tCO, tdTomato, Terrylen, Terrylendiimid, testdye,
Tetra-t-Butylazaporphine, Tetra-t-Butylnaphthalocyanine, Tetracen,
Tetrakis(o-Aminophenyl)Porphyrin, Tetramesitylporphyrin,
Tetramethylrhodamine, tetramethylrhodamine, Tetraphenylporphyrin,
Tetraphenylporphyrin, Texas Red, Texas Red DHPE, Texas Red-X,
ThiolTracker Violet, Thionin acetate, TMRE, TO-PRO-1, TO-PRO-3,
Toluene, Topaz (Tsien1998), TOTO-1, TOTO-3,
Tris(2,2-Bipyridyl)Ruthenium(II) chloride,
Tris(4,4-diphenyl-2,2-bipyridine) ruthenium(II) chloride,
Tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) TMS, TRITC
(Weiss), TRITC Dextran (Weiss), Tryptophan, Tyrosine, Vex1, Vybrant
DyeCycle Green stain, Vybrant DyeCycle Orange stain, Vybrant
DyeCycle Violet stain, WEGFP (post-activation), WellRED D2, WellRED
D3, WellRED D4, WtGFP, WtGFP (Tsien1998), X-rhod-1, Yakima Yellow,
YFP, YO-PRO-1, YO-PRO-3, YOYO-1, YoYo-1, YoYo-1 dsDNA, YoYo-1
ssDNA, YOYO-3, Zinc Octaethylporphyrin, Zinc Phthalocyanine, Zinc
Tetramesitylporphyrin, Zinc Tetraphenylporphyrin, ZsGreen1, or
ZsYellow1.
[0075] In embodiments, the detectable moiety is a moiety of a
derivative of one of the detectable moieties described immediately
above, wherein the derivative differs from one of the detectable
moieties immediately above by a modification resulting from the
conjugation of the detectable moiety to a compound described
herein.
[0076] In embodiments, the detectable label is a fluorescent dye.
In embodiments, the detectable label is a fluorescent dye capable
of exchanging energy with another fluorescent dye (e.g.,
fluorescence resonance energy transfer (FRET) chromophores).
[0077] The term "cyanine" or "cyanine moiety" as described herein
refers to a detectable moiety containing two nitrogen groups
separated by a polymethine chain. In embodiments, the cyanine
moiety has 3 methine structures (i.e. cyanine 3 or Cy3). In
embodiments, the cyanine moiety has 5 methine structures (i.e.
cyanine 5 or Cy5). In embodiments, the cyanine moiety has 7 methine
structures (i.e., cyanine 7 or Cy7).
[0078] Descriptions of compounds (e.g., nucleotide analogues) of
the present disclosure are limited by principles of chemical
bonding known to those skilled in the art. Accordingly, where a
group may be substituted by one or more of a number of
substituents, such substitutions are selected so as to comply with
principles of chemical bonding and to give compounds which are not
inherently unstable and/or would be known to one of ordinary skill
in the art as likely to be unstable under ambient conditions, such
as aqueous, neutral, and several known physiological conditions.
For example, a heterocycloalkyl or heteroaryl is attached to the
remainder of the molecule via a ring heteroatom in compliance with
principles of chemical bonding known to those skilled in the art
thereby avoiding inherently unstable compounds.
[0079] The term "pharmaceutically acceptable salts" is meant to
include salts of the active compounds that are prepared with
relatively nontoxic acids or bases, depending on the particular
substituents found on the compounds described herein. When
compounds of the present invention contain relatively acidic
functionalities, base addition salts can be obtained by contacting
the neutral form of such compounds with a sufficient amount of the
desired base, either neat or in a suitable inert solvent. Examples
of pharmaceutically acceptable base addition salts include sodium,
potassium, calcium, ammonium, organic amino, or magnesium salt, or
a similar salt. When compounds of the present invention contain
relatively basic functionalities, acid addition salts can be
obtained by contacting the neutral form of such compounds with a
sufficient amount of the desired acid, either neat or in a suitable
inert solvent. Examples of pharmaceutically acceptable acid
addition salts include those derived from inorganic acids like
hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic,
phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,
monohydrogensulfuric, hydriodic, or phosphorous acids and the like,
as well as the salts derived from relatively nontoxic organic acids
like acetic, propionic, isobutyric, maleic, malonic, benzoic,
succinic, suberic, fumaric, lactic, mandelic, phthalic,
benzenesulfonic, p-tolylsulfonic, citric, tartaric, oxalic,
methanesulfonic, and the like. Also included are salts of amino
acids such as arginate and the like, and salts of organic acids
like glucuronic or galactunoric acids and the like (see, for
example, Berge et al., "Pharmaceutical Salts", Journal of
Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds
of the present invention contain both basic and acidic
functionalities that allow the compounds to be converted into
either base or acid addition salts.
[0080] Thus, the compounds of the present invention may exist as
salts, such as with pharmaceutically acceptable acids. The present
invention includes such salts. Non-limiting examples of such salts
include hydrochlorides, hydrobromides, phosphates, sulfates,
methanesulfonates, nitrates, maleates, acetates, citrates,
fumarates, proprionates, tartrates (e.g., (+)-tartrates,
(-)-tartrates, or mixtures thereof including racemic mixtures),
succinates, benzoates, and salts with amino acids such as glutamic
acid, and quaternary ammonium salts (e.g., methyl iodide, ethyl
iodide, and the like). These salts may be prepared by methods known
to those skilled in the art.
[0081] The neutral forms of the compounds are preferably
regenerated by contacting the salt with a base or acid and
isolating the parent compound in the conventional manner. The
parent form of the compound may differ from the various salt forms
in certain physical properties, such as solubility in polar
solvents.
[0082] In addition to salt forms, the present invention provides
compounds, which are in a prodrug form. Prodrugs of the compounds
described herein are those compounds that readily undergo chemical
changes under physiological conditions to provide the compounds of
the present invention. Prodrugs of the compounds described herein
may be converted in vivo after administration. Additionally,
prodrugs can be converted to the compounds of the present invention
by chemical or biochemical methods in an ex vivo environment, such
as, for example, when contacted with a suitable enzyme or chemical
reagent.
[0083] Certain compounds of the present invention can exist in
unsolvated forms as well as solvated forms, including hydrated
forms. In general, the solvated forms are equivalent to unsolvated
forms and are encompassed within the scope of the present
invention. Certain compounds of the present invention may exist in
multiple crystalline or amorphous forms. In general, all physical
forms are equivalent for the uses contemplated by the present
invention and are intended to be within the scope of the present
invention.
[0084] "Pharmaceutically acceptable excipient" and
"pharmaceutically acceptable carrier" refer to a substance that
aids the administration of an active agent to and absorption by a
subject and can be included in the compositions of the present
invention without causing a significant adverse toxicological
effect on the patient. Non-limiting examples of pharmaceutically
acceptable excipients include water, NaCl, normal saline solutions,
lactated Ringer's, normal sucrose, normal glucose, binders,
fillers, disintegrants, lubricants, coatings, sweeteners, flavors,
salt solutions (such as Ringer's solution), alcohols, oils,
gelatins, carbohydrates such as lactose, amylose or starch, fatty
acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and
colors, and the like. Such preparations can be sterilized and, if
desired, mixed with auxiliary agents such as lubricants,
preservatives, stabilizers, wetting agents, emulsifiers, salts for
influencing osmotic pressure, buffers, coloring, and/or aromatic
substances and the like that do not deleteriously react with the
compounds of the invention. One of skill in the art will recognize
that other pharmaceutical excipients are useful in the present
invention.
[0085] The term "preparation" is intended to include the
formulation of the active compound with encapsulating material as a
carrier providing a capsule in which the active component with or
without other carriers, is surrounded by a carrier, which is thus
in association with it. Similarly, cachets and lozenges are
included. Tablets, powders, capsules, pills, cachets, and lozenges
can be used as solid dosage forms suitable for oral
administration.
[0086] The terms "polypeptide," "peptide" and "protein" are used
interchangeably herein to refer to a polymer of amino acid
residues, wherein the polymer may optionally be conjugated to a
moiety that does not consist of amino acids. The terms apply to
amino acid polymers in which one or more amino acid residue is an
artificial chemical mimetic of a corresponding naturally occurring
amino acid, as well as to naturally occurring amino acid polymers
and non-naturally occurring amino acid polymer.
[0087] A polypeptide, or a cell is "recombinant" when it is
artificial or engineered, or derived from or contains an artificial
or engineered protein or nucleic acid (e.g., non-natural or not
wild type). For example, a polynucleotide that is inserted into a
vector or any other heterologous location, e.g., in a genome of a
recombinant organism, such that it is not associated with
nucleotide sequences that normally flank the polynucleotide as it
is found in nature is a recombinant polynucleotide. A protein
expressed in vitro or in vivo from a recombinant polynucleotide is
an example of a recombinant polypeptide. Likewise, a polynucleotide
sequence that does not appear in nature, for example a variant of a
naturally occurring gene, is recombinant.
[0088] "Hybridize" shall mean the annealing of one single-stranded
nucleic acid (such as a primer) to another nucleic acid based on
the well-understood principle of sequence complementarity. In an
embodiment the other nucleic acid is a single-stranded nucleic
acid. The propensity for hybridization between nucleic acids
depends on the temperature and ionic strength of their milieu, the
length of the nucleic acids and the degree of complementarity. The
effect of these parameters on hybridization is described in, for
example, Sambrook J., Fritsch E. F., Maniatis T., Molecular
cloning: a laboratory manual, Cold Spring Harbor Laboratory Press,
New York (1989). As used herein, hybridization of a primer, or of a
DNA extension product, respectively, is extendable by creation of a
phosphodiester bond with an available nucleotide or nucleotide
analogue capable of forming a phosphodiester bond, therewith.
[0089] "Contacting" is used in accordance with its plain ordinary
meaning and refers to the process of allowing at least two distinct
species (e.g., chemical compounds including biomolecules or cells)
to become sufficiently proximal to react, interact or physically
touch. It should be appreciated; however, the resulting reaction
product can be produced directly from a reaction between the added
reagents or from an intermediate from one or more of the added
reagents that can be produced in the reaction mixture. The term
"contacting" may include allowing two species to react, interact,
or physically touch, wherein the two species may be a compound as
described herein and a protein or enzyme. In some embodiments
contacting includes allowing a compound described herein to
interact with a protein or enzyme that is involved in a signaling
pathway.
[0090] As defined herein, the term "activation", "activate",
"activating", "activator" and the like in reference to a
target-inhibitor interaction means positively affecting (e.g.,
increasing) the activity or function of the target (e.g., protein)
relative to the activity or function of the target (e.g., protein)
in the absence of the activator. In embodiments activation means
positively affecting (e.g., increasing) the concentration or levels
of the target (e.g., protein) relative to the concentration or
level of the target (e.g., protein) in the absence of the
activator. The terms may reference activation, or activating,
sensitizing, or up-regulating signal transduction or enzymatic
activity or the amount of a target (e.g., protein) decreased in a
disease. Thus, activation may include, at least in part, partially
or totally increasing stimulation, increasing or enabling
activation, or activating, sensitizing, or up-regulating signal
transduction or enzymatic activity or the amount of a target (e.g.,
protein) associated with a disease (e.g., a target (e.g., protein)
which is decreased in a disease relative to a non-diseased
control). Activation may include, at least in part, partially or
totally increasing stimulation, increasing or enabling activation,
or activating, sensitizing, or up-regulating signal transduction or
enzymatic activity or the amount of a target (e.g., protein).
[0091] The terms "agonist," "activator," "upregulator," etc. refer
to a substance capable of detectably increasing the expression or
activity of a given target (e.g., gene or protein). The agonist can
increase expression or activity 10%, 20%, 30%, 40%, 50%, 60%, 70%,
80%, 90% or more in comparison to a control in the absence of the
agonist. In certain instances, expression or activity is 1.5-fold,
2-fold, 3-fold, 4-fold, 5-fold, 10-fold or higher than the
expression or activity in the absence of the agonist.
[0092] As defined herein, the term "inhibition," "inhibit,"
"inhibiting" and the like in reference to a target-inhibitor
interaction means negatively affecting (e.g., decreasing) the
activity or function of the target (e.g., protein) relative to the
activity or function of the target (e.g., protein) in the absence
of the inhibitor. In embodiments inhibition means negatively
affecting (e.g., decreasing) the concentration or levels of the
target (e.g., protein) relative to the concentration or level of
the target (e.g., protein) in the absence of the inhibitor. In
embodiments inhibition refers to reduction of a disease or symptoms
of disease. In embodiments, inhibition refers to a reduction in the
activity of a particular target (e.g., protein). Thus, inhibition
includes, at least in part, partially or totally blocking
stimulation, decreasing, preventing, or delaying activation, or
inactivating, desensitizing, or down-regulating signal transduction
or enzymatic activity or the amount of a target (e.g., protein). In
embodiments, inhibition refers to a reduction of activity of a
target (e.g., protein) resulting from a direct interaction (e.g.,
an inhibitor binds to the target (e.g., protein)). In embodiments,
inhibition refers to a reduction of activity of a target (e.g.,
protein) from an indirect interaction (e.g., an inhibitor binds to
a target (e.g., protein) that activates the target (e.g., protein),
thereby preventing target (e.g., protein) activation).
[0093] The terms "inhibitor," "repressor," "antagonist," or
"downregulator" interchangeably refer to a substance capable of
detectably decreasing the expression or activity of a given target
(e.g., gene or protein). The antagonist can decrease expression or
activity 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more in
comparison to a control in the absence of the antagonist. In
certain instances, expression or activity is 1.5-fold, 2-fold,
3-fold, 4-fold, 5-fold, 10-fold or lower than the expression or
activity in the absence of the antagonist.
[0094] The term "streptavidin" refers to a tetrameric protein
(including homologs, isoforms, and functional fragments thereof)
capable of binding biotin. The term includes any recombinant or
naturally-occurring form of streptavidin variants thereof that
maintain streptavidin activity (e.g., within at least 30%, 40%,
50%, 60%, 70%, 80%, 90%, 95%, or 100% activity compared to wildtype
streptavidin).
[0095] The term "expression" includes any step involved in the
production of the polypeptide including, but not limited to,
transcription, post-transcriptional modification, translation,
post-translational modification, and secretion. Expression can be
detected using conventional techniques for detecting protein (e.g.,
ELISA, Western blotting, flow cytometry, immunofluorescence,
immunohistochemistry, etc.).
[0096] An "effective amount" is an amount sufficient for a compound
to accomplish a stated purpose relative to the absence of the
compound (e.g., achieve the effect for which it is administered,
treat a disease, reduce enzyme activity, increase enzyme activity,
reduce a signaling pathway, or reduce one or more symptoms of a
disease or condition). An "activity decreasing amount," as used
herein, refers to an amount of antagonist required to decrease the
activity of an enzyme relative to the absence of the antagonist. A
"function disrupting amount," as used herein, refers to the amount
of antagonist required to disrupt the function of an enzyme or
protein relative to the absence of the antagonist.
[0097] A "cell" as used herein, refers to a cell carrying out
metabolic or other function sufficient to preserve or replicate its
genomic DNA. A cell can be identified by well-known methods in the
art including, for example, presence of an intact membrane,
staining by a particular dye, ability to produce progeny or, in the
case of a gamete, ability to combine with a second gamete to
produce a viable offspring. Cells may include prokaryotic and
eukaroytic cells. Prokaryotic cells include but are not limited to
bacteria. Eukaryotic cells include but are not limited to yeast
cells and cells derived from plants and animals, for example
mammalian, insect (e.g., Spodoptera) and human cells. Cells may be
useful when they are naturally nonadherent or have been treated not
to adhere to surfaces, for example by trypsinization.
[0098] "Control" or "control experiment" is used in accordance with
its plain ordinary meaning and refers to an experiment in which the
subjects or reagents of the experiment are treated as in a parallel
experiment except for omission of a procedure, reagent, or variable
of the experiment. In some instances, the control is used as a
standard of comparison in evaluating experimental effects. In some
embodiments, a control is the measurement of the activity of a
protein in the absence of a compound as described herein (including
embodiments and examples).
[0099] The term "modulate" is used in accordance with its plain
ordinary meaning and refers to the act of changing or varying one
or more properties. "Modulation" refers to the process of changing
or varying one or more properties. For example, as applied to the
effects of a modulator on a target protein, to modulate means to
change by increasing or decreasing a property or function of the
target molecule or the amount of the target molecule.
[0100] The term "aberrant" as used herein refers to different from
normal. When used to describe enzymatic activity or protein
function, aberrant refers to activity or function that is greater
or less than a normal control or the average of normal non-diseased
control samples.
[0101] "Nucleic acid" refers to nucleotides (e.g.,
deoxyribonucleotides or ribonucleotides) and polymers thereof in
either single-, double- or multiple-stranded form, or complements
thereof; or nucleosides (e.g., deoxyribonucleosides or
ribonucleosides). In embodiments, "nucleic acid" does not include
nucleosides. The terms "polynucleotide," "oligonucleotide," "oligo"
or the like refer, in the usual and customary sense, to a linear
sequence of nucleotides. Oligonucleotides are typically from about
5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in
length, up to about 100 nucleotides in length. Nucleic acids and
polynucleotides are a polymers of any length, including longer
lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000,
etc. In certain embodiments the nucleic acids herein contain
phosphodiester bonds. In other embodiments, nucleic acid analogs
are included that may have alternate backbones, comprising, e.g.,
phosphoramidate, phosphorothioate, phosphorodithioate, or
O-methylphosphoroamidite linkages (see Eckstein, Oligonucleotides
and Analogues: A Practical Approach, Oxford University Press); and
peptide nucleic acid backbones and linkages. Other analog nucleic
acids include those with positive backbones; non-ionic backbones,
and non-ribose backbones, including those described in U.S. Pat.
Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium
Series 580, Carbohydrate Modifications in Antisense Research,
Sanghui & Cook, eds. Nucleic acids containing one or more
carbocyclic sugars are also included within one definition of
nucleic acids. Modifications of the ribose-phosphate backbone may
be done for a variety of reasons, e.g., to increase the stability
and half-life of such molecules in physiological environments or as
probes on a biochip. Mixtures of naturally occurring nucleic acids
and analogs can be made; alternatively, mixtures of different
nucleic acid analogs, and mixtures of naturally occurring nucleic
acids and analogs may be made. A residue of a nucleic acid, as
referred to herein, is a monomer of the nucleic acid (e.g., a
nucleotide). The term "nucleoside" refers, in the usual and
customary sense, to a glycosylamine including a nucleobase and a
five-carbon sugar (ribose or deoxyribose). Non limiting examples,
of nucleosides include, cytidine, uridine, adenosine, guanosine,
thymidine and inosine. Nucleosides may be modified at the base
and/or and the sugar. The term "nucleotide" refers, in the usual
and customary sense, to a single unit of a polynucleotide, i.e., a
monomer. Nucleotides can be ribonucleotides, deoxyribonucleotides,
or modified versions thereof. Examples of polynucleotides
contemplated herein include single and double stranded DNA, single
and double stranded RNA, and hybrid molecules having mixtures of
single and double stranded DNA and RNA. Examples of nucleic acid,
e.g., polynucleotides contemplated herein include any types of RNA,
e.g., mRNA, siRNA, miRNA, and guide RNA and any types of DNA,
genomic DNA, plasmid DNA, and minicircle DNA, and any fragments
thereof. The term "duplex" in the context of polynucleotides
refers, in the usual and customary sense, to double strandedness.
Nucleic acids can be linear or branched. For example, nucleic acids
can be a linear chain of nucleotides or the nucleic acids can be
branched, e.g., such that the nucleic acids comprise one or more
arms or branches of nucleotides. Optionally, the branched nucleic
acids are repetitively branched to form higher ordered structures
such as dendrimers and the like. In embodiments, when a nucleic
acid is to be sequenced, it may be referred to as a template
nucleic acid.
[0102] "Nucleotide," as used herein, refers to a
nucleoside-5'-polyphosphate compound, or a structural analog
thereof, which can be incorporated (e.g., partially incorporated as
a nucleoside-5'-monophosphate or derivative thereof) by a nucleic
acid polymerase to extend a growing nucleic acid chain (such as a
primer). Nucleotides may comprise bases such as A, C, G, T, U, or
analogues thereof, and may comprise 2, 3, 4, 5, 6, 7, 8, or more
phosphates in the phosphate group. Nucleotides may be modified at
one or more of the base, sugar, or phosphate group. A nucleotide
may have a label or tag attached (a "labeled nucleotide" or "tagged
nucleotide").
[0103] The terms also encompass nucleic acids containing known
nucleotide analogs or modified backbone residues or linkages, which
are synthetic, naturally occurring, and non-naturally occurring,
which have similar binding properties as the reference nucleic
acid, and which are metabolized in a manner similar to the
reference nucleotides. Examples of such analogs include, without
limitation, phosphodiester derivatives including, e.g.,
phosphoramidate, phosphorodiamidate, phosphorothioate (also known
as phosphothioate having double bonded sulfur replacing oxygen in
the phosphate), phosphorodithioate, phosphonocarboxylic acids,
phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid,
methyl phosphonate, boron phosphonate, or O-methylphosphoroamidite
linkages (see Eckstein, Oligonucleotides and Analogues: A Practical
Approach, Oxford University Press) as well as modifications to the
nucleotide bases such as in 5-methyl cytidine or pseudouridine; and
peptide nucleic acid backbones and linkages. Other analog nucleic
acids include those with positive backbones; non-ionic backbones,
modified sugars, and non-ribose backbones (e.g., phosphorodiamidate
morpholino oligos or locked nucleic acids (LNA) as known in the
art), including those described in U.S. Pat. Nos. 5,235,033 and
5,034,506, and Chapters 6 and 7, ASC Symposium Series 580,
Carbohydrate Modifications in Antisense Research, Sanghui &
Cook, eds. Nucleic acids containing one or more carbocyclic sugars
are also included within one definition of nucleic acids.
Modifications of the ribose-phosphate backbone may be done for a
variety of reasons, e.g., to increase the stability and half-life
of such molecules in physiological environments or as probes on a
biochip. Mixtures of naturally occurring nucleic acids and analogs
can be made; alternatively, mixtures of different nucleic acid
analogs, and mixtures of naturally occurring nucleic acids and
analogs may be made. In embodiments, the internucleotide linkages
in DNA are phosphodiester, phosphodiester derivatives, or a
combination of both.
[0104] In embodiments, "nucleotide analogue," "nucleotide analog,"
or "nucleotide derivative" shall mean an analogue of adenine (A),
cytosine (C), guanine (G), thymine (T), or uracil (U) (that is, an
analogue or derivative of a nucleotide comprising the base adenine
(A), cytosine (C), guanine (G), thymine (T), or uracil (U)),
comprising a phosphate group, which may be recognized by DNA or RNA
polymerase (whichever is applicable) and may be incorporated into a
strand of DNA or RNA (whichever is appropriate). Examples of
nucleotide analogues include, without limitation, 7-deaza-adenine,
7-deaza-guanine, the analogues of deoxynucleotides shown herein,
analogues in which a label is attached through a cleavable linker
to the 5-position of cytosine or thymine or to the 7-position of
deaza-adenine or deaza-guanine, and analogues in which a small
chemical moiety is used to cap the --OH group at the 3'-position of
deoxyribose. Nucleotide analogues and DNA polymerase-based DNA
sequencing are also described in U.S. Pat. No. 6,664,079, which is
incorporated herein by reference in its entirety for all
purposes.
[0105] A "nucleoside" is structurally similar to a nucleotide, but
is missing the phosphate moieties. An example of a nucleoside
analogue would be one in which the label is linked to the base and
there is no phosphate group attached to the sugar molecule.
[0106] A particular nucleic acid sequence also encompasses "splice
variants." Similarly, a particular protein encoded by a nucleic
acid encompasses any protein encoded by a splice variant of that
nucleic acid. "Splice variants," as the name suggests, are products
of alternative splicing of a gene. After transcription, an initial
nucleic acid transcript may be spliced such that different
(alternate) nucleic acid splice products encode different
polypeptides. Mechanisms for the production of splice variants
vary, but include alternate splicing of exons. Alternate
polypeptides derived from the same nucleic acid by read-through
transcription are also encompassed by this definition. Any products
of a splicing reaction, including recombinant forms of the splice
products, are included in this definition. An example of potassium
channel splice variants is discussed in Leicher, et al., J. Biol.
Chem. 273(52):35095-35101 (1998).
[0107] Nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide if it is expressed as a preprotein
that participates in the secretion of the polypeptide; a promoter
or enhancer is operably linked to a coding sequence if it affects
the transcription of the sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to
facilitate translation. Generally, "operably linked" means that the
DNA sequences being linked are near each other, and, in the case of
a secretory leader, contiguous and in reading phase. However,
enhancers do not have to be contiguous. Linking is accomplished by
ligation at convenient restriction sites. If such sites do not
exist, the synthetic oligonucleotide adaptors or linkers are used
in accordance with conventional practice.
[0108] The terms "identical" or "percent identity," in the context
of two or more nucleic acids or polypeptide sequences, refer to two
or more sequences or subsequences that are the same or have a
specified percentage of amino acid residues or nucleotides that are
the same (i.e., about 60% A identity, preferably 61%, 62%, 63%,
64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%,
77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or higher identity
over a specified region when compared and aligned for maximum
correspondence over a comparison window or designated region) as
measured using a BLAST or BLAST 2.0 sequence comparison algorithms
with default parameters described below, or by manual alignment and
visual inspection (see, e.g., NCBI web site or the like). Such
sequences are then said to be "substantially identical." This
definition also refers to, or may be applied to, the compliment of
a test sequence. The definition also includes sequences that have
deletions and/or additions, as well as those that have
substitutions. As described below, the preferred algorithms can
account for gaps and the like. Preferably, identity exists over a
region that is at least about 10 amino acids or 20 nucleotides in
length, or more preferably over a region that is 10-50 amino acids
or 20-50 nucleotides in length. As used herein, percent (%) amino
acid sequence identity is defined as the percentage of amino acids
in a candidate sequence that are identical to the amino acids in a
reference sequence, after aligning the sequences and introducing
gaps, if necessary, to achieve the maximum percent sequence
identity. Alignment for purposes of determining percent sequence
identity can be achieved in various ways that are within the skill
in the art, for instance, using publicly available computer
software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign
(DNASTAR) software. Appropriate parameters for measuring alignment,
including any algorithms needed to achieve maximal alignment over
the full-length of the sequences being compared can be determined
by known methods.
[0109] For sequence comparisons, typically one sequence acts as a
reference sequence, to which test sequences are compared. When
using a sequence comparison algorithm, test and reference sequences
are entered into a computer, subsequence coordinates are
designated, if necessary, and sequence algorithm program parameters
are designated. Preferably, default program parameters can be used,
or alternative parameters can be designated. The sequence
comparison algorithm then calculates the percent sequence
identities for the test sequences relative to the reference
sequence, based on the program parameters.
[0110] A "comparison window," as used herein, includes reference to
a segment of any one of the number of contiguous positions selected
from the group consisting of from 10 to 600, usually about 50 to
about 200, more usually about 100 to about 150 in which a sequence
may be compared to a reference sequence of the same number of
contiguous positions after the two sequences are optimally aligned.
Methods of alignment of sequences for comparison are well-known in
the art. Optimal alignment of sequences for comparison can be
conducted, e.g., by the local homology algorithm of Smith &
Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment
algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),
by the search for similarity method of Pearson & Lipman, Proc.
Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized
implementations of these algorithms (GAP, BESTFIT, FASTA, and
TFASTA in the Wisconsin Genetics Software Package, Genetics
Computer Group, 575 Science Dr., Madison, Wis.), or by manual
alignment and visual inspection (see, e.g., Current Protocols in
Molecular Biology (Ausubel et al., eds. 1995 supplement)).
[0111] As used herein, the term "bioconjugate reactive moiety" and
"bioconjugate reactive group" refers to a moiety or group capable
of forming a bioconjugate (e.g., covalent linker) as a result of
the association between atoms or molecules of bioconjugate reactive
groups. The association can be direct or indirect. For example, a
conjugate between a first bioconjugate reactive group (e.g.,
--NH.sub.2--, --COOH, --N-hydroxysuccinimide, or maleimide) and a
second bioconjugate reactive group (e.g., sulfhydryl,
sulfur-containing amino acid, amine, amine sidechain containing
amino acid, or carboxylate) provided herein can be direct, e.g., by
covalent bond or linker (e.g., a first linker of second linker), or
indirect, e.g., by non-covalent bond (e.g., electrostatic
interactions (e.g., ionic bond, hydrogen bond, halogen bond), van
der Waals interactions (e.g., dipole-dipole, dipole-induced dipole,
London dispersion), ring stacking (pi effects), hydrophobic
interactions and the like). In embodiments, bioconjugates or
bioconjugate linkers are formed using bioconjugate chemistry (i.e.
the association of two bioconjugate reactive groups) including, but
are not limited to nucleophilic substitutions (e.g., reactions of
amines and alcohols with acyl halides, active esters),
electrophilic substitutions (e.g., enamine reactions) and additions
to carbon-carbon and carbon-heteroatom multiple bonds (e.g.,
Michael reaction, Diels-Alder addition). These and other useful
reactions are discussed in, for example, March, ADVANCED ORGANIC
CHEMISTRY, 3rd Ed., John Wiley & Sons, New York, 1985;
Hermanson, BIOCONJUGATE TECHNIQUES, Academic Press, San Diego,
1996; and Feeney et al., MODIFICATION OF PROTEINS; Advances in
Chemistry Series, Vol. 198, American Chemical Society, Washington,
D.C., 1982. In embodiments, the first bioconjugate reactive group
(e.g., maleimide moiety) is covalently attached to the second
bioconjugate reactive group (e.g., a sulfhydryl). In embodiments,
the first bioconjugate reactive group (e.g., haloacetyl moiety) is
covalently attached to the second bioconjugate reactive group
(e.g., a sulfhydryl). In embodiments, the first bioconjugate
reactive group (e.g., pyridyl moiety) is covalently attached to the
second bioconjugate reactive group (e.g., a sulfhydryl). In
embodiments, the first bioconjugate reactive group (e.g.,
--N-hydroxysuccinimide moiety) is covalently attached to the second
bioconjugate reactive group (e.g., an amine). In embodiments, the
first bioconjugate reactive group (e.g., maleimide moiety) is
covalently attached to the second bioconjugate reactive group
(e.g., a sulfhydryl). In embodiments, the first bioconjugate
reactive group (e.g., --sulfo-N-hydroxysuccinimide moiety) is
covalently attached to the second bioconjugate reactive group
(e.g., an amine).
[0112] Useful bioconjugate reactive groups used for bioconjugate
chemistries herein include, for example: (a) carboxyl groups and
various derivatives thereof including, but not limited to,
N-hydroxysuccinimide esters, N-hydroxybenzotriazole esters, acid
halides, acyl imidazoles, thioesters, p-nitrophenyl esters, alkyl,
alkenyl, alkynyl and aromatic esters; (b) hydroxyl groups which can
be converted to esters, ethers, aldehydes, etc.; (c) haloalkyl
groups wherein the halide can be later displaced with a
nucleophilic group such as, for example, an amine, a carboxylate
anion, thiol anion, carbanion, or an alkoxide ion, thereby
resulting in the covalent attachment of a new group at the site of
the halogen atom; (d) dienophile groups which are capable of
participating in Diels-Alder reactions such as, for example,
maleimido or maleimide groups; (e) aldehyde or ketone groups such
that subsequent derivatization is possible via formation of
carbonyl derivatives such as, for example, imines, hydrazones,
semicarbazones or oximes, or via such mechanisms as Grignard
addition or alkyllithium addition; (f) sulfonyl halide groups for
subsequent reaction with amines, for example, to form sulfonamides;
(g) thiol groups, which can be converted to disulfides, reacted
with acyl halides, or bonded to metals such as gold, or react with
maleimides; (h) amine or sulfhydryl groups (e.g., present in
cysteine), which can be, for example, acylated, alkylated or
oxidized;(i) alkenes, which can undergo, for example,
cycloadditions, acylation, Michael addition, etc.; (j) epoxides,
which can react with, for example, amines and hydroxyl
compounds;(k) phosphoramidites and other standard functional groups
useful in nucleic acid synthesis; (l) metal silicon oxide bonding;
(m) metal bonding to reactive phosphorus groups (e.g., phosphines)
to form, for example, phosphate diester bonds; (n) azides coupled
to alkynes using copper catalyzed cycloaddition click chemistry;
(o) biotin conjugate can react with avidin or strepavidin to form a
avidin-biotin complex or streptavidin-biotin complex.
[0113] The term "monophosphate" is used in accordance with its
ordinary meaning in the arts and refers to a moiety having the
formula:
##STR00003##
or ionized forms thereof. The term "polyphosphate" refers to at
least two phosphate groups, having the formula:
##STR00004##
or ionized forms thereof, wherein np is an integer of 1 or greater.
In embodiments, np is an integer from 1 to 5. In embodiments, np is
an integer from 1 to 2. In embodiments, np is 2. The term
"diphosphate" is used in accordance with its ordinary meaning in
the arts and refers to a moiety having the formula:
##STR00005##
or ionized forms thereof. The term "triphosphate" is used in
accordance with its ordinary meaning in the arts and refers to a
moiety having the formula:
##STR00006##
or ionized forms thereof. In embodiments, a polyphosphate is a
diphosphate. In embodiments, a polyphosphate is a triphosphate.
[0114] The term "nucleobase" or "base" as used herein refers to a
divalent purine or pyrimidine compound or a derivative thereof,
that may be a constituent of nucleic acid (i.e., DNA or RNA, or a
derivative thereof). In embodiments, the base is a derivative of a
naturally occurring DNA or RNA base (e.g., a base analogue). In
embodiments the base is a hybridizing base. In embodiments the base
hybridizes to a complementary base. In embodiments, the base is
capable of forming at least one hydrogen bond with a complementary
base (e.g., adenine hydrogen bonds with thymine, adenine hydrogen
bonds with uracil, guanine pairs with cytosine). Non-limiting
examples of a base includes cytosine or a derivative thereof (e.g.,
cytosine analogue), guanine or a derivative thereof (e.g., guanine
analogue), adenine or a derivative thereof (e.g., adenine
analogue), thymine or a derivative thereof (e.g., thymine
analogue), uracil or a derivative thereof (e.g., uracil analogue),
hypoxanthine or a derivative thereof (e.g., hypoxanthine analogue),
xanthine or a derivative thereof (e.g., xanthine analogue),
7-methylguanine or a derivative thereof (e.g., 7-methylguanine
analogue), deaza-adenine or a derivative thereof (e.g.,
deaza-adenine analogue), deaza-guanine or a derivative thereof
(e.g., deaza-guanine), deaza-hypoxanthine or a derivative thereof,
5,6-dihydrouracil or a derivative thereof (e.g., 5,6-dihydrouracil
analogue), 5-methylcytosine or a derivative thereof (e.g.,
5-methylcytosine analogue), or 5-hydroxymethylcytosine or a
derivative thereof (e.g., 5-hydroxymethylcytosine analogue)
moieties. In embodiments, the base is adenine, guanine,
hypoxanthine, xanthine, theobromine, caffeine, uric acid, or
isoguanine, which may be optionally substituted or modified. In
embodiments, the base is
##STR00007##
which may be optionally substituted or modified. In embodiments,
the base includes
##STR00008##
which may be optionally substituted or modified.
[0115] The term "non-covalent linker" is used in accordance with
its ordinary meaning and refers to a divalent moiety which includes
at least two molecules that are not covalently linked to each other
but are capable of interacting with each other via a non-covalent
bond (e.g., electrostatic interactions (e.g., ionic bond, hydrogen
bond, halogen bond) or van der Waals interactions (e.g.,
dipole-dipole, dipole-induced dipole, London dispersion). In
embodiments, the non-covalent linker is the result of two molecules
that are not covalently linked to each other that interact with
each other via a non-covalent bond.
[0116] The term "anchor moiety" as used herein refers to a chemical
moiety capable of interacting (e.g., covalently or non-covalently)
with a second, optionally different, chemical moiety (e.g.,
complementary anchor moiety binder). In embodiments, the anchor
moiety is a bioconjugate reactive group capable of interacting
(e.g., covalently) with a complementary bioconjugate reactive group
(e.g., complementary anchor moiety reactive group, complementary
anchor moiety binder). In embodiments, an anchor moiety is a click
chemistry reactant moiety. In embodiments, the anchor moiety (an
"affinity anchor moiety") is capable of non-covalently interacting
with a second chemical moiety (e.g., complementary affinity anchor
moiety binder). Non-limiting examples of an anchor moiety include
biotin, azide, trans-cyclooctene (TCO) (Blackman, M. L., et al., J.
Am. Chem. Soc., 2008, 130, 13518-13519; Debets, M. F., et al. Org.
Biomol. Chem., 2013, 11, 6439-6455) and phenyl boric acid (PBA)
(Bergseid M., et al., BioTechniques, 2000, 29, 1126-1133). In
embodiments, an affinity anchor moiety (e.g., biotin moiety)
interacts non-covalently with a complementary affinity anchor
moiety binder (e.g., streptavidin moiety). In embodiments, an
anchor moiety (e.g., azide moiety, trans-cyclooctene (TCO) moiety,
phenyl boric acid (PBA) moiety) covalently binds a complementary
anchor moiety binder (e.g., dibenzocyclooctyne (DBCO) moiety
(Jewett J. C. and Bertozzi C. R. J. Am. Chem. Soc., 2010, 132,
3688-3690), tetrazine (TZ) moiety, salicylhydroxamic acid (SHA)
moiety).
[0117] The terms "cleavable linker" or "cleavable moiety" as used
herein refers to a divalent or monovalent, respectively, moiety
which is capable of being separated (e.g., detached, split,
disconnected, hydrolyzed, a stable bond within the moiety is
broken) into distinct entities. In embodiments, a cleavable linker
is cleavable (e.g., specifically cleavable) in response to external
stimuli (e.g., enzymes, nucleophilic/basic reagents, reducing
agents, photo-irradiation, electrophilic/acidic reagents,
organometallic and metal reagents, or oxidizing reagents). In
embodiments, a cleavable linker is a self-immolative linker, a
trivalent linker, or a linker capable of dendritic amplication of
signal, or a self-immolative dendrimer containing linker (e.g., all
as described in US 2007/0009980, US 2006/0003383, and US
2009/0047699, which are incorporated by reference in their entirety
for any purpose). A chemically cleavable linker refers to a linker
which is capable of being split in response to the presence of a
chemical (e.g., acid, base, oxidizing agent, reducing agent, Pd(0),
tris-(2-carboxyethyl)phosphine, dilute nitrous acid, fluoride,
tris(3-hydroxypropyl)phosphine), sodium dithionite
(Na.sub.2S.sub.2O.sub.4), hydrazine (N.sub.2H.sub.4)). A chemically
cleavable linker is non-enzymatically cleavable. In embodiments,
the cleavable linker is cleaved by contacting the cleavable linker
with a cleaving agent (e.g., a reducing agent). In embodiments, the
cleaving agent is sodium dithionite (Na.sub.2S.sub.2O.sub.4), weak
acid, hydrazine (N.sub.2H.sub.4), Pd(0), or light-irradiation
(e.g., ultraviolet radiation). The term "self-immolative" referring
to a linker is used in accordance with its well understood meaning
in Chemistry and Biology as used in US 2007/0009980, US
2006/0003383, and US 2009/0047699, which are incorporated by
reference in their entirety for any purpose. In embodiments
"self-immolative" referring to a linker refers to a linker that is
capable of additional cleavage following initial cleavage by an
external stimuli. The term dendrimer is used in accordance with its
well understood meaning in Chemistry. In embodiments, the term
"self-immolative dendrimer" is used as described in US
2007/0009980, US 2006/0003383, and US 2009/0047699, which are
incorporated by reference in their entirety for any purpose and in
embodiments refers to a dendrimer that is capable of releasing all
of its tail units through a self-immolative fragmentation following
initial cleavage by an external stimulus.
[0118] A photocleavable linker (e.g., including or consisting of an
o-nitrobenzyl group) refers to a linker which is capable of being
split in response to photo-irradiation (e.g., ultraviolet
radiation). An acid-cleavable linker refers to a linker which is
capable of being split in response to a change in the pH (e.g.,
increased acidity). A base-cleavable linker refers to a linker
which is capable of being split in response to a change in the pH
(e.g., decreased acidity). An oxidant-cleavable linker refers to a
linker which is capable of being split in response to the presence
of an oxidizing agent. A reductant-cleavable linker refers to a
linker which is capable of being split in response to the presence
of an reducing agent (e.g., tris(3-hydroxypropyl)phosphine). In
embodiments, the cleavable linker is a dialkylketal linker
(Binaulda S., et al., Chem. Commun., 2013, 49, 2082-2102; Shenoi R.
A., et al., J. Am. Chem. Soc., 2012, 134, 14945-14957), an azo
linker (Rathod, K. M., et al., Chem. Sci. Tran., 2013, 2, 25-28;
Leriche G., et al., Eur. J. Org. Chem., 2010, 23, 4360-64), an
allyl linker, a cyanoethyl linker, a
1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl linker, or a
nitrobenzyl linker.
[0119] The term "orthogonally cleavable linker" or "orthogonal
cleavable linker" as used herein refer to a cleavable linker that
is cleaved by a first cleaving agent (e.g., enzyme,
nucleophilic/basic reagent, reducing agent, photo-irradiation,
electrophilic/acidic reagent, organometallic and metal reagent,
oxidizing reagent) in a mixture of two or more different cleaving
agents and is not cleaved by any other different cleaving agent in
the mixture of two or more cleaving agents. For example, two
different cleavable linkers are both orthogonal cleavable linkers
when a mixture of the two different cleavable linkers are reacted
with two different cleaving agents and each cleavable linker is
cleaved by only one of the cleaving agents and not the other
cleaving agent and the agent that cleaves each cleavable linker is
different. In embodiments, an orthogonally is a cleavable linker
that following cleavage the two separated entities (e.g.,
fluorescent dye, bioconjugate reactive group) do not further react
and form a new orthogonally cleavable linker.
[0120] The term "orthogonal detectable label" or "orthogonal
detectable moiety" as used herein refer to a detectable label
(e.g., fluorescent dye or detectable dye) that is capable of being
detected and identified (e.g., by use of a detection means (e.g.,
emission wavelength, physical characteristic measurement)) in a
mixture or a panel (collection of separate samples) of two or more
different detectable labels. For example, two different detectable
labels that are fluorescent dyes are both orthogonal detectable
labels when a panel of the two different fluorescent dyes is
subjected to a wavelength of light that is absorbed by one
fluorescent dye but not the other and results in emission of light
from the fluorescent dye that absorbed the light but not the other
fluorescent dye. Orthogonal detectable labels may be separately
identified by different absorbance or emission intensities of the
orthogonal detectable labels compared to each other and not only be
the absolute presence of absence of a signal. An example of a set
of four orthogonal detectable labels is the set of Rox-Labeled
Tetrazine, Alexa488-Labeled SHA, Cy5-Labeled Streptavidin, and
R6G-Labeled Dibenzocyclooctyne.
[0121] The term "polymerase-compatible cleavable moiety" as used
herein refers to a cleavable moiety which does not interfere with
the function of a polymerase (e.g., DNA polymerase, modified DNA
polymerase). Methods for determining the function of a polymerase
contemplated herein are described in B. Rosenblum et al. (Nucleic
Acids Res. 1997 Nov. 15; 25(22): 4500-4504); and Z. Zhu et al.
(Nucleic Acids Res. 1994 Aug. 25; 22(16): 3418-3422), which are
incorporated by reference herein in their entirety for all
purposes. In embodiments the polymerase-compatible cleavable moiety
does not decrease the function of a polymerase relative to the
absence of the polymerase-compatible cleavable moiety. In
embodiments, the polymerase-compatible cleavable moiety does not
negatively affect DNA polymerase recognition. In embodiments, the
polymerase-compatible cleavable moiety does not negatively affect
(e.g., limit) the read length of the DNA polymerase. Additional
examples of a polymerase-compatible cleavable moiety may be found
in U.S. Pat. No. 6,664,079, Ju J. et al. (2006) Proc Natl Acad Sci
USA 103(52):19635-19640; Ruparel H. et al. (2005) Proc Natl Acad
Sci USA 102(17):5932-5937; Wu J. et al. (2007) Proc Natl Acad Sci
USA 104(104):16462-16467; Guo J. et al. (2008) Proc Natl Acad Sci
USA 105(27): 9145-9150 Bentley D. R. et al. (2008) Nature
456(7218):53-59; or Hutter D. et al. (2010) Nucleosides Nucleotides
& Nucleic Acids 29:879-895, which are incorporated herein by
reference in their entirety for all purposes. In embodiments, a
polymerase-compatible cleavable moiety includes an azido moiety or
a dithiol linking moiety. In embodiments, the polymerase-compatible
cleavable moiety is independently --NH.sub.2, --CN, --CH.sub.3,
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2),
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3), or --CH.sub.2N.sub.3.
In embodiments, the polymerase-compatible cleavable moiety
comprises a disulfide moiety. In embodiments, a
polymerase-compatible cleavable moiety is a cleavable moiety on a
nucleotide, nucleobase, nucleoside, or nucleic acid that does not
interfere with the function of a polymerase (e.g., DNA polymerase,
modified DNA polymerase). In embodiments, a polymerase-compatible
cleavable moiety is a moiety described herein.
[0122] In embodiments, the polymerase-compatible cleavable moiety
may be referred to as a "reversible terminator". The terms
"reversible terminator" and "reversible terminator moiety" are used
in accordance with their plain and ordinary meanings and refers to
a cleavable moiety on the 3' position of a nucleotide which does
not interfere with the function of a polymerase (e.g., DNA
polymerase, modified DNA polymerase). In embodiments, the
reversible terminator moiety is
##STR00009##
[0123] The term "allyl" as described herein refers to an
unsubstituted methylene attached to a vinyl group (i.e.,
--CH.dbd.CH.sub.2), having the formula
##STR00010##
An "allyl linker" refers to a divalent unsubstituted methylene
attached to a vinyl group, having the formula
##STR00011##
[0124] The term "polymer" refers to a molecule including repeating
subunits (e.g., polymerized monomers). For example, polymeric
molecules may be based upon polyethylene glycol (PEG),
tetraethylene glycol (TEG), polyvinylpyrrolidone (PVP),
poly(xylene), or poly(p-xylylene). The term "polymerizable monomer"
is used in accordance with its meaning in the art of polymer
chemistry and refers to a compound that may covalently bind
chemically to other monomer molecules (such as other polymerizable
monomers that are the same or different) to form a polymer.
[0125] The term "polymerase-compatible moiety" as used herein
refers a moiety which does not interfere with the function of a
polymerase (e.g., DNA polymerase, modified DNA polymerase). Methods
for determining the function of a polymerase contemplated herein
are described in B. Rosenblum et al. (Nucleic Acids Res. 1997 Nov.
15; 25(22): 4500-4504); and Z. Zhu et al. (Nucleic Acids Res. 1994
Aug. 25; 22(16): 3418-3422), which are incorporated by reference
herein in their entirety for all purposes. In embodiments the
polymerase-compatible moiety does not decrease the function of a
polymerase relative to the absence of the polymerase-compatible
moiety. In embodiments, the polymerase-compatible moiety does not
negatively affect DNA polymerase recognition. In embodiments, the
polymerase-compatible moiety does not negatively affect (e.g.,
limit) the read length of the DNA polymerase. Additional examples
of a polymerase-compatible moiety may be found in U.S. Pat. No.
6,664,079, Ju J. et al. (2006) Proc Natl Acad Sci USA
103(52):19635-19640; Ruparel H. et al. (2005) Proc Natl Acad Sci
USA 102(17):5932-5937; Wu J. et al. (2007) Proc Natl Acad Sci USA
104(104):16462-16467; Guo J. et al. (2008) Proc Natl Acad Sci USA
105(27): 9145-9150 Bentley D. R. et al. (2008) Nature
456(7218):53-59; or Hutter D. et al. (2010) Nucleosides Nucleotides
& Nucleic Acids 29:879-895, which are incorporated herein by
reference in their entirety for all purposes. In embodiments, a
polymerase-compatible moiety includes hydrogen, --N.sub.3, --CN, or
halogen. In embodiments, a polymerase-compatible moiety is a moiety
on a nucleotide, nucleobase, nucleoside, or nucleic acid that does
not interfere with the function of a polymerase (e.g., DNA
polymerase, modified DNA polymerase).
[0126] The term "DNA polymerase" and "nucleic acid polymerase" are
used in accordance with their plain ordinary meaning and refer to
enzymes capable of synthesizing nucleic acid molecules from
nucleotides (e.g., deoxyribonucleotides). Typically, a DNA
polymerase adds nucleotides to the 3'-end of a DNA strand, one
nucleotide at a time. In embodiments, the DNA polymerase is a Pol I
DNA polymerase, Pol II DNA polymerase, Pol III DNA polymerase, Pol
IV DNA polymerase, Pol V DNA polymerase, Pol .beta. DNA polymerase,
Pol .mu. DNA polymerase, Pol .lamda. DNA polymerase, Pol .sigma.
DNA polymerase, Pol .alpha. DNA polymerase, Pol .delta. DNA
polymerase, Pol .epsilon. DNA polymerase, Pol .eta. DNA polymerase,
Pol DNA polymerase, Pol .kappa. DNA polymerase, Pol .zeta. DNA
polymerase, Pol .gamma. DNA polymerase, Pol .theta. DNA polymerase,
Pol .upsilon. DNA polymerase, or a thermophilic nucleic acid
polymerase (e.g., Taq polymerase, Therminator .gamma., 9.degree. N
polymerase (exo-), Therminator II, Therminator III, or Therminator
IX).
[0127] The term "thermophilic nucleic acid polymerase" as used
herein refers to a family of DNA polymerases (e.g., 9.degree.
N.TM.) and mutants thereof derived from the DNA polymerase
originally isolated from the hyperthermophilic archaea,
Thermococcus sp. 9 degrees N-7, found in hydrothermal vents at that
latitude (East Pacific Rise) (Southworth M. W., et al. PNAS. 1996;
93(11):5281-5285). A thermophilic nucleic acid polymerase is a
member of the family B DNA polymerases. Site-directed mutagenesis
of the 3'-5' exo motif I (Asp-Ile-Glu) to Asp-Ile-Asp resulted in
reduction of 3'-5' exonuclease activity to <1% of wild-type,
while maintaining other properties of the polymerase including its
high strand displacement activity. Subsequent mutagenesis of key
amino acids results in an increased ability of the enzyme to
incorporate dideoxynucleotides, ribonucleotides and
acyclonucleotides (e.g., Therminator II enzyme from New England
Biolabs with D141A/E143A/Y409V/A485L mutations); 3'-amino-dNTPs,
3'-azido-dNTPs and other 3'-modified nucleotides (e.g., NEB
Therminator III DNA Polymerase with D141A/E143A/L408S/Y409A/P410V
mutations, NEB Therminator IX DNA polymerase), or .gamma.-phosphate
labeled nucleotides (e.g., Therminator .gamma.:
D141A/E143A/W355A/L408W/R460A/Q461S/K464E/D480V/R484W/A485L).
Typically these enzymes do not have 5'-3' exonuclease activity.
Additional information about thermophilic nucleic acid polymerases
may be found in (Southworth M W, et al. PNAS. 1996;
93(11):5281-5285; Bergen K., et al. ChemBioChem. 2013;
14(9):1058-1062; Kumar S., et al. Scientific Reports. 2012; 2:684;
Fuller C. W., et al. 2016; 113(19):5233-5238; Guo J., et al.
Proceedings of the National Academy of Sciences of the United
States of America. 2008; 105(27):9145-9150), which are incorporated
herein in their entirety for all purposes.
[0128] The term "primer," as used herein, is defined to be one or
more nucleic acid fragments that specifically hybridize to a
nucleic acid template. A primer can be of any length depending on
the particular technique it will be used for. For example, PCR
primers are generally between 10 and 40 nucleotides in length. The
length and complexity of the nucleic acid fixed onto the nucleic
acid template is not critical to the invention. One of skill can
adjust these factors to provide optimum hybridization and signal
production for a given hybridization procedure, and to provide the
required resolution among different genes or genomic locations. The
primer permits the addition of a nucleotide residue thereto, or
oligonucleotide or polynucleotide synthesis therefrom, under
suitable conditions well-known in the art. In an embodiment the
primer is a DNA primer, i.e., a primer consisting of, or largely
consisting of, deoxyribonucleotide residues. The primers are
designed to have a sequence that is the complement of a region of
template/target DNA to which the primer hybridizes. The addition of
a nucleotide residue to the 3' end of a primer by formation of a
phosphodiester bond results in a DNA extension product. The
addition of a nucleotide residue to the 3' end of the DNA extension
product by formation of a phosphodiester bond results in a further
DNA extension product. In another embodiment the primer is an RNA
primer. In embodiments, a primer is hybridized to a target nucleic
acid.
[0129] The phrase "stringent hybridization conditions" refers to
conditions under which a primer will hybridize to its target
subsequence, typically in a complex mixture of nucleic acids, but
to no other sequences. Stringent conditions are sequence-dependent
and will be different in different circumstances. Longer sequences
hybridize specifically at higher temperatures. An extensive guide
to the hybridization of nucleic acids is found in Tijssen,
Techniques in Biochemistry and Molecular Biology--Hybridization
with Nucleic Probes, "Overview of principles of hybridization and
the strategy of nucleic acid assays" (1993). Generally, stringent
conditions are selected to be about 5-10.degree. C. lower than the
thermal melting point (T.sub.m) for the specific sequence at a
defined ionic strength pH. The T.sub.m is the temperature (under
defined ionic strength, pH, and nucleic concentration) at which 50%
of the probes complementary to the target hybridize to the target
sequence at equilibrium (as the target sequences are present in
excess, at T.sub.m, 50% of the probes are occupied at equilibrium).
Stringent conditions may also be achieved with the addition of
destabilizing agents such as formamide. For selective or specific
hybridization, a positive signal is at least two times background,
preferably 10 times background hybridization. Exemplary stringent
hybridization conditions can be as following: 50% formamide,
5.times.SSC, and 1% SDS, incubating at 42.degree. C., or,
5.times.SSC, 1% SDS, incubating at 65.degree. C., with wash in
0.2.times.SSC, and 0.1% SDS at 65.degree. C.
[0130] "Solid substrate" shall mean any suitable medium present in
the solid phase to which a nucleic acid or an agent may be affixed.
Non-limiting examples include chips, beads and columns. The solid
substrate can be non-porous or porous. Exemplary solid substrates
include, but are not limited to, glass and modified or
functionalized glass, plastics (including acrylics, polystyrene and
copolymers of styrene and other materials, polypropylene,
polyethylene, polybutylene, polyurethanes, Teflon.TM., cyclic
olefins, polyimides etc.), nylon, ceramics, resins, Zeonor, silica
or silica-based materials including silicon and modified silicon,
carbon, metals, inorganic glasses, optical fiber bundles, and
polymers.
[0131] Nucleic acids that do not hybridize to each other under
stringent conditions are still substantially identical if the
polypeptides which they encode are substantially identical. This
occurs, for example, when a copy of a nucleic acid is created using
the maximum codon degeneracy permitted by the genetic code. In such
cases, the nucleic acids typically hybridize under moderately
stringent hybridization conditions. Exemplary "moderately stringent
hybridization conditions" include a hybridization in a buffer of
40% formamide, 1 M NaCl, 1% SDS at 37.degree. C., and a wash in
1.times.SSC at 45.degree. C. A positive hybridization is at least
twice background. Those of ordinary skill will readily recognize
that alternative hybridization and wash conditions can be utilized
to provide conditions of similar stringency. Additional guidelines
for determining hybridization parameters are provided in numerous
references, e.g., Current Protocols in Molecular Biology, ed.
Ausubel, et al., supra.
[0132] The term "thio-trigger moiety" refers to a substituent
having the formula
##STR00012##
wherein X is --O--, --NH--, or --S--; R.sup.100 is --SR.sup.102 or
CN; and R.sup.102 and R.sup.102a are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. In embodiments, the thio-trigger
moiety has the formula:
##STR00013##
wherein R.sup.100 and R.sup.102a are as described herein.
[0133] A "thio-trigger containing linker" refers to a covalent
linker that includes a thio-trigger moiety. For example, when a
reducing agent (e.g., dithiothreitol, THPP, or TCEP) contacts a
thio-trigger containing linker, the heteroatom represented by the
symbol X (e.g., oxygen) of the thio-trigger moiety is reduced, and
breaks the linker, according to the mechanism:
##STR00014##
[0134] As used herein, the term "kit" refers to any delivery system
for delivering materials. In the context of reaction assays, such
delivery systems include systems that allow for the storage,
transport, or delivery of reaction reagents (e.g.,
oligonucleotides, enzymes, etc. in the appropriate containers)
and/or supporting materials (e.g., buffers, written instructions
for performing the assay, etc.) from one location to another. For
example, kits include one or more enclosures (e.g., boxes)
containing the relevant reaction reagents and/or supporting
materials. As used herein, the term "fragmented kit" refers to a
delivery system comprising two or more separate containers that
each contain a subportion of the total kit components. The
containers may be delivered to the intended recipient together or
separately. For example, a first container may contain an enzyme
for use in an assay, while a second container contains
oligonucleotides. In contrast, a "combined kit" refers to a
delivery system containing all of the components of a reaction
assay in a single container (e.g., in a single box housing each of
the desired components). The term "kit" includes both fragmented
and combined kits.
[0135] As used herein, the term "salt" refers to acid or base salts
of the compounds described herein. Illustrative examples of
acceptable salts are mineral acid (hydrochloric acid, hydrobromic
acid, phosphoric acid, and the like) salts, organic acid (acetic
acid, propionic acid, glutamic acid, citric acid and the like)
salts, quaternary ammonium (methyl iodide, ethyl iodide, and the
like) salts. In embodiments, compounds may be presented with a
positive charge, for example
##STR00015##
and it is understood an appropriate counter-ion (e.g., chloride
ion, fluoride ion, or acetate ion) may also be present, though not
explicitly shown. Likewise, for compounds having a negative
charge
##STR00016##
it is understood an appropriate counter-ion (e.g., a proton, sodium
ion, potassium ion, or ammonium ion) may also be present, though
not explicitly shown. The protonation state of the compound (e.g.,
a compound described herein) depends on the local environment
(i.e., the pH of the environment), therefore, in embodiments, the
compound may be described as having a moiety in a protonated
state
##STR00017##
or an ionic state
##STR00018##
and it is understood these are interchangeable. In embodiments, the
counter-ion is represented by the symbol M (e.g., M.sup.+ or
M.sup.-).
[0136] As used herein, the terms "sequencing", "sequence
determination", and "determining a nucleotide sequence", are used
in accordance with their ordinary meaning in the art, and refer to
determination of partial as well as full sequence information of
the nucleic acid being sequenced, and particular physical processes
for generating such sequence information. That is, the term
includes sequence comparisons, fingerprinting, and like levels of
information about a target nucleic acid, as well as the express
identification and ordering of nucleotides in a target nucleic
acid. The term also includes the determination of the
identification, ordering, and locations of one, two, or three of
the four types of nucleotides within a target nucleic acid.
[0137] As used herein, the term "extension" or "elongation" is used
in accordance with its plain and ordinary meanings and refer to
synthesis by a polymerase of a new polynucleotide strand
complementary to a template strand by adding free nucleotides
(e.g., dNTPs) from a reaction mixture that are complementary to the
template in the 5'-to-3' direction. Extension includes condensing
the 5'-phosphate group of the dNTPs with the 3'-hydroxy group at
the end of the nascent (elongating) DNA strand.
[0138] As used herein, the term "sequencing cycle" is used in
accordance with its plain and ordinary meaning and refers to
incorporating one or more nucleotides (e.g., a compound described
herein) to the 3' end of a polynucleotide with a polymerase, and
detecting one or more labels that identify the one or more
nucleotides incorporated. The sequencing may be accomplished by,
for example, sequencing by synthesis, pyrosequencing, and the like.
In embodiments, a sequencing cycle includes extending a
complementary polynucleotide by incorporating a first nucleotide
using a polymerase, wherein the polynucleotide is hybridized to a
template nucleic acid, detecting the first nucleotide, and
identifying the first nucleotide. In embodiments, to begin a
sequencing cycle, one or more differently labeled nucleotides and a
DNA polymerase can be introduced. Following nucleotide addition,
signals produced (e.g., via excitation and emission of a detectable
label) can be detected to determine the identity of the
incorporated nucleotide (based on the labels on the nucleotides).
Reagents can then be added to remove the 3' reversible terminator
and to remove labels from each incorporated base. Reagents, enzymes
and other substances can be removed between steps by washing.
Cycles may include repeating these steps, and the sequence of each
cluster is read over the multiple repetitions.
II. Compositions
[0139] In an aspect is provided a compound having the formula:
##STR00019##
[0140] B is a divalent nucleobase.
[0141] R.sup.1 is independently hydrogen, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, substituted or unsubstituted heteroaryl, a 5'-nucleoside
protecting group, monophosphate moiety or derivative thereof (e.g.,
phosphoramidate moiety, phosphorothioate moiety, phosphorodithioate
moiety, or O-methylphosphoroamidite moiety), polyphosphate moiety
or derivative thereof (e.g., including a phosphoramidate,
phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite),
or nucleic acid moiety or derivative thereof (e.g., including a
phosphoramidate, phosphorothioate, phosphorodithioate, or
O-methylphosphoroamidite).
[0142] R.sup.2 and R.sup.3 are independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety.
[0143] L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are
independently a bond, --NH--, --S--, --O--, --C(O)--, --C(O)O--,
--OC(O)--, --NHC(O)--, --C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--,
--C(S)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene; a bioconjugate linker; a cleavable
linker, a self-immolative linker, a linker capable of dendritic
amplification of signal (e.g., capable of increasing fluorescence
by releasing fluorophores from the remainder of the linker), a
trivalent linker, or a self-immolative dendrimer linker (e.g.,
capable of increasing fluorescence by releasing fluorophores from
the remainder of the linker). In embodiments, L.sup.101, L.sup.103,
L.sup.104, and L.sup.105 are independently a bond, --NH--, --S--,
--O--, --C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; a bioconjugate linker;
or a cleavable linker. In embodiments, L.sup.101, L.sup.103,
L.sup.104, and L.sup.105 are independently a bond, --NH--, --S--,
--O--, --C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene.
[0144] R.sup.100 is --SR.sup.102 or --CN.
[0145] R.sup.102 and R.sup.102a are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0146] R.sup.4 is a detectable moiety.
[0147] In embodiments, R.sup.100 is R.sup.102. In embodiments,
R.sup.100 is --CN.
[0148] In embodiments, the compound has the formula:
##STR00020##
R.sup.1, R.sup.2, R.sup.3, B, L.sup.101, R.sup.102, R.sup.102a,
L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as described
herein.
[0149] In embodiments, the compound has the formula:
##STR00021##
R.sup.1, R.sup.2, R.sup.3, B, L.sup.101, R.sup.102a, L.sup.103,
L.sup.104, L.sup.105, and R.sup.4 are as described herein.
[0150] In embodiments, R.sup.1 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted (e.g., substituted with a
substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, size-limited substituent group, or lower substituent group)
or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered),
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered), a 5'-nucleoside protecting group,
monophosphate moiety or derivative thereof (e.g., phosphoramidate
moiety, phosphorothioate moiety, phosphorodithioate moiety, or
O-methylphosphoroamidite moiety), polyphosphate moiety or
derivative thereof (e.g., including a phosphoramidate,
phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite),
or nucleic acid moiety or derivative thereof (e.g., including a
phosphoramidate, phosphorothioate, phosphorodithioate, or
O-methylphosphoroamidite). In embodiments, R.sup.1 is independently
a 5'-nucleoside protecting group, monophosphate moiety,
polyphosphate moiety, or nucleic acid moiety
[0151] In embodiments, a substituted R.sup.1 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.1 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.1 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.1 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.1 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.1 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.1 is substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when R.sup.1 is substituted, it
is substituted with 1 to 10 lower substituent groups. In
embodiments, when R.sup.1 is substituted, it is substituted with 1
to 5 substituent groups. In embodiments, when R.sup.1 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when R.sup.1 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when R.sup.1 is substituted, it is substituted with a substituent
group. In embodiments, when R.sup.1 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when R.sup.1 is substituted, it is substituted with a lower
substituent group.
[0152] In embodiments, R.sup.1 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, or a 5'-nucleoside
protecting group; or R.sup.1 is a monophosphate moiety,
polyphosphate moiety, or nucleic acid moiety. In embodiments,
R.sup.1 is independently hydrogen, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SH, --SO.sub.3H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl. In embodiments, R.sup.1 is
a 5'-nucleoside protecting group. In embodiments, R.sup.1 is a
monophosphate moiety, polyphosphate moiety, or nucleic acid moiety.
In embodiments, R.sup.1 is a monophosphate moiety. In embodiments,
R.sup.1 is a polyphosphate moiety. In embodiments, R.sup.1 is a
nucleic acid moiety. In embodiments, R.sup.1 is hydrogen. In
embodiments, R.sup.1 is a triphosphate moiety. In embodiments,
R.sup.1 is --OH.
[0153] In embodiments, R.sup.1 is hydrogen. In embodiments, R.sup.1
is --OH. In embodiments, R.sup.1 is a monophosphate moiety. In
embodiments, R.sup.1 is a polyphosphate moiety. In embodiments,
R.sup.1 is a triphosphate moiety. In embodiments, R.sup.1 is a
nucleic acid moiety. In embodiments, R.sup.1 is --OH. In
embodiments, R.sup.1 is a derivative of a monophosphate moiety. In
embodiments, R.sup.1 is a derivative of a polyphosphate moiety. In
embodiments, R.sup.1 is a derivative of a triphosphate moiety. In
embodiments, R.sup.1 is a derivative of a nucleic acid moiety.
[0154] In embodiments, R.sup.1 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl, a 5'-nucleoside protecting group,
monophosphate moiety, polyphosphate moiety, or nucleic acid moiety.
In embodiments, R.sup.1 is independently a monophosphate moiety
including a phosphodiester derivative. In embodiments, R.sup.1 is
independently a polyphosphate moiety including a phosphodiester
derivative. In embodiments, R.sup.1 is independently a nucleic acid
moiety including a phosphodiester derivative. In embodiments,
R.sup.1 is independently a phosphoramidate moiety. In embodiments,
R.sup.1 is independently a polyphosphate moiety including a
phosphoramidate. In embodiments, R.sup.1 is independently a nucleic
acid moiety including a phosphoramidate. In embodiments, R.sup.1 is
independently a phosphorothioate moiety. In embodiments, R.sup.1 is
independently a polyphosphate moiety including a phosphorothioate.
In embodiments, R.sup.1 is independently a nucleic acid moiety
including a phosphorothioate. In embodiments, R.sup.1 is
independently a phosphorodithioate moiety. In embodiments, R.sup.1
is independently a polyphosphate moiety including a
phosphorodithioate. In embodiments, R.sup.1 is independently a
nucleic acid moiety including a phosphorodithioate. In embodiments,
R.sup.1 is independently an O-methylphosphoroamidite moiety. In
embodiments, R.sup.1 is independently a polyphosphate moiety
including an O-methylphosphoroamidite. In embodiments, R.sup.1 is
independently a nucleic acid moiety including an
O-methylphosphoroamidite. In embodiments, R.sup.1 is independently
a nucleic acid moiety including a nucleotide analog. In
embodiments, R.sup.1 is independently a nucleic acid moiety
including a plurality of optionally different nucleotide
analogs.
[0155] In embodiments, R.sup.1 is independently a 5'-nucleoside
protecting group; and the 5'-nucleoside protecting group is
##STR00022##
wherein R.sup.9 is substituted or unsubstituted C.sub.1-C.sub.4
alkyl. R.sup.10 and R.sup.11 are each independently halogen,
--CF.sub.3, --Cl.sub.3, --CI.sub.3, --CBr.sub.3, --CHF.sub.2,
--CHCl.sub.2, --CHI.sub.2, --CHBr.sub.2, --OCH.sub.2F,
--OCH.sub.2Cl, --OCH.sub.2I, --OCH.sub.2Br, --OCHF.sub.2,
--CHCl.sub.2, --OCHI.sub.2, --OCHBr.sub.2, --OCF.sub.3,
--OCI.sub.3, --OCI.sub.3, --OCBr.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --N.sub.3, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl. The symbols z10 and z11
are each independently integers from 0 to 5. In embodiments, z10
and z11 are 0.
[0156] In embodiments, R.sup.9 is substituted (e.g., substituted
with a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted C.sub.1-C.sub.4 alkyl.
[0157] In embodiments, a substituted R.sup.9 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.9 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.9 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.9 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.9 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.9 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.9 is substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when R.sup.9 is substituted, it
is substituted with 1 to 10 lower substituent groups. In
embodiments, when R.sup.9 is substituted, it is substituted with 1
to 5 substituent groups. In embodiments, when R.sup.9 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when R.sup.9 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when R.sup.9 is substituted, it is substituted with a substituent
group. In embodiments, when R.sup.9 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when R.sup.9 is substituted, it is substituted with a lower
substituent group.
[0158] In embodiments, R.sup.9 is independently substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) C.sub.1-C.sub.4 alkyl. In
embodiments, R.sup.9 is an unsubstituted methyl. In embodiments,
R.sup.9 is an unsubstituted C.sub.2 alkyl. In embodiments, R.sup.9
is an unsubstituted C.sub.3 alkyl. In embodiments, R.sup.9 is an
unsubstituted C.sub.4 alkyl. In embodiments, R.sup.9 is an
unsubstituted tert-butyl.
[0159] In embodiments, R.sup.10 and R.sup.11 are each independently
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), substituted (e.g., substituted with
a substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted cycloalkyl (e.g., C.sub.3
-C.sub.8, C.sub.3 -C.sub.6, C.sub.4-C.sub.6, or C.sub.5-C.sub.6),
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered),
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.10 and R.sup.11 are each
independently unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl.
[0160] In embodiments, R.sup.10 and R.sup.11 are each independently
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl, substituted (e.g., substituted with a
substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted heteroalkyl, substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl,
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkyl, substituted (e.g., substituted with
a substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted aryl, or substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted heteroaryl. In
embodiments, R.sup.10 and R.sup.11 are each independently
unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted
cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or
unsubstituted heteroaryl.
[0161] In embodiments, a substituted R.sup.10 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.10 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.10 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.10 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.10 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.10 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.10 is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.10 is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.10 is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.10 is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.10 is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.10 is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.10 is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.10 is substituted, it is substituted with a
lower substituent group.
[0162] In embodiments, a substituted R.sup.11 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.11 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.11 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.11 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.11 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.11 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.11 is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.11 is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.11 is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.11 is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.11 is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.11 is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.11 is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.1 is substituted, it is substituted with a
lower substituent group.
[0163] In embodiments, R.sup.2 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl. In embodiments, R.sup.2 is independently
a polymerase-compatible cleavable moiety. In embodiments, R.sup.2
is independently an --O-polymerase-compatible cleavable moiety.
[0164] In embodiments, R.sup.2 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted (e.g., substituted with a
substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.2 is independently a
polymerase-compatible cleavable moiety. In embodiments, R.sup.2 is
independently a --O-polymerase-compatible cleavable moiety.
[0165] In embodiments, a substituted R.sup.2 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.2 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups;
[0166] each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, when R.sup.2 is substituted, it is substituted with at
least one substituent group. In embodiments, when R.sup.2 is
substituted, it is substituted with at least one size-limited
substituent group. In embodiments, when R.sup.2 is substituted, it
is substituted with at least one lower substituent group. In
embodiments, when R.sup.2 is substituted, it is substituted with 1
to 10 substituent groups. In embodiments, when R.sup.2 is
substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when R.sup.2 is substituted, it
is substituted with 1 to 10 lower substituent groups. In
embodiments, when R.sup.2 is substituted, it is substituted with 1
to 5 substituent groups. In embodiments, when R.sup.2 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when R.sup.2 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when R.sup.2 is substituted, it is substituted with a substituent
group. In embodiments, when R.sup.2 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when R.sup.2 is substituted, it is substituted with a lower
substituent group.
[0167] In embodiments, R.sup.2 is hydrogen. In embodiments, R.sup.2
is OH. In embodiments, R.sup.2 is --O-polymerase-compatible
cleavable moiety.
[0168] In embodiments, R.sup.2 is an --O-polymerase-compatible
cleavable moiety. In embodiments, the polymerase-compatible
cleavable moiety is independently --NH.sub.2, --NO.sub.2, --CN,
--CH.sub.3, C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2), methoxyalkyl (e.g.,
--CH.sub.2--O--CH.sub.3), or --CH.sub.2N.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently --NH.sub.2.
In embodiments, the polymerase-compatible cleavable moiety is
independently --CN. In embodiments, the polymerase-compatible
cleavable moiety is independently --CH.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2). In
embodiments, the polymerase-compatible cleavable moiety is
independently methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3). In
embodiments, the polymerase-compatible cleavable moiety is
independently CH.sub.2N.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently NH.sub.2.
In embodiments, the polymerase-compatible cleavable moiety is
independently NO.sub.2. In embodiments, the polymerase-compatible
cleavable moiety is independently CH.sub.2N.sub.3. In embodiments,
the polymerase-compatible cleavable moiety is independently
##STR00023##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00024##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00025##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00026##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00027##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00028##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00029##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00030##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00031##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00032##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00033##
In embodiments, the polymerase-compatible cleavable moiety is
independently CH.sub.2--O--CH.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently NH.sub.2,
CH.sub.2N.sub.3,
##STR00034##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00035##
[0169] In embodiments, R.sup.2 is --NH.sub.2, --CN, --CH.sub.3,
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2),
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3), or --CH.sub.2N.sub.3.
In embodiments, R.sup.2 is --NH.sub.2. In embodiments, R.sup.2 is
--CN. In embodiments, R.sup.2 is --CH.sub.3. In embodiments,
R.sup.2 is C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2).
[0170] In embodiments, R.sup.2 is methoxyalkyl (e.g.,
--CH.sub.2--O--CH.sub.3). In embodiments, R.sup.2 is
--CH.sub.2N.sub.3. In embodiments, R.sup.2 is
##STR00036##
In embodiments, R.sup.2 is
##STR00037##
In embodiments, R.sup.2 is
##STR00038##
In embodiments, R.sup.2 is
##STR00039##
In embodiments, R.sup.2 is
##STR00040##
In embodiments, R.sup.2 is
##STR00041##
In embodiments, R.sup.2 is
##STR00042##
In embodiments, R.sup.2 is
##STR00043##
In embodiments, R.sup.2 is
##STR00044##
In embodiments, R.sup.2 is
##STR00045##
In embodiments, R.sup.2 is
##STR00046##
In embodiments, R.sup.2 is --CH.sub.2--O--CH.sub.3. In embodiments,
R.sup.2 is --NH.sub.2, --CH.sub.2N.sub.3,
##STR00047##
[0171] In embodiments, R.sup.2 is
##STR00048##
[0172] In embodiments, R.sup.2 is
##STR00049##
[0173] In embodiments, R.sup.2 is
##STR00050##
[0174] In embodiments, R.sup.2 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00051##
R.sup.5A is independently hydrogen, halogen, --CX.sup.5A.sub.3,
--CHX.sup.5A.sub.2, --CH.sub.2X.sup.5A, --OCX.sup.5A.sub.3,
--OCH.sub.2X.sup.5A, --OCHX.sup.5A.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl, substituted (e.g., substituted with a
substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted heteroalkyl, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkyl, substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted aryl, or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroaryl.
R.sup.5B is independently hydrogen, halogen, --CX.sup.5B.sub.3,
--CHX.sup.5B.sub.2, --CH.sub.2X.sup.5B, --OCX.sup.5B.sub.3,
--OCH.sub.2X.sup.5B, --OCHX.sup.5B.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl, substituted (e.g., substituted with a
substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted heteroalkyl, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkyl, substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted aryl, or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroaryl. In
embodiments, R.sup.5A and R.sup.5B are combined to form an oxo.
R.sup.5C is hydrogen, halogen, --CX.sup.5C.sub.3,
--CHX.sup.5C.sub.2, --CH.sub.2X.sup.5C, --OCX.sup.5C.sub.3,
--OCH.sub.2X.sup.5C, --OCHX.sup.5C.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substitutent group) or
unsubstituted alkyl, substituted (e.g., substituted with a
substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted heteroalkyl, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl,
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkyl, substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted aryl, or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroaryl. In
embodiments, R.sup.5C is unsubstituted C.sub.1-C.sub.4 alkyl. In
embodiments, R.sup.5C is unsubstituted methyl. In embodiments,
R.sup.5C is unsubstituted tert-butyl. The symbols X.sup.5A,
X.sup.5B, and X.sup.5C are independently --F, --Cl, --Br, or
--I.
[0175] In embodiments, R.sup.2 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00052##
R.sup.5A is independently hydrogen, halogen, --CX.sup.5A.sub.3,
--CHX.sup.5A.sub.2, --CH.sub.2X.sup.5A, --OCX.sup.5A.sub.3,
--OCH.sub.2X.sup.5A, --OCHX.sup.5A.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), substituted (e.g., substituted with
a substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). R.sup.5B is independently hydrogen, halogen,
--CX.sup.5B.sub.3, --CHX.sup.5B.sub.2, --CH.sub.2X.sup.5B,
--OCX.sup.5B.sub.3, --OCH.sub.2X.sup.5B, --OCHX.sup.5B.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.5A and R.sup.5B are
combined to form an oxo. R.sup.5C is hydrogen, halogen,
--CX.sup.5C.sub.3, --CHX.sup.5C.sub.2, --CH.sub.2X.sup.5C,
--OCX.sup.5C.sub.3, --OCH.sub.2X.sup.5C, --OCHX.sup.5C.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.5C is unsubstituted
C.sub.1-C.sub.4 alkyl. In embodiments, R.sup.5C is unsubstituted
methyl. In embodiments, R.sup.5C is unsubstituted tert-butyl. The
symbols X.sup.5A, X.sup.5B, and X.sup.5C are independently --F,
--Cl, --Br, or --I.
[0176] In embodiments, a substituted R.sup.5A (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.5A is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.5A is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.5A is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.5A is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.5A is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.5A is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.5A is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.5A is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.5A is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.5A is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.5A is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.5A is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.5A is substituted, it is substituted with a
lower substituent group.
[0177] In embodiments, a substituted R.sup.5B (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.5B is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.5B is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.5B is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.5B is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.5B is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.5B is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.5B is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.5B is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.5B is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.5B is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.5B is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.5B is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.5B is substituted, it is substituted with a
lower substituent group.
[0178] In embodiments, a substituted R.sup.5 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.5C is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.5C is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.5C is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.5C is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.5C is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.5C is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.5C is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.5C is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.5C is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.5C is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.5C is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.5C is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.5C is substituted, it is substituted with a
lower substituent group.
[0179] In embodiments, R.sup.2 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00053##
In embodiments, R.sup.5A is independently hydrogen, halogen,
--CX.sup.5A.sub.3, --CHX.sup.5A.sub.2, --CH.sub.2X.sup.5A,
--OCX.sup.5A.sub.3, --OCH.sub.2X.sup.5A, --OCHX.sup.5A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5D-substituted or unsubstituted alkyl,
R.sup.5D-substituted or unsubstituted heteroalkyl,
R.sup.5D-substituted or unsubstituted cycloalkyl,
R.sup.5D-substituted or unsubstituted heterocycloalkyl,
R.sup.5D-substituted or unsubstituted aryl, or R.sup.5D-substituted
or unsubstituted heteroaryl. R.sup.5D is independently halogen,
oxo, --CX.sup.5D.sub.3, --CHX.sup.5D.sub.2, --CH.sub.2X.sup.5D,
--OCX.sup.5D.sub.3, --OCH.sub.2X.sup.5D, --OCHX.sup.5D.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5E-substituted or unsubstituted alkyl,
R.sup.5E-substituted or unsubstituted heteroalkyl,
R.sup.5E-substituted or unsubstituted cycloalkyl,
R.sup.5E-substituted or unsubstituted heterocycloalkyl,
R.sup.5E-substituted or unsubstituted aryl, or R.sup.5E-substituted
or unsubstituted heteroaryl. R.sup.5E is independently halogen,
oxo, --CX.sup.5E.sub.3, --CHX.sup.5E.sub.2, --CH.sub.2X.sup.5E,
--OCX.sup.5E.sub.3, --OCH.sub.2X.sup.5E, --OCHX.sup.5E.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.5B is independently hydrogen, halogen, --CX.sup.5B.sub.3,
--CHX.sup.5B.sub.2, --CH.sub.2X.sup.5B, --OCX.sup.5B.sub.3,
--OCH.sub.2X.sup.5B, --OCHX.sup.5B.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5F-substituted or unsubstituted alkyl, R.sup.5F-substituted
or unsubstituted heteroalkyl, R.sup.5F-substituted or unsubstituted
cycloalkyl, R.sup.5F-substituted or unsubstituted heterocycloalkyl,
R.sup.5F-substituted or unsubstituted aryl, or R.sup.5F-substituted
or unsubstituted heteroaryl. R.sup.5F is independently halogen,
oxo, --CX.sup.5F.sub.3, --CHX.sup.5F.sub.2, --CH.sub.2X.sup.5F,
--OCX.sup.5F.sub.3, --OCH.sub.2X.sup.5F, --OCHX.sup.5F.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5G-substituted or unsubstituted alkyl,
R.sup.5G-substituted or unsubstituted heteroalkyl,
R.sup.5G-substituted or unsubstituted cycloalkyl,
R.sup.5G-substituted or unsubstituted heterocycloalkyl,
R.sup.5G-substituted or unsubstituted aryl, or R.sup.5G-substituted
or unsubstituted heteroaryl. R.sup.5G is independently halogen,
oxo, --CX.sup.5G.sub.3, --CHX.sup.5G.sub.2, --CH.sub.2X.sup.5G,
--OCX.sup.5G.sub.3, --OCH.sub.2X.sup.5G, --OCHX.sup.5G.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.5A and R.sup.5B are combined to form an oxo. In embodiments,
R.sup.5C is independently hydrogen, halogen, --CX.sup.5C.sub.3,
--CHX.sup.5C.sub.2, --CH.sub.2X.sup.5C, --OCX.sup.5C.sub.3,
--OCH.sub.2X.sup.5C, --OCHX.sup.5C.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5H-substituted or unsubstituted alkyl, R.sup.5H-substituted
or unsubstituted heteroalkyl, R.sup.5H-substituted or unsubstituted
cycloalkyl, R.sup.5H-substituted or unsubstituted heterocycloalkyl,
R.sup.5H-substituted or unsubstituted aryl, or R.sup.5H-substituted
or unsubstituted heteroaryl. R.sup.5H is independently halogen,
oxo, --CX.sup.5H.sub.3, --CHX.sup.5H.sub.2, --CH.sub.2X.sup.5H,
--OCX.sup.5H.sub.3, --OCH.sub.2X.sup.5H, --OCHX.sup.5H.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5I-substituted or unsubstituted alkyl,
R.sup.5I-substituted or unsubstituted heteroalkyl,
R.sup.5I-substituted or unsubstituted cycloalkyl,
R.sup.5I-substituted or unsubstituted heterocycloalkyl,
R.sup.5I-substituted or unsubstituted aryl, or R.sup.5I-substituted
or unsubstituted heteroaryl. R.sup.5I is independently halogen,
oxo, --CX.sup.5I.sub.3, --CHX.sup.5I.sub.2, --CH.sub.2X.sup.5I,
--OCX.sup.5I.sub.3, --OCH.sub.2X.sup.5I, --OCHX.sup.5I.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.5C is unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments,
R.sup.5C is unsubstituted methyl. In embodiments, R.sup.5C is
unsubstituted tert-butyl. The symbols X.sup.5A, X.sup.5B, X.sup.5C,
X.sup.5D, X.sup.5E, X.sup.5F, X.sup.5G, X.sup.5H, and X.sup.5I are
independently --F, --Cl, --Br, or --I.
[0180] In embodiments, R.sup.2 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00054##
In embodiments, R.sup.5A is independently hydrogen, halogen,
--CX.sup.5A.sub.3, --CHX.sup.5A.sub.2, --CH.sub.2X.sup.5A,
--OCX.sup.5A.sub.3, --OCH.sub.2X.sup.5A, --OCHX.sup.5A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5D-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, C.sub.1-C.sub.4, or
C.sub.1-C.sub.2), R.sup.5D-substituted or unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), R.sup.5D-substituted or
unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6,
C.sub.4-C.sub.6, or C.sub.5-C.sub.6), R.sup.5D-substituted or
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5D-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5D-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5D is independently halogen, oxo, --CX.sup.5D.sub.3,
--CHX.sup.5D.sub.2, --CH.sub.2X.sup.5D, --OCX.sup.5D.sub.3,
--OCH.sub.2X.sup.5D, --OCHX.sup.5D.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5E-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.5E-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.5E-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.5E-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5E-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5E-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5E is independently halogen, oxo, --CX.sup.5E.sub.3,
--CHX.sup.5E.sub.2, --CH.sub.2X.sup.5E, --OCX.sup.5E.sub.3,
--OCH.sub.2X.sup.5E, --OCHX.sup.5E.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.5B is
independently hydrogen, halogen, --CX.sup.5B.sub.3,
--CHX.sup.5B.sub.2, --CH.sub.2X.sup.5B, --OCX.sup.5B.sub.3,
--OCH.sub.2X.sup.5B, --OCHX.sup.5B.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5F-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.5F-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.5F-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.5F-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5F-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5F-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5F is independently halogen, oxo, --CX.sup.5F.sub.3,
--CHX.sup.5F.sub.2, --CH.sub.2X.sup.5F, --OCX.sup.5F.sub.3,
--OCH.sub.2X.sup.5F, --OCHX.sup.5F.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5G-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.5G-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.5G-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.5G-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5G-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5G-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5G is independently halogen, oxo, --CX.sup.5G.sub.3,
--CHX.sup.5G.sub.2, --CH.sub.2X.sup.5G, --OCX.sup.5G.sub.3,
--OCH.sub.2X.sup.5G, --OCHX.sup.5G.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.5A and
R.sup.5B are combined to form an oxo. In embodiments, R.sup.5C is
independently hydrogen, halogen, --CX.sup.5C.sub.3,
--CHX.sup.5C.sub.2, --CH.sub.2X.sup.5C, --OCX.sup.5C.sub.3,
--OCH.sub.2X.sup.5C, --OCHX.sup.5C.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5H-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.5H-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.5H-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.5H-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5H-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5H-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5H is independently halogen, oxo, --CX.sup.5H.sub.3,
--CHX.sup.5H.sub.2, --CH.sub.2X.sup.5H, --OCX.sup.5H.sub.3,
--OCH.sub.2X.sup.5H, --OCHX.sup.5H.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5I-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.5I-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.5I-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.5I-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.5I-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.5I-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.5I is independently halogen, oxo, --CX.sup.5I.sub.3,
--CHX.sup.5I.sub.2, --CH.sub.2X.sup.5I, --OCX.sup.5I.sub.3,
--OCH.sub.2X.sup.5I, --OCHX.sup.5I.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.5C is
unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments, R.sup.5C is
unsubstituted methyl. In embodiments, R.sup.5C is unsubstituted
tert-butyl. The symbols X.sup.5A, X.sup.5B, X.sup.5C, X.sup.5D,
X.sup.5E, X.sup.5F, X.sup.5G, X.sup.5H, and X.sup.5I are
independently --F, --Cl, --Br, or --I.
[0181] In embodiments, R.sup.5A is independently hydrogen, halogen,
--CX.sup.5A.sub.3, --CHX.sup.5A.sub.2, --CH.sub.2X.sup.5A,
--OCX.sup.5A.sub.3, --OCH.sub.2X.sup.5A, --OCHX.sup.5A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.5D-substituted C.sub.1-C.sub.4 alkyl (e.g.,
R.sup.5D-substituted C.sub.1-C.sub.3 alkyl, R.sup.5D-substituted
C.sub.1-C.sub.2 alkyl, or R.sup.5D-substituted methyl) or
R.sup.5D-substituted 2 to 8 membered heteroalkyl (e.g., 2 to 6
membered heteroalkyl, R.sup.5D-substituted 2 to 5 membered
heteroalkyl, or R.sup.5D-substituted 2 to 4 membered heteroalkyl).
In embodiments, R.sup.5D is independently halogen, oxo,
--CX.sup.5D.sub.3, --CHX.sup.5D.sub.2, --CH.sub.2X.sup.5D,
--OCX.sup.5D.sub.3, --OCH.sub.2X.sup.5D, --OCHX.sup.5D.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, or
--ONO.sub.2. In embodiments, R.sup.5B is independently hydrogen,
halogen, --CX.sup.5B.sub.3, --CHX.sup.5B.sub.2, --CH.sub.2X.sup.5B,
--OCX.sup.5B.sub.3, --OCH.sub.2X.sup.5B, --OCHX.sup.5B.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.5F-substituted C.sub.1-C.sub.4 alkyl, (e.g.,
R.sup.5F-substituted C.sub.1-C.sub.3 alkyl, R.sup.5F-substituted
C.sub.1-C.sub.2 alkyl, or R.sup.5F-substituted methyl) or
R.sup.5F-substituted 2 to 8 membered heteroalkyl (e.g.,
R.sup.5F-substituted 2 to 6 membered heteroalkyl,
R.sup.5F-substituted 2 to 5 membered heteroalkyl, or
R.sup.5F-substituted 2 to 4 membered heteroalkyl). In embodiments,
R.sup.5F is independently halogen, oxo, --CX.sup.5F.sub.3,
--CHX.sup.5F.sub.2, --CH.sub.2X.sup.5F, --OCX.sup.5F.sub.3,
--OCH.sub.2X.sup.5F, --OCHX.sup.5F.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, or --ONO.sub.2. In
embodiments, R.sup.5A and R.sup.5B are be combined to form an oxo
group. The symbols X.sup.5A, X.sup.5B, X.sup.5D, and X.sup.5F are
independently --F, --Cl, --Br, or --I.
[0182] In embodiments, R.sup.2 is independently hydrogen, oxo,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, R.sup.2A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.2A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.2A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.2A-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.2A-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.2A-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered), or --OR.sup.2A. In embodiments, R.sup.2 is independently
--OR.sup.2A.
[0183] R.sup.2A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.2B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.2B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.2B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.2B-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.2B-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), R.sup.2B-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered), or a polymerase-compatible cleavable moiety. In
embodiments, R.sup.2A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.2B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.2B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.2B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.2B-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.2B-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.2B-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, R.sup.2A is independently a
polymerase-compatible cleavable moiety.
[0184] R.sup.2B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.2C-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.2C-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.2C-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3 -C.sub.6, or C.sub.5-C.sub.6),
R.sup.2C-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.2C-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.2C-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered).
[0185] R.sup.2C is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0186] In embodiments, R.sup.2A is a polymerase-compatible
cleavable moiety; and the polymerase-compatible cleavable moiety is
independently
##STR00055##
R.sup.5A, R.sup.5B, and R.sup.5C are as described herein, including
in embodiments.
[0187] In embodiments, R.sup.2A is independently:
##STR00056## ##STR00057## ##STR00058## ##STR00059##
[0188] In embodiments, R.sup.2A is independently:
##STR00060## ##STR00061## ##STR00062## ##STR00063##
[0189] In embodiments, R.sup.2A is independently:
##STR00064## ##STR00065## ##STR00066## ##STR00067##
[0190] In embodiments, R.sup.2A is
##STR00068##
[0191] In embodiments, R.sup.2A is
##STR00069##
[0192] In embodiments, R.sup.2A is
##STR00070##
[0193] In embodiments, R.sup.2A is independently
##STR00071##
[0194] In embodiments, R.sup.2A is independently
##STR00072##
[0195] In embodiments, R.sup.2A is independently
##STR00073##
[0196] In embodiments, R.sup.3 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl. In embodiments, R.sup.3 is independently
a polymerase-compatible cleavable moiety. In embodiments, R.sup.3
is independently an --O-polymerase-compatible cleavable moiety.
[0197] In embodiments, R.sup.3 is independently hydrogen, halogen,
--CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2,
--CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br,
--CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted (e.g., substituted with a
substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.3 is independently a
polymerase-compatible cleavable moiety. In embodiments, R.sup.3 is
independently an --O-polymerase-compatible cleavable moiety.
[0198] In embodiments, a substituted R.sup.3 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.3 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.3 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.3 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.3 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.3 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.3 is substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when R.sup.3 is substituted, it
is substituted with 1 to 10 lower substituent groups. In
embodiments, when R.sup.3 is substituted, it is substituted with 1
to 5 substituent groups. In embodiments, when R.sup.3 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when R.sup.3 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when R.sup.3 is substituted, it is substituted with a substituent
group. In embodiments, when R.sup.3 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when R.sup.3 is substituted, it is substituted with a lower
substituent group.
[0199] In embodiments, R.sup.3 is hydrogen. In embodiments, R.sup.3
is a polymerase-compatible cleavable moiety. In embodiments,
R.sup.3 is a polymerase-compatible cleavable moiety including an
azido moiety. In embodiments, R.sup.3 is a polymerase-compatible
cleavable moiety including a dithiol linker. In embodiments,
R.sup.3 is an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is --CH.sub.2N.sub.3.
[0200] In embodiments, R.sup.3 is an --O-polymerase-compatible
cleavable moiety. In embodiments, the polymerase-compatible
cleavable moiety is independently --NH.sub.2, --NO.sub.2, --CN,
--CH.sub.3, C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2), methoxyalkyl (e.g.,
--CH.sub.2--O--CH.sub.3), or CH.sub.2N.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently --NH.sub.2.
In embodiments, the polymerase-compatible cleavable moiety is
independently --CN. In embodiments, the polymerase-compatible
cleavable moiety is independently --CH.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2). In
embodiments, the polymerase-compatible cleavable moiety is
independently methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3). In
embodiments, the polymerase-compatible cleavable moiety is
independently --CH.sub.2N.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently --NH.sub.2.
In embodiments, the polymerase-compatible cleavable moiety is
independently --NO.sub.2. In embodiments, the polymerase-compatible
cleavable moiety is independently --CH.sub.2N.sub.3. In
embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00074##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00075##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00076##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00077##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00078##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00079##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00080##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00081##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00082##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00083##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00084##
In embodiments, the polymerase-compatible cleavable moiety is
independently CH.sub.2--O--CH.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently NH.sub.2,
CH.sub.2N.sub.3,
##STR00085##
or CH.sub.2--O--CH.sub.3.
[0201] In embodiments, R.sup.3 is --NH.sub.2, --CN, --CH.sub.3,
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2),
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3), or CH.sub.2N.sub.3.
In embodiments, R.sup.3 is --NH.sub.2. In embodiments, R.sup.3 is
--CN. In embodiments, R.sup.3 is --CH.sub.3. In embodiments,
R.sup.3 is C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2). In embodiments, R.sup.3 is
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3). In embodiments,
R.sup.3 is CH.sub.2N.sub.3. In embodiments, R.sup.3 is
##STR00086##
In embodiments, R.sup.3 is
##STR00087##
In embodiments, R.sup.3 is
##STR00088##
In embodiments, R.sup.3 is
##STR00089##
In embodiments, R.sup.3 is
##STR00090##
In embodiments, R.sup.3 is
##STR00091##
In embodiments, R.sup.3 is
##STR00092##
In embodiments, R.sup.3 is
##STR00093##
In embodiments, R.sup.3 is
##STR00094##
In embodiments, R.sup.3 is
##STR00095##
In embodiments, R.sup.3 is
##STR00096##
In embodiments, R.sup.3 is --CH.sub.2--O--CH.sub.3. In embodiments,
R.sup.3 is --NH.sub.2, --CH.sub.2N.sub.3,
##STR00097##
or --CH.sub.2--O--CH.sub.3.
[0202] In embodiments, R.sup.3 is
##STR00098##
[0203] In embodiments, R.sup.3 is
##STR00099##
[0204] In embodiments, R.sup.3 is
##STR00100##
[0205] In embodiments, R.sup.3 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00101##
R.sup.6A is independently hydrogen, halogen, --CX.sup.6A.sub.3,
--CHX.sup.6A.sub.2, --CH.sub.2X.sup.6A, --OCX.sup.6A.sub.3,
--OCH.sub.2X.sup.6A, --OCHX.sup.6A.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), substituted (e.g., substituted with
a substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). R.sup.6B is independently hydrogen, halogen,
--CX.sup.6B.sub.3, --CHX.sup.6B.sub.2, --CH.sub.2X.sup.6B,
--OCX.sup.6B.sub.3, --OCH.sub.2X.sup.6B, --OCHX.sup.6B.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.6A and R.sup.6B are
combined to form an oxo. R.sup.6C is hydrogen, halogen,
--CX.sup.6C.sub.3, --CHX.sup.6C.sub.2, --CH.sub.2X.sup.6C,
--OCX.sup.6C.sub.3, --OCH.sub.2X.sup.6C, --OCHX.sup.6C.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2), substituted
(e.g., substituted with a substituent group, a size-limited
substituent group, or lower substituent group) or unsubstituted
heteroalkyl (e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6
membered, 2 to 3 membered, or 4 to 5 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3
to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6
membered), substituted (e.g., substituted with a substituent group,
a size-limited substituent group, or lower substituent group) or
unsubstituted aryl (e.g., C.sub.6-C.sub.10 or phenyl), or
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered,
or 5 to 6 membered). In embodiments, R.sup.6C is unsubstituted
C.sub.1-C.sub.4 alkyl. In embodiments, R.sup.6C is unsubstituted
methyl. In embodiments, R.sup.6C is unsubstituted tert-butyl. The
symbols X.sup.6A, X.sup.6B, and X.sup.6C are independently --F,
--Cl, --Br, or --I.
[0206] In embodiments, a substituted R.sup.6A (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.6A is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.6A is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.6A is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.6A is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.6A is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.6A is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.6A is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.6A is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.6A is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.6A is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.6A is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.6A is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.6A is substituted, it is substituted with a
lower substituent group.
[0207] In embodiments, a substituted R.sup.6B (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.6B is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.6B is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.6B is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.6B is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.6B is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.6B is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.6B is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.6B is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.6B is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.6B is substituted,
it is substituted with 1 to 5 lower substituent groups. In
embodiments, when R.sup.6B is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.6B is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.6B is substituted, it is substituted with a
lower substituent group.
[0208] In embodiments, a substituted R.sup.6C (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.6C is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.6C is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.6C is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.6C is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.6C is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.6C is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.6C is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.6C is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.6C is substituted, it is substituted with 1 to 5 size-limited
substituent groups. In embodiments, when R.sup.6C is substituted,
it is substituted with 1 to S lower substituent groups. In
embodiments, when R.sup.6C is substituted, it is substituted with a
substituent group. In embodiments, when R.sup.6C is substituted, it
is substituted with a size-limited substituent group. In
embodiments, when R.sup.6C is substituted, it is substituted with a
lower substituent group.
[0209] In embodiments, R.sup.3 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00102##
In embodiments, R.sup.6A is independently hydrogen, halogen,
--CX.sup.6A.sub.3, --CHX.sup.6A.sub.2, --CH.sub.2X.sup.6A,
--OCX.sup.6A.sub.3, --OCH.sub.2X.sup.6A, --OCHX.sup.6A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6D-substituted or unsubstituted alkyl,
R.sup.6D-substituted or unsubstituted heteroalkyl,
R.sup.6D-substituted or unsubstituted cycloalkyl,
R.sup.6D-substituted or unsubstituted heterocycloalkyl,
R.sup.6D-substituted or unsubstituted aryl, or R.sup.6D-substituted
or unsubstituted heteroaryl. R.sup.6D is independently halogen,
oxo, --CX.sup.6D.sub.3, --CHX.sup.6D.sub.2, --CH.sub.2X.sup.6D,
--OCX.sup.6D.sub.3, --OCH.sub.2X.sup.6D, --OCHX.sup.6D.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6E-substituted or unsubstituted alkyl,
R.sup.6E-substituted or unsubstituted heteroalkyl,
R.sup.6E-substituted or unsubstituted cycloalkyl,
R.sup.6E-substituted or unsubstituted heterocycloalkyl,
R.sup.6E-substituted or unsubstituted aryl, or R.sup.6E-substituted
or unsubstituted heteroaryl. R.sup.6E is independently halogen,
oxo, --CX.sup.6E.sub.3, --CHX.sup.6E.sub.2, --CH.sub.2X.sup.6E,
--OCX.sup.6E.sub.3, --OCH.sub.2X.sup.6E, --OCHX.sup.6E.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.6B is independently hydrogen, halogen, --CX.sup.6B.sub.3,
--CHX.sup.6B.sub.2, --CH.sub.2X.sup.6B, --OCX.sup.6B.sub.3,
--OCH.sub.2X.sup.6B, --OCHX.sup.6B.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6F-substituted or unsubstituted alkyl, R.sup.6F-substituted
or unsubstituted heteroalkyl, R.sup.6F-substituted or unsubstituted
cycloalkyl, R.sup.6F-substituted or unsubstituted heterocycloalkyl,
R.sup.6F-substituted or unsubstituted aryl, or R.sup.6F-substituted
or unsubstituted heteroaryl. R.sup.6F is independently halogen,
oxo, --CX.sup.6F.sub.3, CHX.sup.6F.sub.2, --CH.sub.2X.sup.6F,
--OCX.sup.6F.sub.3, --OCH.sub.2X.sup.6F, --OCHX.sup.6F.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6G-substituted or unsubstituted alkyl,
R.sup.6G-substituted or unsubstituted heteroalkyl,
R.sup.6G-substituted or unsubstituted cycloalkyl,
R.sup.6G-substituted or unsubstituted heterocycloalkyl,
R.sup.6G-substituted or unsubstituted aryl, or R.sup.6G-substituted
or unsubstituted heteroaryl. R.sup.6G is independently halogen,
oxo, --CX.sup.6G.sub.3, --CHX.sup.6G.sub.2, --CH.sub.2X.sup.6G,
--OCX.sup.6G.sub.3, --OCH.sub.2X.sup.6G, --OCHX.sup.6G.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.6A and R.sup.6B are combined to form an oxo. In embodiments,
R.sup.6C is independently hydrogen, halogen, --CX.sup.6C.sub.3,
--CHX.sup.6C.sub.2, --CH.sub.2X.sup.6C, --OCX.sup.6C.sub.3,
--OCH.sub.2X.sup.6C, --OCHX.sup.6C.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6H-substituted or unsubstituted alkyl, R.sup.6H-substituted
or unsubstituted heteroalkyl, R.sup.6H-substituted or unsubstituted
cycloalkyl, R.sup.6H-substituted or unsubstituted heterocycloalkyl,
R.sup.6H-substituted or unsubstituted aryl, or R.sup.6H-substituted
or unsubstituted heteroaryl. R.sup.6H is independently halogen,
oxo, --CX.sup.6H.sub.3, --CHX.sup.6H.sub.2, --CH.sub.2X.sup.6H,
--OCX.sup.6H.sub.3, --OCH.sub.2X.sup.6H, --OCHX.sup.6H.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6I-substituted or unsubstituted alkyl,
R.sup.6I-substituted or unsubstituted heteroalkyl,
R.sup.6I-substituted or unsubstituted cycloalkyl,
R.sup.6I-substituted or unsubstituted heterocycloalkyl,
R.sup.6I-substituted or unsubstituted aryl, or R.sup.6I-substituted
or unsubstituted heteroaryl. R.sup.6I is independently halogen,
oxo, --CX.sup.6I.sub.3, --CHX.sup.6I.sub.2, --CH.sub.2X.sup.6I,
--OCX.sup.6I.sub.3, --OCH.sub.2X.sup.6I, --OCHX.sup.6I.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl, unsubstituted heteroalkyl,
unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,
unsubstituted aryl, or unsubstituted heteroaryl. In embodiments,
R.sup.6C is unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments,
R.sup.6C is unsubstituted methyl. In embodiments, R.sup.6C is
unsubstituted tert-butyl. The symbols X.sup.6A, X.sup.6B, X.sup.6C,
X.sup.6D, X.sup.6E, X.sup.6F, X.sup.6G, X.sup.6H, and X.sup.6I are
independently --F, --Cl, --Br, or --I.
[0210] In embodiments, R.sup.3 is a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; and the
polymerase-compatible cleavable moiety is independently
##STR00103##
In embodiments, R.sup.6A is independently hydrogen, halogen,
--CX.sup.6A.sub.3, --CHX.sup.6A.sub.2, --CH.sub.2X.sup.6A,
--OCX.sup.6A.sub.3, --OCH.sub.2X.sup.6A, --OCHX.sup.6A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6D-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, C.sub.1-C.sub.4, or
C.sub.1-C.sub.2), R.sup.6D-substituted or unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), R.sup.6D-substituted or
unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6,
C.sub.4-C.sub.6, or C.sub.5-C.sub.6), R.sup.6D-substituted or
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, 4 to 6 membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6D-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6D-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6D is independently halogen, oxo, --CX.sup.6D.sub.3,
--CHX.sup.6D.sub.2, --CH.sub.2X.sup.6D, --OCX.sup.6D.sub.3,
--OCH.sub.2X.sup.6D, --OCHX.sup.6D.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6E-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.6E-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.6E-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.6E-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6E-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6E-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6E is independently halogen, oxo, --CX.sup.6E.sub.3,
--CHX.sup.6E.sub.2, --CH.sub.2X.sup.6E, --OCX.sup.6E.sub.3,
--OCH.sub.2X.sup.6E, --OCHX.sup.6E.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.6B is
independently hydrogen, halogen, --CX.sup.6B.sub.3,
--CHX.sup.6B.sub.2, --CH.sub.2X.sup.6B, --OCX.sup.6B.sub.3,
--OCH.sub.2X.sup.6B, --OCHX.sup.6B.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6F-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.6F-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.6F-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.6F-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6F-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6F-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6F is independently halogen, oxo, --CX.sup.6F.sub.3,
--CHX.sup.6F.sub.2, --CH.sub.2X.sup.6F, --OCX.sup.6F.sub.3,
--OCH.sub.2X.sup.6F, --OCHX.sup.6F.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6G-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.6G-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.6G-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.6G-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6G-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6G-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6G is independently halogen, oxo, --CX.sup.6G.sub.3,
--CHX.sup.6G.sub.2, --CH.sub.2X.sup.6G, --OCX.sup.6G.sub.3,
--OCH.sub.2X.sup.6G, --OCHX.sup.6G.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.6A and
R.sup.6B are combined to form an oxo. In embodiments, R.sup.6C is
independently hydrogen, halogen, --CX.sup.6C.sub.3,
--CHX.sup.6C.sub.2, --CH.sub.2X.sup.6C, --OCX.sup.6C.sub.3,
--OCH.sub.2X.sup.6C, --OCHX.sup.6C.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6H-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.6H-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.6H-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.6H-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6H-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6H-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6H is independently halogen, oxo, --CX.sup.6H.sub.3,
--CHX.sup.6H.sub.2, --CH.sub.2X.sup.6H, --OCX.sup.6H.sub.3,
--OCH.sub.2X.sup.6H, --OCHX.sup.6H.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.6I-substituted or unsubstituted alkyl (e.g., C.sub.1-C.sub.8,
C.sub.1-C.sub.6, C.sub.1-C.sub.4, or C.sub.1-C.sub.2),
R.sup.6I-substituted or unsubstituted heteroalkyl (e.g., 2 to 8
membered, 2 to 6 membered, 4 to 6 membered, 2 to 3 membered, or 4
to 5 membered), R.sup.6I-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, C .sub.4-C.sub.6, or
C.sub.5-C.sub.6), R.sup.6I-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered),
R.sup.6I-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10
or phenyl), or R.sup.6I-substituted or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
R.sup.6I is independently halogen, oxo, --CX.sup.6I.sub.3,
--CHX.sup.6I.sub.2, --CH.sub.2X.sup.6I, --OCX.sup.6I.sub.3,
--OCH.sub.2X.sup.6I, --OCHX.sup.6I.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.-,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
unsubstituted alkyl (e.g., C.sub.1-C.sub.8, C.sub.1-C.sub.6,
C.sub.1-C.sub.4, or C.sub.1-C.sub.2), unsubstituted heteroalkyl
(e.g., 2 to 8 membered, 2 to 6 membered, 4 to 6 membered, 2 to 3
membered, or 4 to 5 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, C.sub.4-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or 5
to 6 membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10 or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered). In embodiments, R.sup.6C is
unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments, R.sup.6C is
unsubstituted methyl. In embodiments, R.sup.6C is unsubstituted
tert-butyl. The symbols X.sup.6A, X.sup.6B, X.sup.6C, X.sup.6D,
X.sup.6E, X.sup.6F, X.sup.6G, X.sup.6H, and X.sup.6I are
independently --F, --Cl, --Br, or --I.
[0211] In embodiments, R.sup.6A is independently hydrogen, halogen,
--CX.sup.6A.sub.3, --CHX.sup.6A.sub.2, --CH.sub.2X.sup.6A,
--OCX.sup.6A.sub.3, --OCH.sub.2X.sup.6A, --OCHX.sup.6A.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6D-substituted C.sub.1-C.sub.4 alkyl (e.g.,
R.sup.6D-substituted C.sub.1-C.sub.3 alkyl, R.sup.6D-substituted
C.sub.1-C.sub.2 alkyl, or R.sup.6D-substituted methyl) or
R.sup.6D-substituted 2 to 8 membered heteroalkyl (e.g.,
R.sup.6D-substituted 2 to 6 membered heteroalkyl,
R.sup.6D-substituted 2 to 5 membered heteroalkyl, or
R.sup.6D-substituted 2 to 4 membered heteroalkyl). In embodiments,
R.sup.6D is independently halogen, oxo, --CX.sup.6D.sub.3,
--CHX.sup.6D.sub.2, --CH.sub.2X.sup.6D, --OCX.sup.6D.sub.3,
--OCH.sub.2X.sup.6D, --OCHX.sup.6D.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, or --ONO.sub.2. In
embodiments, R.sup.6B is independently hydrogen, halogen,
--CX.sup.6B.sub.3, --CHX.sup.6B.sub.2, --CH.sub.2X.sup.6B,
--OCX.sup.6B.sub.3, --OCH.sub.2X.sup.6B, --OCHX.sup.6B.sub.2, --CN,
--OH, --SH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.6F-substituted C.sub.1-C.sub.4 alkyl, (e.g.,
R.sup.6F-substituted C.sub.1-C.sub.3 alkyl, R.sup.6F-substituted
C.sub.1-C.sub.2 alkyl, or R.sup.6F-substituted methyl) or
R.sup.6F-substituted 2 to 8 membered heteroalkyl (e.g.,
R.sup.6F-substituted 2 to 6 membered heteroalkyl,
R.sup.6F-substituted 2 to 5 membered heteroalkyl, or
R.sup.6F-substituted 2 to 4 membered heteroalkyl). In embodiments,
R.sup.6F is independently halogen, oxo, --CX.sup.6F.sub.3,
--CHX.sup.6F.sub.2, --CH.sub.2X.sup.6F, --OCX.sup.6F.sub.3,
--OCH.sub.2X.sup.6F, --OCHX.sup.6F.sub.2, --CN, --OH, --SH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, or --ONO.sub.2. In
embodiments, R.sup.6A and R.sup.6B are combined to form an oxo. The
symbols X.sup.6A, X.sup.6B, X.sup.6D, and X.sup.6F are
independently --F, --Cl, --Br, or --I.
[0212] In embodiments, R.sup.3 is independently hydrogen, oxo,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCBr.sub.3,
--OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2,
--OCHF.sub.2, --N.sub.3, --SF.sub.5, --NH.sub.3.sup.+,
--SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN, --ONO.sub.2,
R.sup.3A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.3A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.3A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.3A-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.3A-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.3A-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered), or --OR.sup.3A.
[0213] In embodiments, R.sup.3 is independently hydrogen, oxo,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.3A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.3A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.3A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.3A-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.3A-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.3A-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered), or --OR.sup.3A. In embodiments, R.sup.3 is independently
--OR.sup.3A. In embodiments, R.sup.3 is independently a reversible
terminator moiety.
[0214] R.sup.3A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.3B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.3B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.3B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.3B-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.3B-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), R.sup.3B-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered), or a polymerase-compatible cleavable moiety. In
embodiments, R.sup.3A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.3B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.3B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.3B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or Cs--CO,
R.sup.3B-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.3B-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.3B-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, R.sup.3A is independently a
polymerase-compatible cleavable moiety.
[0215] R.sup.3B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, R.sup.3C-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.3C-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.3C-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3 -C.sub.6, or C.sub.5-C.sub.6),
R.sup.3C-substituted or unsubstituted heterocycloalkyl (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.3C-substituted or unsubstituted aryl (e.g., C.sub.6-C.sub.10,
C.sub.10, or phenyl), or R.sup.3C-substituted or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered).
[0216] R.sup.3C is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2,
--CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F,
--CH.sub.2I, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2,
--NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3,
--OCF.sub.3, --OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2,
--OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl,
--OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5,
--NH.sub.3.sup.+, --SO.sub.3.sup.-, --OPO.sub.3H.sup.-, --SCN,
--ONO.sub.2, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0217] In embodiments, R.sup.3 is an --O-polymerase-compatible
cleavable moiety. In embodiments, the -polymerase-compatible
cleavable moiety is independently (substituted or unsubstituted
alkylene)-SS-(unsubstituted alkyl). In embodiments, the
-polymerase-compatible cleavable moiety is independently
(halo-substituted or unsubstituted C.sub.1-C.sub.3
alkylene)-SS-(unsubstituted C.sub.1-C.sub.4 alkyl).
[0218] In embodiments, R.sup.3 is --OR.sup.3A. In embodiments,
R.sup.3 is --OH. In embodiments, R.sup.3A is hydrogen. In
embodiments, R.sup.3A is a polymerase-compatible cleavable moiety.
In embodiments, R.sup.3A is a polymerase-compatible cleavable
moiety including an azido moiety. In embodiments, R.sup.3A is a
polymerase-compatible cleavable moiety including a dithiol linker.
In embodiments, R.sup.3A is a polymerase-compatible cleavable
moiety; and the polymerase-compatible cleavable moiety is
independently CH.sub.2N.sub.3.
[0219] In embodiments, the polymerase-compatible cleavable moiety
is independently --NH.sub.2, --NO.sub.2, --CN, --CH.sub.3,
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2),
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3), or CH.sub.2N.sub.3.
In embodiments, the polymerase-compatible cleavable moiety is
independently --NH.sub.2. In embodiments, the polymerase-compatible
cleavable moiety is independently --CN. In embodiments, the
polymerase-compatible cleavable moiety is independently --CH.sub.3.
In embodiments, the polymerase-compatible cleavable moiety is
independently C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2). In embodiments, the
polymerase-compatible cleavable moiety is independently
methoxyalkyl (e.g., --CH.sub.2--O--CH.sub.3). In embodiments, the
polymerase-compatible cleavable moiety is independently
CH.sub.2N.sub.3. In embodiments, the polymerase-compatible
cleavable moiety is independently NH.sub.2. In embodiments, the
polymerase-compatible cleavable moiety is independently NO.sub.2.
In embodiments, the polymerase-compatible cleavable moiety is
independently CH.sub.2N.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently
##STR00104##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00105##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00106##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00107##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00108##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00109##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00110##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00111##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00112##
In embodiments, the polymerase-compatible cleavable moiety is
independently
##STR00113##
In embodiments, the polymerase-compatible cleavable moiety is
##STR00114##
In embodiments, the polymerase-compatible cleavable moiety is
independently --CH.sub.2--O--CH.sub.3. In embodiments, the
polymerase-compatible cleavable moiety is independently --NH.sub.2,
--CH.sub.2N.sub.3
##STR00115##
[0220] In embodiments, R.sup.3A is independently --NH.sub.2, --CN,
--CH.sub.3, C.sub.2-C.sub.6 allyl (e.g.,
--CH.sub.2--CH.dbd.CH.sub.2), methoxyalkyl (e.g.,
--CH.sub.2--O--CH.sub.3), or CH.sub.2N.sub.3. In embodiments,
R.sup.3A independently is --NH.sub.2. In embodiments, R.sup.3A is
independently --CN. In embodiments, R.sup.3A is independently
--CH.sub.3. In embodiments, R.sup.3A is independently
C.sub.2-C.sub.6 allyl (e.g., --CH.sub.2--CH.dbd.CH.sub.2). In
embodiments, R.sup.3A independently is methoxyalkyl (e.g.,
--CH.sub.2--O--CH.sub.3). In embodiments, R.sup.3A is independently
CH.sub.2N.sub.3. In embodiments, R.sup.3A is independently
##STR00116##
In embodiments, R.sup.3A is independently
##STR00117##
In embodiments, R.sup.3A is independently
##STR00118##
In embodiments, R.sup.3A is
##STR00119##
In embodiments, R.sup.3A is
##STR00120##
In embodiments, R.sup.3A is independently
##STR00121##
In embodiments, R.sup.3A is independently
##STR00122##
In embodiments, R.sup.3A is independently
##STR00123##
In embodiments, R.sup.3A is independently
##STR00124##
In embodiments, R.sup.3A is independently
##STR00125##
In embodiments, R.sup.3A is independently
##STR00126##
In embodiments, R.sup.3A is independently --CH.sub.2--O--CH.sub.3.
In embodiments, R.sup.3A is independently --NH.sub.2,
--CH.sub.2N.sub.3,
##STR00127##
[0221] In embodiments, R.sup.3A is a polymerase-compatible
cleavable moiety; and the polymerase-compatible cleavable moiety is
independently
##STR00128##
R.sup.6A, R.sup.6B, and R.sup.6C are as described herein, including
in embodiments.
[0222] In embodiments, R.sup.3A is independently:
##STR00129## ##STR00130## ##STR00131## ##STR00132##
[0223] In embodiments, R.sup.3A is independently:
##STR00133## ##STR00134## ##STR00135## ##STR00136##
[0224] In embodiments, R.sup.3A is independently:
##STR00137## ##STR00138## ##STR00139## ##STR00140##
[0225] In embodiments, R.sup.3A is
##STR00141##
[0226] In embodiments, R.sup.3A is
##STR00142##
[0227] In embodiments, R.sup.3A is
##STR00143##
[0228] In embodiments, R.sup.3A is independently
##STR00144##
[0229] In embodiments, R.sup.3A is independently
##STR00145##
[0230] In embodiments, R.sup.3A is independently
##STR00146##
[0231] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00147## ##STR00148## ##STR00149## ##STR00150##
[0232] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00151## ##STR00152## ##STR00153## ##STR00154##
[0233] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00155## ##STR00156## ##STR00157## ##STR00158##
[0234] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00159##
[0235] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00160##
[0236] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00161##
[0237] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00162##
[0238] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00163##
[0239] In embodiments, the -polymerase-compatible cleavable moiety
is independently:
##STR00164##
[0240] In embodiments, B is a divalent cytosine or a derivative
thereof, divalent guanine or a derivative thereof, divalent adenine
or a derivative thereof, divalent thymine or a derivative thereof,
divalent uracil or a derivative thereof, divalent hypoxanthine or a
derivative thereof, divalent xanthine or a derivative thereof,
divalent 7-methylguanine or a derivative thereof, divalent
5,6-dihydrouracil or a derivative thereof, divalent
5-methylcytosine or a derivative thereof, or divalent
5-hydroxymethylcytosine or a derivative thereof.
[0241] In embodiments, B is
##STR00165##
[0242] In embodiments, B is a divalent cytosine or a derivative
thereof. In embodiments, B is a divalent guanine or a derivative
thereof. In embodiments, B is a divalent adenine or a derivative
thereof. In embodiments, B is a divalent thymine or a derivative
thereof. In embodiments, B is a divalent uracil or a derivative
thereof. In embodiments, B is a divalent hypoxanthine or a
derivative thereof. In embodiments, B is a divalent xanthine or a
derivative thereof. In embodiments, B is a divalent 7-methylguanine
or a derivative thereof. In embodiments, B is a divalent
5,6-dihydrouracil or a derivative thereof. In embodiments, B is a
divalent 5-methylcytosine or a derivative thereof. In embodiments,
B is a divalent 5-hydroxymethylcytosine or a derivative
thereof.
[0243] In embodiments, B is a divalent cytosine. In embodiments, B
is a divalent guanine. In embodiments, B is a divalent adenine. In
embodiments, B is a divalent thymine. In embodiments, B is a
divalent uracil. In embodiments, B is a divalent hypoxanthine. In
embodiments, B is a divalent xanthine. In embodiments, B is a
divalent 7-methylguanine. In embodiments, B is a divalent
5,6-dihydrouracil. In embodiments, B is a divalent
5-methylcytosine. In embodiments, B is a divalent
5-hydroxymethylcytosine.
[0244] In embodiments, B is independently
##STR00166##
In embodiments, B is independently
##STR00167##
In embodiments, B is independently
##STR00168##
In embodiments, B is independently
##STR00169##
[0245] In embodiments, L.sup.101 is independently a bond, --NH--,
--O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--,
--OC(O)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene.
[0246] In embodiments, L.sup.101 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted
or unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), substituted or unsubstituted cycloalkylene (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6), substituted
or unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted or
unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0247] In embodiments, L.sup.101 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkylene
(e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10 membered, 2 to 8
membered, 2 to 6 membered, or 2 to 4 membered), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkylene
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroarylene
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0248] In embodiments, a substituted L.sup.101 (e.g., substituted
alkylene, substituted heteroalkylene, substituted cycloalkylene,
substituted heterocycloalkylene, substituted arylene, and/or
substituted heteroarylene) is substituted with at least one
substituent group, size-limited substituent group, or lower
substituent group; wherein if the substituted L.sup.101 is
substituted with a plurality of groups selected from substituent
groups, size-limited substituent groups, and lower substituent
groups; each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, when L.sup.101 is substituted, it is substituted with
at least one substituent group. In embodiments, when L.sup.101 is
substituted, it is substituted with at least one size-limited
substituent group. In embodiments, when L.sup.101 is substituted,
it is substituted with at least one lower substituent group. In
embodiments, when L.sup.101 is substituted, it is substituted with
1 to 10 substituent groups. In embodiments, when L.sup.101 is
substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when L.sup.101 is substituted,
it is substituted with 1 to 10 lower substituent groups. In
embodiments, when L.sup.101 is substituted, it is substituted with
1 to 5 substituent groups. In embodiments, when L.sup.101 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when L.sup.101 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when L.sup.101 is substituted, it is substituted with a substituent
group. In embodiments, when L.sup.101 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when L.sup.101 is substituted, it is substituted with a lower
substituent group.
[0249] In embodiments, L.sup.101 is a bond, --NH--, --NR.sup.101--,
--S--, --O--, --C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--,
--C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--, --C(S)--,
R.sup.101-substituted or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.101-substituted or
unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.101-substituted or unsubstituted
cycloalkylene (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or
C.sub.5-C.sub.6), R.sup.101-substituted or unsubstituted
heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, or 5
to 6 membered), R.sup.101-substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or
R.sup.101-substituted or unsubstituted heteroarylene (e.g., 5 to 10
membered, 5 to 9 membered, or 5 to 6 membered). In embodiments,
L.sup.101 is a bond. In embodiments, L.sup.101 is --NH--. In
embodiments, L.sup.101 is --NR.sup.101--. In embodiments, L.sup.101
is --S--. In embodiments, L.sup.101 is --O--. In embodiments,
L.sup.101 is --C(O)--. In embodiments, L.sup.101 is --C(O)O--. In
embodiments, L.sup.101 is --OC(O)--. In embodiments, L.sup.101 is
--NHC(O)--. In embodiments, L.sup.101 is --C(O)NH--. In
embodiments, L.sup.101 is --NHC(O)NH--. In embodiments, L.sup.101
is --NHC(NH)NH--. In embodiments, L.sup.101 is --C(S)--. In
embodiments, L.sup.101 is R.sup.101-substituted or unsubstituted
C.sub.1-C.sub.20 alkylene. In embodiments, L.sup.101 is
R.sup.101-substituted or unsubstituted 2 to 20 membered
heteroalkylene. In embodiments, L.sup.101 is R.sup.101-substituted
or unsubstituted C.sub.3-C.sub.8 cycloalkylene. In embodiments,
L.sup.101 is R.sup.101-substituted or unsubstituted 3 to 8 membered
heterocycloalkylene. In embodiments, L.sup.101 is
R.sup.101-substituted or unsubstituted C.sub.6-C.sub.10 arylene. In
embodiments, L.sup.101 is R.sup.101-substituted or unsubstituted 5
to 10 membered heteroarylene.
[0250] In embodiments, L.sup.101 is --(CH.sub.2CH.sub.2O).sub.b--.
In embodiments, L.sup.101 is
--CCCH.sub.2(OCH.sub.2CH.sub.2).sub.a--NHC(O)--(CH.sub.2).sub.c(OCH.sub.2-
CH.sub.2).sub.b--. In embodiments, L.sup.101 is
--CHCHCH.sub.2--NHC(O)--(CH.sub.2).sub.c(OCH.sub.2CH.sub.2).sub.b--.
In embodiments, L.sup.101 is
--CCCH.sub.2--NHC(O)--(CH.sub.2).sub.c(OCH.sub.2CH.sub.2).sub.b--.
In embodiments, L.sup.101 is --CCCH.sub.2--. The symbol a is an
integer from 0 to 8. In embodiments, a is 1. In embodiments, a is
0. The symbol b is an integer from 0 to 8. In embodiments, b is 1
or 2. In embodiments, b is an integer from 2 to 8. In embodiments,
b is 1. The symbol c is an integer from 0 to 8. In embodiments, c
is 3. In embodiments, c is 1. In embodiments, c is 2.
[0251] R.sup.101 is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.101A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.101A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.101A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.101A-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.101A-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.101A-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0252] In embodiments, R.sup.101 is independently --NH.sub.2. In
embodiments, R.sup.101 is independently --OH. In embodiments,
R.sup.101 is independently halogen. In embodiments, R.sup.101 is
independently --CN. In embodiments, R.sup.101 is independently oxo.
In embodiments, R.sup.101 is independently --CF.sub.3. In
embodiments, R.sup.101 is independently --COOH. In embodiments,
R.sup.101 is independently --CONH.sub.2. In embodiments, R.sup.101
is independently --F. In embodiments, R.sup.101 is independently
--Cl. In embodiments, R.sup.101 is independently --Br. In
embodiments, R.sup.101 is independently --I.
[0253] R.sup.101A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.101B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), R.sup.101B-substituted or unsubstituted
heteroalkyl (e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10
membered, 2 to 8 membered, 2 to 6 membered, or 2 to 4 membered),
R.sup.101B-substituted or unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.101B-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.101B-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.101B-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0254] R.sup.101B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0255] In embodiments, R.sup.102 and R.sup.102a are independently
hydrogen, halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3,
--CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2,
--CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H,
--NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3,
--OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2,
--OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I,
--OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted (e.g., substituted
with a substituent group, a size-limited substituent group, or
lower substituent group) or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, C.sub.1-C.sub.4, or
C.sub.1-C.sub.2), substituted (e.g., substituted with a substituent
group, a size-limited substituent group, or lower substituent
group) or unsubstituted heteroalkyl (e.g., 2 to 8 membered, 2 to 6
membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5 membered),
substituted (e.g., substituted with a substituent group, a
size-limited substituent group, or lower substituent group) or
unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6,
C.sub.4-C.sub.6, or C.sub.5-C.sub.6), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, 4 to 6
membered, 4 to 5 membered, or 5 to 6 membered), substituted (e.g.,
substituted with a substituent group, a size-limited substituent
group, or lower substituent group) or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10 or phenyl), or substituted (e.g., substituted with
a substituent group, a size-limited substituent group, or lower
substituent group) or unsubstituted heteroaryl (e.g., 5 to 10
membered, 5 to 9 membered, or 5 to 6 membered).
[0256] In embodiments, a substituted R.sup.102 (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.102 is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.102 is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.102 is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.102 is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.102 is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.102 is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.102 is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.102 is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.102 is substituted, it is substituted with 1 to 5
size-limited substituent groups. In embodiments, when R.sup.102 is
substituted, it is substituted with 1 to 5 lower substituent
groups. In embodiments, when R.sup.102 is substituted, it is
substituted with a substituent group. In embodiments, when
R.sup.102 is substituted, it is substituted with a size-limited
substituent group. In embodiments, when R.sup.102 is substituted,
it is substituted with a lower substituent group.
[0257] In embodiments, a substituted R.sup.102a (e.g., substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, and/or substituted heteroaryl)
is substituted with at least one substituent group, size-limited
substituent group, or lower substituent group; wherein if the
substituted R.sup.102a is substituted with a plurality of groups
selected from substituent groups, size-limited substituent groups,
and lower substituent groups; each substituent group, size-limited
substituent group, and/or lower substituent group may optionally be
different. In embodiments, when R.sup.102a is substituted, it is
substituted with at least one substituent group. In embodiments,
when R.sup.102a is substituted, it is substituted with at least one
size-limited substituent group. In embodiments, when R.sup.102a is
substituted, it is substituted with at least one lower substituent
group. In embodiments, when R.sup.102a is substituted, it is
substituted with 1 to 10 substituent groups. In embodiments, when
R.sup.102a is substituted, it is substituted with 1 to 10
size-limited substituent groups. In embodiments, when R.sup.102a is
substituted, it is substituted with 1 to 10 lower substituent
groups. In embodiments, when R.sup.102a is substituted, it is
substituted with 1 to 5 substituent groups. In embodiments, when
R.sup.102a is substituted, it is substituted with 1 to 5
size-limited substituent groups. In embodiments, when R.sup.102a is
substituted, it is substituted with 1 to 5 lower substituent
groups. In embodiments, when R.sup.6B is substituted, it is
substituted with a substituent group. In embodiments, when
R.sup.102a is substituted, it is substituted with a size-limited
substituent group. In embodiments, when R.sup.102a is substituted,
it is substituted with a lower substituent group.
[0258] In embodiments, L.sup.103 is independently a bond, --NH--,
--O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--,
--OC(O)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene.
[0259] In embodiments, L.sup.103 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted or unsubstituted
heteroalkylene (e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10
membered, 2 to 8 membered, 2 to 6 membered, or 2 to 4 membered),
substituted or unsubstituted cycloalkylene (e.g., C.sub.3-C.sub.8,
C.sub.3-C.sub.6, or C.sub.5-C.sub.6), substituted or unsubstituted
heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, or 5
to 6 membered), substituted or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted or
unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0260] In embodiments, L.sup.103 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted (e.g.,
substituted with a group, size-limited substituent group, or lower
substituent group) or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), substituted (e.g., substituted with a group,
size-limited substituent group, or lower substituent group) or
unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), substituted (e.g., substituted with a group,
size-limited substituent group, or lower substituent group) or
unsubstituted cycloalkylene (e.g., C.sub.3-C.sub.8,
C.sub.3-C.sub.6, or C.sub.5-C.sub.6), substituted (e.g.,
substituted with a group, size-limited substituent group, or lower
substituent group) or unsubstituted heterocycloalkylene (e.g., 3 to
8 membered, 3 to 6 membered, or 5 to 6 membered), substituted
(e.g., substituted with a group, size-limited substituent group, or
lower substituent group) or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted (e.g.,
substituted with a group, size-limited substituent group, or lower
substituent group) or unsubstituted heteroarylene (e.g., 5 to 10
membered, 5 to 9 membered, or 5 to 6 membered).
[0261] In embodiments, a substituted L.sup.103 (e.g., substituted
alkylene, substituted heteroalkylene, substituted cycloalkylene,
substituted heterocycloalkylene, substituted arylene, and/or
substituted heteroarylene) is substituted with at least one
substituent group, size-limited substituent group, or lower
substituent group; wherein if the substituted L.sup.103 is
substituted with a plurality of groups selected from substituent
groups, size-limited substituent groups, and lower substituent
groups; each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, when L.sup.103 is substituted, it is substituted with
at least one substituent group. In embodiments, when L.sup.103 is
substituted, it is substituted with at least one size-limited
substituent group. In embodiments, when L.sup.103 is substituted,
it is substituted with at least one lower substituent group. In
embodiments, when L.sup.103 is substituted, it is substituted with
1 to 10 substituent groups. In embodiments, when L.sup.103 is
substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when L.sup.103 is substituted,
it is substituted with 1 to 10 lower substituent groups. In
embodiments, when L.sup.103 is substituted, it is substituted with
1 to 5 substituent groups. In embodiments, when L.sup.103 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when L.sup.103 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when L.sup.103 is substituted, it is substituted with a substituent
group. In embodiments, when L.sup.103 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when L.sup.103 is substituted, it is substituted with a lower
substituent group.
[0262] In embodiments, L.sup.103 is a bond, --NH--, --NR.sup.103--,
--S--, --O--, --C(O)--, --OC(O)O--, --C(O)--, --NHC(O)--,
--C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--, --C(S)--,
R.sup.103-substituted or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.103-substituted or
unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.103-substituted or unsubstituted
cycloalkylene (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or
C.sub.5-C.sub.6), R.sup.103-substituted or unsubstituted
heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, or 5
to 6 membered), R.sup.103-substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or
R.sup.103-substituted or unsubstituted heteroarylene (e.g., 5 to 10
membered, 5 to 9 membered, or 5 to 6 membered). In embodiments,
L.sup.103 is a bond. In embodiments, L.sup.103 is --NH--. In
embodiments, L.sup.103 is --NR.sup.103--. In embodiments, L.sup.103
is --S--. In embodiments, L.sup.103 is --O--. In embodiments,
L.sup.103 is --C(O)--. In embodiments, L.sup.103 is --C(O)O--. In
embodiments, L.sup.103 is --OC(O)--. In embodiments, L.sup.103 is
--NHC(O)--. In embodiments, L.sup.103 is --C(O)NH--. In
embodiments, L.sup.103 is --NHC(O)NH--. In embodiments, L.sup.103
is --NHC(NH)NH--. In embodiments, L.sup.103 is --C(S)--. In
embodiments, L.sup.103 is R.sup.103-substituted or unsubstituted
C.sub.1-C.sub.20 alkylene. In embodiments, L.sup.103 is
R.sup.103-substituted or unsubstituted 2 to 20 membered
heteroalkylene. In embodiments, L.sup.103 is R.sup.103-substituted
or unsubstituted C.sub.3-C.sub.8 cycloalkylene. In embodiments,
L.sup.103 is R.sup.103-substituted or unsubstituted 3 to 8 membered
heterocycloalkylene. In embodiments, L.sup.103 is
R.sup.103-substituted or unsubstituted C.sub.6-C.sub.10 arylene. In
embodiments, L.sup.103 is unsubstituted phenylene. In embodiments,
L.sup.103 is R.sup.103-substituted or unsubstituted 5 to 10
membered heteroarylene.
[0263] In embodiments, L.sup.103 is --(CH.sub.2CH.sub.2O).sub.d--.
In embodiments, L.sup.103 is --(CH.sub.2O).sub.d--. In embodiments,
L.sup.103 is --(CH.sub.2).sub.d--. In embodiments, L.sup.103 is
--(CH.sub.2).sub.d--NH--. In embodiments, L.sup.103 is
-(unsubstituted phenylene)-. In embodiments, L.sup.103 is
##STR00170##
In embodiments, L.sup.103 is -(unsubstituted phenylene)--C(O)NH--.
In embodiments, L.sup.103 is
##STR00171##
In embodiments, L.sup.103 is -(unsubstituted phenylene)--NHC(O)--.
In embodiments, L.sup.103 is
##STR00172##
The symbol d is an integer from 0 to 8. In embodiments, d is 3. In
embodiments, d is 2. In embodiments, d is 1. In embodiments, d is
0.
[0264] R.sup.103 is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.103A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), R.sup.103A-substituted or unsubstituted
heteroalkyl (e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10
membered, 2 to 8 membered, 2 to 6 membered, or 2 to 4 membered),
R.sup.103A-substituted or unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.103A-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.103A-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.103A-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0265] In embodiments, R.sup.103 is independently --NH.sub.2. In
embodiments, R.sup.103 is independently --OH. In embodiments,
R.sup.103 is independently halogen. In embodiments, R.sup.103 is
independently --CN. In embodiments, R.sup.103 is independently oxo.
In embodiments, R.sup.103 is independently --CF.sub.3. In
embodiments, R.sup.103 is independently --COOH. In embodiments,
R.sup.103 is independently --CONH.sub.2. In embodiments, R.sup.103
is independently --F. In embodiments, R.sup.103 is independently
--Cl. In embodiments, R.sup.103 is independently --Br. In
embodiments, R.sup.103 is independently --I.
[0266] R.sup.103A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.103B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.103B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.103B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
substituted or unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.103B-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.103B-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0267] R.sup.103B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0268] In embodiments, L.sup.104 is independently a bond, --NH--,
--O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--,
--OC(O)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene.
[0269] In embodiments, L.sup.104 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted
or unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), substituted or unsubstituted cycloalkylene (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6), substituted
or unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted or
unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0270] In embodiments, L.sup.104 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkylene
(e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10 membered, 2 to 8
membered, 2 to 6 membered, or 2 to 4 membered), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkylene
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroarylene
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0271] In embodiments, a substituted L.sup.104 (e.g., substituted
alkylene, substituted heteroalkylene, substituted cycloalkylene,
substituted heterocycloalkylene, substituted arylene, and/or
substituted heteroarylene) is substituted with at least one
substituent group, size-limited substituent group, or lower
substituent group; wherein if the substituted L.sup.104 is
substituted with a plurality of groups selected from substituent
groups, size-limited substituent groups, and lower substituent
groups; each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, when L.sup.104 is substituted, it is substituted with
at least one substituent group. In embodiments, when L.sup.104 is
substituted, it is substituted with at least one size-limited
substituent group. In embodiments, when L.sup.104 is substituted,
it is substituted with at least one lower substituent group. In
embodiments, when L.sup.104 is substituted, it is substituted with
1 to 10 substituent groups. In embodiments, when L.sup.104 is
substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when L.sup.104 is substituted,
it is substituted with 1 to 10 lower substituent groups. In
embodiments, when L.sup.104 is substituted, it is substituted with
1 to 5 substituent groups. In embodiments, when L.sup.104 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when L.sup.104 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when L.sup.104 is substituted, it is substituted with a substituent
group. In embodiments, when L.sup.104 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when L.sup.104 is substituted, it is substituted with a lower
substituent group.
[0272] In embodiments, L.sup.104 is a bond, --NH--, --NR.sup.104--,
--S--, --O--, --C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--,
--C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--, --C(S)--,
R.sup.104-substituted or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.104-substituted or
unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.104-substituted or unsubstituted
cycloalkylene (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or
C.sub.5-C.sub.6), R.sup.104-substituted or unsubstituted
heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6 membered, or 5
to 6 membered), R.sup.104-substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or
R.sup.104-substituted or unsubstituted heteroarylene (e.g., 5 to 10
membered, 5 to 9 membered, or 5 to 6 membered). In embodiments,
L.sup.104 is a bond. In embodiments, L.sup.104 is --NH--. In
embodiments, L.sup.104 is --NR.sup.104--. In embodiments, L.sup.104
is --S--. In embodiments, L.sup.104 is --O--. In embodiments,
L.sup.104 is --C(O)--. In embodiments, L.sup.104 is --C(O)O--. In
embodiments, L.sup.104 is --OC(O)--. In embodiments, L.sup.104 is
--NHC(O)--. In embodiments, L.sup.104 is --C(O)NH--. In
embodiments, L.sup.104 is --NHC(O)NH--. In embodiments, L.sup.104
is --NHC(NH)NH--. In embodiments, L.sup.104 is --C(S)--. In
embodiments, L.sup.104 is R.sup.104-substituted or unsubstituted
C.sub.1-C.sub.20 alkylene. In embodiments, L.sup.104 is
R.sup.104-substituted or unsubstituted 2 to 20 membered
heteroalkylene. In embodiments, L.sup.104 is R.sup.104-substituted
or unsubstituted C.sub.3-C.sub.8 cycloalkylene. In embodiments,
L.sup.104 is R.sup.104-substituted or unsubstituted 3 to 8 membered
heterocycloalkylene. In embodiments, L.sup.104 is
R.sup.104-substituted or unsubstituted C.sub.6-C.sub.10 arylene. In
embodiments, L.sup.104 is unsubstituted phenylene. In embodiments,
L.sup.104 is R.sup.104-substituted or unsubstituted 5 to 10
membered heteroarylene.
[0273] In embodiments, L.sup.104 is --(CH.sub.2CH.sub.2O).sub.e--.
In embodiments, L.sup.104 is --(CH.sub.2O).sub.e--. In embodiments,
L.sup.104 is --(CH.sub.2).sub.e--. In embodiments, L.sup.104 is
(CH.sub.2).sub.e--NH--. In embodiments, L.sup.104 is
-(unsubstituted phenylene)-. In embodiments, L.sup.104 is
##STR00173##
In embodiments, L.sup.104 is -(unsubstituted phenylene)--C(O)NH--.
In embodiments, L.sup.104 is
##STR00174##
In embodiments, L.sup.104 is -(unsubstituted phenylene)--NHC(O)--.
In embodiments, L.sup.104 is
##STR00175##
The symbol e is an integer from 0 to 8. In embodiments, e is 3. In
embodiments, e is 1. In embodiments, e is 2.
[0274] R.sup.104 is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.104A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.104A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.104A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.104A-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.104A-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.104A-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0275] In embodiments, R.sup.104 is independently --NH.sub.2. In
embodiments, R.sup.104 is independently --OH. In embodiments,
R.sup.104 is independently halogen. In embodiments, R.sup.104 is
independently --CN. In embodiments, R.sup.104 is independently oxo.
In embodiments, R.sup.104 is independently --CF.sub.3. In
embodiments, R.sup.104 is independently --COOH. In embodiments,
R.sup.104 is independently --CONH.sub.2. In embodiments, R.sup.104
is independently --F. In embodiments, R.sup.104 is independently
--Cl. In embodiments, R.sup.104 is independently --Br. In
embodiments, R.sup.104 is independently --I.
[0276] R.sup.104A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.104B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.104B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.104B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.104B-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.104B-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.104B-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0277] R.sup.104B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0278] In embodiments, L.sup.105 is independently a bond, --NH--,
--O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--,
--OC(O)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene.
[0279] In embodiments, L.sup.105 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted or unsubstituted
alkylene (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted
or unsubstituted heteroalkylene (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), substituted or unsubstituted cycloalkylene (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6), substituted
or unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted or unsubstituted arylene
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted or
unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0280] In embodiments, L.sup.105 is a bond, --NH--, --S--, --O--,
--C(O)--, --C(O)O--, --OC(O)--, --NHC(O)--, --C(O)NH--,
--NHC(O)NH--, --NHC(NH)NH--, --C(S)--, substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroalkylene
(e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10 membered, 2 to 8
membered, 2 to 6 membered, or 2 to 4 membered), substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted cycloalkylene
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
substituted (e.g., substituted with a substituent group,
size-limited substituent group, or lower substituent group) or
unsubstituted heterocycloalkylene (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), substituted (e.g., substituted with
a substituent group, size-limited substituent group, or lower
substituent group) or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or substituted (e.g.,
substituted with a substituent group, size-limited substituent
group, or lower substituent group) or unsubstituted heteroarylene
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0281] In embodiments, a substituted L.sup.105 (e.g., substituted
alkylene, substituted heteroalkylene, substituted cycloalkylene,
substituted heterocycloalkylene, substituted arylene, and/or
substituted heteroarylene) is substituted with at least one
substituent group, size-limited substituent group, or lower
substituent group; wherein if the substituted L.sup.105 is
substituted with a plurality of groups selected from substituent
groups, size-limited substituent groups, and lower substituent
groups; each substituent group, size-limited substituent group,
and/or lower substituent group may optionally be different. In
embodiments, when L.sup.105 is substituted, it is substituted with
at least one substituent group. In embodiments, when L.sup.105 is
substituted, it is substituted with at least one size-limited
substituent group. In embodiments, when L.sup.105 is substituted,
it is substituted with at least one lower substituent group. In
embodiments, when L.sup.105 is substituted, it is substituted with
1 to 10 substituent groups. In embodiments, when L.sup.105 is
substituted, it is substituted with 1 to 10 size-limited
substituent groups. In embodiments, when L.sup.105 is substituted,
it is substituted with 1 to 10 lower substituent groups. In
embodiments, when L.sup.105 is substituted, it is substituted with
1 to 5 substituent groups. In embodiments, when L.sup.105 is
substituted, it is substituted with 1 to 5 size-limited substituent
groups. In embodiments, when L.sup.105 is substituted, it is
substituted with 1 to 5 lower substituent groups. In embodiments,
when L.sup.105 is substituted, it is substituted with a substituent
group. In embodiments, when L.sup.105 is substituted, it is
substituted with a size-limited substituent group. In embodiments,
when L.sup.105 is substituted, it is substituted with a lower
substituent group.
[0282] In embodiments, L.sup.105 is a bond, --NH--, --NR.sup.105--,
--S--, --O--, --C(O)--, --OC(O)O--, --C(O)--, --NHC(O)--,
--C(O)NH--, --NHC(O)NH--, --NHC(NH)NH--, --C(S)--,
R.sup.105-substituted or unsubstituted alkylene (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), R.sup.105-substituted or unsubstituted
heteroalkylene (e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10
membered, 2 to 8 membered, 2 to 6 membered, or 2 to 4 membered),
R.sup.105-substituted or unsubstituted cycloalkylene (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.105-substituted or unsubstituted heterocycloalkylene (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.105-substituted or unsubstituted arylene (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenylene), or R.sup.105-substituted
or unsubstituted heteroarylene (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered). In embodiments, L.sup.105 is a bond.
In embodiments, L.sup.105 is --NH--. In embodiments, L.sup.105 is
--NR.sup.105--. In embodiments, L.sup.105 is --S--. In embodiments,
L.sup.105 is --O--. In embodiments, L.sup.105 is --C(O)--. In
embodiments, L.sup.105 is --C(O)O--. In embodiments, L.sup.105 is
--OC(O)--. In embodiments, L.sup.105 is --NHC(O)--. In embodiments,
L.sup.105 is --C(O)NH--. In embodiments, L.sup.105 is --NHC(O)NH--.
In embodiments, L.sup.105 is --NHC(NH)NH--. In embodiments,
L.sup.105 is --C(S)--. In embodiments, L.sup.105 is
R.sup.105-substituted or unsubstituted C.sub.1-C.sub.20 alkylene.
In embodiments, L.sup.105 is R.sup.105-substituted or unsubstituted
2 to 20 membered heteroalkylene. In embodiments, L.sup.105 is
oxo-substituted 2 to 20 membered heteroalkylene. In embodiments,
L.sup.105 is R.sup.105-substituted or unsubstituted C.sub.3-C.sub.8
cycloalkylene. In embodiments, L.sup.105 is R.sup.105-substituted
or unsubstituted 3 to 8 membered heterocycloalkylene. In
embodiments, L.sup.105 is oxo-substituted 3 to 8 membered
heterocycloalkylene. In embodiments, L.sup.105 is
R.sup.105-substituted or unsubstituted C.sub.6-C.sub.10 arylene. In
embodiments, L.sup.105 is R.sup.105-substituted or unsubstituted 5
to 10 membered heteroarylene. In embodiments, L.sup.105 is
oxo-substituted 5 to 10 membered heteroarylene.
[0283] In embodiments, L.sup.105 is --(CH.sub.2CH.sub.2O).sub.f--.
In embodiments, L.sup.105 is --(CH.sub.2O).sub.f--. In embodiments,
L.sup.105 is --(CH.sub.2).sub.f--. In embodiments, L.sup.105 is
--(CH.sub.2).sub.f--NH--. In embodiments, L.sup.105 is
--C(O)NH(CH.sub.2).sub.f--NH--. In embodiments, L.sup.105 is
--(CH.sub.2CH.sub.2O).sub.f--(CH.sub.2).sub.g--NH--. In
embodiments, L.sup.105 is --(CH.sub.2).sub.g--. In embodiments,
L.sup.105 is --(CH.sub.2).sub.g--NH--. In embodiments, L.sup.105 is
--NHC(O)--(CH.sub.2).sub.f--NH--. In embodiments, L.sup.105 is
--NHC(O)--(CH.sub.2).sub.f--NH--. In embodiments, L.sup.105 is
--NHC(O)--(CH.sub.2CH.sub.2O).sub.f--(CH.sub.2).sub.g--NH--. In
embodiments, L.sup.105 is --NHC(O)--(CH.sub.2).sub.g--. In
embodiments, L.sup.105 is --NHC(O)--(CH.sub.2).sub.g--NH--. In
embodiments, L.sup.105 is --C(O)NH(CH.sub.2).sub.f--NH--. In
embodiments, L.sup.105 is
--C(O)NH--(CH.sub.2CH.sub.2O).sub.f--(CH.sub.2).sub.g--NH--. In
embodiments, L.sup.105 is --C(O)NH--(CH.sub.2).sub.g--. In
embodiments, L.sup.105 is --C(O)NH--(CH.sub.2).sub.g--NH--. The
symbol f is an integer from 0 to 8. In embodiments, f is 3. In
embodiments, f is 1. In embodiments, f is 2. In embodiments, f is
0. The symbol g is an integer from 0 to 8. In embodiments, g is 3.
In embodiments, g is 1. In embodiments, g is 2. In embodiments, g
is 0.
[0284] R.sup.105 is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.105A-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.105A-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.105A-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.105A-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.105A-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.105A-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0285] In embodiments, R.sup.105 is independently --NH.sub.2. In
embodiments, R.sup.105 is independently --OH. In embodiments,
R.sup.105 is independently halogen. In embodiments, R.sup.105 is
independently --CN. In embodiments, R.sup.105 is independently oxo.
In embodiments, R.sup.105 is independently --CF.sub.3. In
embodiments, R.sup.105 is independently --COOH. In embodiments,
R.sup.105 is independently --CONH.sub.2. In embodiments, R.sup.105
is independently --F. In embodiments, R.sup.105 is independently
--Cl. In embodiments, R.sup.105 is independently --Br. In
embodiments, R.sup.105 is independently --I.
[0286] R.sup.105A is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.105B-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.105B-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.105B-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.105B-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.105B-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.105B-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0287] R.sup.105B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.6, or C.sub.1-C.sub.4),
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8,
C.sub.3-C.sub.6, or C.sub.5-C.sub.6), unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6
membered), unsubstituted aryl (e.g., C.sub.6-C.sub.10, C.sub.10, or
phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to
9 membered, or 5 to 6 membered).
[0288] In embodiments, L.sup.101, L.sup.103, L.sup.104, and
L.sup.105 are independently a bond, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene.
[0289] In embodiments, L.sup.101, L.sup.103, L.sup.104, and
L.sup.105 are independently a bond, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and R.sup.102 and
R.sup.102a are independently hydrogen or unsubstituted alkyl.
[0290] In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene.
[0291] In embodiments, L.sup.103 is independently a bond or
substituted or unsubstituted 2 to 10 membered heteroalkylene.
[0292] In embodiments, L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene.
[0293] In embodiments, L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene.
[0294] In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; L.sup.105 is independently
bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and R.sup.102 is unsubstituted C.sub.1-C.sub.4
alkyl; and R.sup.102a is hydrogen or unsubstituted methyl.
[0295] In embodiments, L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene.
[0296] In embodiments, L.sup.104 is unsubstituted phenylene.
[0297] In embodiments, L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; L.sup.104 is unsubstituted phenylene; and R.sup.102
and R.sup.102a are independently hydrogen or unsubstituted
alkyl.
[0298] In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene.
[0299] In embodiments, L.sup.103 is independently a bond or
substituted or unsubstituted 2 to 10 membered heteroalkylene.
[0300] In embodiments, L.sup.104 is independently an unsubstituted
phenylene.
[0301] In embodiments, L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene.
[0302] In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; L.sup.104 is independently an
unsubstituted phenylene; L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
R.sup.102 is unsubstituted C.sub.1-C.sub.4 alkyl; and R.sup.102a is
hydrogen or unsubstituted methyl.
[0303] In embodiments, L.sup.101, L.sup.103, L.sup.104, and
L.sup.105 are independently a bond, --NH--, --O--, --C(O)--,
--C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--,
substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; and R.sup.102 is unsubstituted C.sub.1-C.sub.4
alkyl.
[0304] In embodiments, L.sup.101, L.sup.103, L.sup.104, and
L.sup.105 are independently a bond, --NH--, --O--, --C(O)--,
--C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--,
substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene.
[0305] In embodiments, R.sup.102 is unsubstituted C.sub.1-C.sub.4
alkyl.
[0306] In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; L.sup.105 is independently
bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and R.sup.102 is unsubstituted C.sub.1-C.sub.4
alkyl. In embodiments, L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene. In embodiments,
L.sup.103 is independently a bond or substituted or unsubstituted 2
to 10 membered heteroalkylene. In embodiments, L.sup.104 is
independently a bond, substituted or unsubstituted 4 to 18 membered
heteroalkylene, or substituted or unsubstituted phenylene. In
embodiments, L.sup.105 is independently bond or substituted or
unsubstituted 4 to 18 membered heteroalkylene.
[0307] In embodiments, L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; L.sup.104 is unsubstituted phenylene; and R.sup.102
is unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments, L.sup.101,
L.sup.103 and L.sup.105 are independently a bond, --NH--, --O--,
--C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--, --C(O)O--,
--OC(O)--, substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, or substituted or
unsubstituted heteroarylene. In embodiments, L.sup.104 is
unsubstituted phenylene.
[0308] In embodiments, R.sup.102 is independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --N.sub.3, R.sup.102B-substituted or
unsubstituted alkyl (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, or C.sub.1-C.sub.4),
R.sup.102B-substituted or unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), R.sup.102B-substituted or
unsubstituted cycloalkyl (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6,
or C.sub.5-C.sub.6), R.sup.102B-substituted or unsubstituted
heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6
membered), R.sup.102B-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.102B-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0309] In embodiments, R.sup.102 is independently unsubstituted
alkyl (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.6,
or C.sub.1-C.sub.4). In embodiments, R.sup.102 is independently
unsubstituted C.sub.1-C.sub.6 alkyl. In embodiments, R.sup.102 is
independently unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments,
R.sup.102 is independently unsubstituted methyl. In embodiments,
R.sup.102 is independently unsubstituted ethyl. In embodiments,
R.sup.102 is independently unsubstituted propyl (e.g., n-propyl or
isopropyl). In embodiments, R.sup.102 is independently
unsubstituted butyl (e.g., n-butyl, s-butyl, t-butyl, or isobutyl).
In embodiments, R.sup.102 is independently unsubstituted
tert-butyl. In embodiments, R.sup.102 is independently
hydrogen.
[0310] R.sup.102B is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, R.sup.102C-substituted or unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), R.sup.102C-substituted or
unsubstituted heteroalkyl (e.g., 2 to 20 membered, 8 to 20
membered, 2 to 10 membered, 2 to 8 membered, 2 to 6 membered, or 2
to 4 membered), R.sup.102C-substituted or unsubstituted cycloalkyl
(e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
R.sup.102C-substituted or unsubstituted heterocycloalkyl (e.g., 3
to 8 membered, 3 to 6 membered, or 5 to 6 membered),
R.sup.102C-substituted or unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or R.sup.102C-substituted
or unsubstituted heteroaryl (e.g., 5 to 10 membered, 5 to 9
membered, or 5 to 6 membered).
[0311] R.sup.102C is independently oxo, halogen, --CCl.sub.3,
--CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--N.sub.3, unsubstituted alkyl (e.g., C.sub.1-C.sub.20,
C.sub.10-C.sub.20, C.sub.1-C.sub.8, C.sub.1-C.sub.6, or
C.sub.1-C.sub.4), unsubstituted heteroalkyl (e.g., 2 to 20
membered, 8 to 20 membered, 2 to 10 membered, 2 to 8 membered, 2 to
6 membered, or 2 to 4 membered), unsubstituted cycloalkyl (e.g.,
C.sub.3-C.sub.8, C.sub.3-C.sub.6, or C.sub.5-C.sub.6),
unsubstituted heterocycloalkyl (e.g., 3 to 8 membered, 3 to 6
membered, or 5 to 6 membered), unsubstituted aryl (e.g.,
C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted heteroaryl
(e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6 membered).
[0312] In embodiments, R.sup.102a is independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --N.sub.3, unsubstituted alkyl (e.g.,
C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4), unsubstituted heteroalkyl
(e.g., 2 to 20 membered, 8 to 20 membered, 2 to 10 membered, 2 to 8
membered, 2 to 6 membered, or 2 to 4 membered), unsubstituted
cycloalkyl (e.g., C.sub.3-C.sub.8, C.sub.3-C.sub.6, or
C.sub.5-C.sub.6), unsubstituted heterocycloalkyl (e.g., 3 to 8
membered, 3 to 6 membered, or 5 to 6 membered), unsubstituted aryl
(e.g., C.sub.6-C.sub.10, C.sub.10, or phenyl), or unsubstituted
heteroaryl (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6
membered). In embodiments, R.sup.102a is independently hydrogen or
unsubstituted alkyl (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20,
C.sub.1-C.sub.8, C.sub.1-C.sub.6, or C.sub.1-C.sub.4).
[0313] In embodiments, R.sup.102a is independently unsubstituted
alkyl (e.g., C.sub.1-C.sub.20, C.sub.10-C.sub.20, C.sub.1-C.sub.8,
C.sub.1-C.sub.6, or C.sub.1-C.sub.4). In embodiments, R.sup.102a is
independently unsubstituted C.sub.1-C.sub.6 alkyl. In embodiments,
R.sup.102a is independently unsubstituted C.sub.1-C.sub.4 alkyl. In
embodiments, R.sup.102a is independently unsubstituted methyl. In
embodiments, R.sup.102a is independently unsubstituted tert-butyl.
In embodiments, R.sup.102a is independently hydrogen.
[0314] In embodiments, R.sup.102 and R.sup.102a are independently
hydrogen or unsubstituted alkyl. In embodiments, R.sup.102 is
unsubstituted C.sub.1-C.sub.4 alkyl. In embodiments, R.sup.102a is
hydrogen or unsubstituted methyl.
[0315] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00176##
[0316] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00177## ##STR00178##
[0317] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00179##
[0318] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00180##
[0319] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00181## ##STR00182##
[0320] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00183##
[0321] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00184##
[0322] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00185## ##STR00186##
[0323] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00187##
[0324] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00188##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00189##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00190##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00191##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00192##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00193##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00194##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00195##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00196##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00197##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00198##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00199##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00200##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.10-
5)- is
##STR00201##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00202##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00203##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00204##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00205##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00206##
In embodiments,
-L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.10-
5)- is
##STR00207##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00208##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00209##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00210##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00211##
[0325] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00212##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00213##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00214##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is,
##STR00215##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00216##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is,
##STR00217##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00218##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00219##
[0326] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00220##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00221##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00222##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00223##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00224##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00225##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00226##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00227##
[0327] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00228##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00229##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00230##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00231##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00232##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00233##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00234##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00235##
[0328] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00236##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00237##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00238##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00239##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00240##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00241##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00242##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00243##
[0329] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00244##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00245##
In embodiments,
-L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.10-
5)- is
##STR00246##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00247##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.204)-(L.sup.1-
05)- is
##STR00248##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00249##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.204)-(L.sup.1-
05)- is
##STR00250##
[0330] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00251##
[0331] In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00252##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00253##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00254##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00255##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is,
##STR00256##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00257##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00258##
In embodiments,
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00259##
[0332] In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00260##
[0333] In embodiments,
-(L.sup.101)-OC(SCN)((R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00261##
[0334] In embodiments,
-(L.sup.101)-OC(SCN)((R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00262##
[0335] In embodiments,
-(L.sup.101)-OC(SCN)((R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00263##
In embodiments,
-(L.sup.101)-OC(SCN)((R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00264##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00265##
In embodiments,
-(L.sup.101)-OC(SCN)((R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00266##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00267##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00268##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00269##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00270##
[0336] In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00271##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00272##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00273##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00274##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00275##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00276##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00277##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00278##
[0337] In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00279##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00280##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00281##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00282##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00283##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.204)-(L.sup.105)-
is
##STR00284##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.204)-(L.sup.105)-
is
##STR00285##
In embodiments,
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00286##
[0338] In embodiments, R.sup.4 is a fluorescent dye moiety. In
embodiments, R.sup.4 is a detectable moiety described herein (e.g.,
Table 1). In embodiments, R.sup.4 is a detectable moiety described
in Table 1.
[0339] In embodiments, R.sup.4 is
##STR00287##
[0340] In embodiments, R.sup.4 is
##STR00288##
In embodiments, R.sup.4 is
##STR00289##
In embodiments, R.sup.4 is
##STR00290##
In embodiments, R.sup.4 is
##STR00291##
[0341] In embodiments, the compound has the formula:
##STR00292##
R.sup.3, B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, R.sup.102,
and R.sup.4 are as described herein, including in embodiments. In
embodiments, R.sup.3 is an --O-polymerase-compatible cleavable
moiety. In embodiments, R.sup.102 is an unsubstituted
C.sub.1-C.sub.4 alkyl.
[0342] In embodiments, the compound has the formula:
##STR00293##
R.sup.3, B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4
are as described herein, including in embodiments. In embodiments,
R.sup.3 is an --O-polymerase-compatible cleavable moiety.
[0343] In embodiments, the compound has the formula:
##STR00294##
B, R.sup.1, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105,
R.sup.102, and R.sup.4 are as described herein.
[0344] In embodiments, compound has the formula:
##STR00295##
B, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105, R.sup.102,
and R.sup.4 are as described herein.
[0345] In embodiments, the compound has the formula:
##STR00296##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, R.sup.102, and
R.sup.4 are as described herein.
[0346] In embodiments, the compound has the formula:
##STR00297##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0347] In embodiments, the compound has the formula:
##STR00298##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0348] In embodiments, the compound has the formula:
##STR00299##
B, R.sup.1, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105,
and R.sup.4 are as described herein.
[0349] In embodiments, compound has the formula:
##STR00300##
B, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4
are as described herein.
[0350] In embodiments, the compound has the formula:
##STR00301##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0351] In embodiments, the compound has the formula:
##STR00302##
B, R.sup.1, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105,
R.sup.102, and R.sup.4 are as described herein.
[0352] In embodiments, the compound has the formula:
##STR00303##
B, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105, R.sup.102,
and R.sup.4 are as described herein.
[0353] In embodiments, the compound has the formula:
##STR00304##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, R.sup.102, and
R.sup.4 are as described herein.
[0354] In embodiments, the compound has the formula:
##STR00305##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0355] In embodiments, the compound has the formula:
##STR00306##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0356] In embodiments, the compound has the formula:
##STR00307##
B, R.sup.1, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105,
and R.sup.4 are as described herein.
[0357] In embodiments, the compound has the formula:
##STR00308##
B, R.sup.2, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4
are as described herein.
[0358] In embodiments, the compound has the formula:
##STR00309##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0359] In embodiments, the compound has the formula:
##STR00310##
wherein R.sup.3A, B, L.sup.101, L.sup.103, R.sup.102, and R.sup.4
are as described herein, including in embodiments. In embodiments,
the compound has the formula:
##STR00311##
wherein R.sup.3A, B, L.sup.101, L.sup.103, and R.sup.4 are as
described herein, including in embodiments. In embodiments, L.sup.1
is
##STR00312##
In embodiments, L.sup.1 is
##STR00313##
In embodiments, L.sup.1 is
##STR00314##
In embodiments, R.sup.3A is independently:
##STR00315## ##STR00316## ##STR00317## ##STR00318##
[0360] In embodiments, R.sup.2 is hydrogen. In embodiments, R.sup.2
is --OH.
[0361] In embodiments, R.sup.102 is unsubstituted methyl. In
embodiments, R.sup.102 is unsubstituted ethyl. In embodiments,
R.sup.102 is unsubstituted propyl. In embodiments, R.sup.102 is
unsubstituted isopropyl. In embodiments, R.sup.102 is unsubstituted
butyl. In embodiments, R.sup.102 is unsubstituted tert-butyl.
[0362] In embodiments, L.sup.101 is
##STR00319##
In embodiments, L.sup.101 is
##STR00320##
In embodiments, L.sup.101 is CCCH.sub.2--. In embodiments,
L.sup.101 is
##STR00321##
In embodiments, L.sup.101 is
##STR00322##
In embodiments, L.sup.101 is
##STR00323##
[0363] In embodiments, L.sup.103 is
##STR00324##
In embodiments, L.sup.103 is
##STR00325##
In embodiments, L.sup.103 is
##STR00326##
In embodiments, L.sup.103 is
##STR00327##
In embodiments, L.sup.103 is
##STR00328##
In embodiments, L.sup.103 is a bond.
[0364] In embodiments, L.sup.104 is
##STR00329##
In embodiments, L.sup.104 is
##STR00330##
In embodiments, L.sup.104 is
##STR00331##
In embodiments, L.sup.104 is
##STR00332##
In embodiments, L.sup.104 is
##STR00333##
In embodiments, L.sup.104 is a bond.
[0365] In embodiments, L.sup.105 is
##STR00334##
In embodiments, L.sup.105 is
##STR00335##
In embodiments, L.sup.105 is
##STR00336##
In embodiments, L.sup.105 is
##STR00337##
In embodiments, L.sup.105 is
##STR00338##
In embodiments, L.sup.105 is a bond.
[0366] In embodiments, L.sup.103-L.sup.104-L.sup.105- is
##STR00339##
In embodiments, L.sup.103-L.sup.104-L.sup.105- is
##STR00340##
In embodiments, L.sup.103-L.sup.104-L.sup.105- is
##STR00341##
In embodiments, L.sup.103-L.sup.104-L.sup.105- is
##STR00342##
In embodiments, L.sup.103-L.sup.104-L.sup.105- is
##STR00343##
[0367] In embodiments, the compound has the formula:
##STR00344##
R.sup.3, R.sup.4, and R.sup.102 are as described herein, including
in embodiments. In embodiments, R.sup.3 is an
--O-polymerase-compatible cleavable moiety. In embodiments,
R.sup.102 is an unsubstituted C.sub.1-C.sub.4 alkyl.
[0368] In embodiments, the compound has the formula:
##STR00345##
R.sup.3 and R.sup.4 are as described herein, including in
embodiments. In embodiments, R.sup.3 is an
--O-polymerase-compatible cleavable moiety.
[0369] In embodiments, the compound has the formula:
##STR00346##
R.sup.3, R.sup.4, and R.sup.102 are as described herein, including
in embodiments. In embodiments, R.sup.3 is an
--O-polymerase-compatible cleavable moiety. In embodiments,
R.sup.100 is an unsubstituted C.sub.1-C.sub.4 alkyl.
[0370] In embodiments, the compound has the formula:
##STR00347##
R.sup.3 and R.sup.4 are as described herein, including in
embodiments. In embodiments, R.sup.3 is an
--O-polymerase-compatible cleavable moiety.
[0371] In embodiments, the compound has the formula:
##STR00348##
B, R.sup.2, and R.sup.4 are as described herein.
[0372] In embodiments, the compound has the formula:
##STR00349##
B, R.sup.2, and R.sup.4 are as described herein.
[0373] In embodiments, the compound has the formula:
##STR00350##
B and R.sup.4 are as described herein.
[0374] In embodiments, the compound has the formula:
##STR00351##
B and R.sup.4 are as described herein.
[0375] In embodiments, the compound has the formula:
##STR00352##
B, R.sup.2, and R.sup.4 are as described herein.
[0376] In embodiments, the compound has the formula:
##STR00353##
B and R.sup.4 are as described herein.
[0377] In embodiments, the compound has the formula:
##STR00354##
B, R.sup.2, and R.sup.4 are as described herein.
[0378] In embodiments, the compound has the formula:
##STR00355##
B, R.sup.2, and R.sup.4 are as described herein.
[0379] In embodiments, the compound has the formula:
##STR00356##
B and R.sup.4 are as described herein.
[0380] In embodiments, the compound has the formula:
##STR00357##
B and R.sup.4 are as described herein.
[0381] In embodiments, the compound has the formula:
##STR00358##
B, R.sup.2, and R.sup.4 are as described herein.
[0382] In embodiments, the compound has the formula:
##STR00359##
B and R.sup.4 are as described herein.
[0383] In embodiments, the compound has the formula:
##STR00360##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (IV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(IV), R.sup.100 is --CN.
[0384] In embodiments, the compound has the formula:
##STR00361##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0385] In embodiments, the compound has the formula:
##STR00362##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0386] In embodiments, the compound has the formula:
##STR00363##
B and R.sup.4 are as described herein. In embodiments of Formula
(V), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (V), R.sup.100 is --CN.
[0387] In embodiments, the compound has the formula:
##STR00364##
B and R.sup.4 are as described herein. In embodiments of Formula
(VI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (VI), R.sup.100 is --CN.
[0388] In embodiments, the compound has the formula:
##STR00365##
B and R.sup.4 are as described herein.
[0389] In embodiments, the compound has the formula:
##STR00366##
B and R.sup.4 are as described herein.
[0390] In embodiments, the compound has the formula:
##STR00367##
B and R.sup.4 are as described herein.
[0391] In embodiments, the compound has the formula:
##STR00368##
B and R.sup.4 are as described herein.
[0392] In embodiments, the compound has the formula:
##STR00369##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (VII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(VII), R.sup.100 is --CN.
[0393] In embodiments, the compound has the formula:
##STR00370##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0394] In embodiments, the compound has the formula:
##STR00371##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0395] In embodiments, the compound has the formula:
##STR00372##
B and R.sup.4 are as described herein. In embodiments of Formula
(VIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (VIII), R.sup.100 is --CN.
[0396] In embodiments, the compound has the formula:
##STR00373##
B and R.sup.4 are as described herein. In embodiments of Formula
(IX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (IX), R.sup.100 is --CN.
[0397] In embodiments, the compound has the formula:
##STR00374##
B and R.sup.4 are as described herein.
[0398] In embodiments, the compound has the formula:
##STR00375##
B and R.sup.4 are as described herein.
[0399] In embodiments, the compound has the formula:
##STR00376##
B and R.sup.4 are as described herein.
[0400] In embodiments, the compound has the formula:
##STR00377##
B and R.sup.4 are as described herein.
[0401] In embodiments, the compound has the formula:
##STR00378##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (X), R.sup.100 is
--SR.sup.102 and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(X), R.sup.100 is --CN.
[0402] In embodiments, the compound has the formula:
##STR00379##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0403] In embodiments, the compound has the formula:
##STR00380##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0404] In embodiments, the compound has the formula:
##STR00381##
B and R.sup.4 are as described herein. In embodiments of Formula
(XI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XI), R.sup.100 is --CN.
[0405] In embodiments, the compound has the formula:
##STR00382##
B and R.sup.4 are as described herein.
[0406] In embodiments, the compound has the formula:
##STR00383##
B and R.sup.4 are as described herein.
[0407] In embodiments, the compound has the formula:
##STR00384##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XII), R.sup.100 is --CN.
[0408] In embodiments, the compound has the formula:
##STR00385##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0409] In embodiments, the compound has the formula:
##STR00386##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0410] In embodiments, the compound has the formula:
##STR00387##
B and R.sup.4 are as described herein. In embodiments of Formula
(XIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XIII), R.sup.100 is --CN.
[0411] In embodiments, the compound has the formula:
##STR00388##
B and R.sup.4 are as described herein.
[0412] In embodiments, the compound has the formula:
##STR00389##
B and R.sup.4 are as described herein.
[0413] In embodiments, the compound has the formula:
##STR00390##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XIV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XIV), R.sup.100 is --CN.
[0414] In embodiments, the compound has the formula:
##STR00391##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0415] In embodiments, the compound has the formula:
##STR00392##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0416] In embodiments, the compound has the formula:
##STR00393##
B and R.sup.4 are as described herein. In embodiments of Formula
(XV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XV), R.sup.100 is --CN.
[0417] In embodiments, the compound has the formula:
##STR00394##
B and R.sup.4 are as described herein.
[0418] In embodiments, the compound has the formula:
##STR00395##
B and R.sup.4 are as described herein.
[0419] In embodiments, the compound has the formula:
##STR00396##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XVI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XVI), R.sup.100 is --CN.
[0420] In embodiments, the compound has the formula:
##STR00397##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0421] In embodiments, the compound has the formula:
##STR00398##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0422] In embodiments, the compound has the formula:
##STR00399##
B and R.sup.4 are as described herein. In embodiments of Formula
(XVII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XVII), R.sup.100 is --CN.
[0423] In embodiments, the compound has the formula:
##STR00400##
B and R.sup.4 are as described herein. In embodiments of Formula
(XVIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XVIII), R.sup.100 is --CN.
[0424] In embodiments, the compound has the formula:
##STR00401##
B and R.sup.4 are as described herein.
[0425] In embodiments, the compound has the formula:
##STR00402##
B and R.sup.4 are as described herein.
[0426] In embodiments, the compound has the formula:
##STR00403##
B and R.sup.4 are as described herein.
[0427] In embodiments, the compound has the formula:
##STR00404##
B and R.sup.4 are as described herein.
[0428] In embodiments, the compound has the formula:
##STR00405##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XIX), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XIX), R.sup.100 is --CN.
[0429] In embodiments, the compound has the formula:
##STR00406##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0430] In embodiments, the compound has the formula:
##STR00407##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0431] In embodiments, the compound has the formula:
##STR00408##
B and R.sup.4 are as described herein. In embodiments of Formula
(XX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XX), R.sup.100 is --CN.
[0432] In embodiments, the compound has the formula:
##STR00409##
B and R.sup.4 are as described herein.
[0433] In embodiments, the compound has the formula:
##STR00410##
B and R.sup.4 are as described herein.
[0434] In embodiments, the compound has the formula:
##STR00411##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXI), R.sup.100 is --CN.
[0435] In embodiments, the compound has the formula:
##STR00412##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0436] In embodiments, the compound has the formula:
##STR00413##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0437] In embodiments, the compound has the formula:
##STR00414##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXII), R.sup.100 is --CN.
[0438] In embodiments, the compound has the formula:
##STR00415##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXIII), R.sup.100 is --CN.
[0439] In embodiments, the compound has the formula:
##STR00416##
B and R.sup.4 are as described herein.
[0440] In embodiments, the compound has the formula:
##STR00417##
B and R.sup.4 are as described herein.
[0441] In embodiments, the compound has the formula:
##STR00418##
B and R.sup.4 are as described herein.
[0442] In embodiments, the compound has the formula:
##STR00419##
B and R.sup.4 are as described herein.
[0443] In embodiments, the compound has the formula:
##STR00420##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXIV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXIV), R.sup.100 is --CN.
[0444] In embodiments, the compound has the formula:
##STR00421##
B, L.sup.101, L.sup.103, L.sup.1014, L.sup.105, and R.sup.4 are as
described herein.
[0445] In embodiments, the compound has the formula:
##STR00422##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0446] In embodiments, the compound has the formula:
##STR00423##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXV), R.sup.100 is --CN.
[0447] In embodiments, the compound has the formula:
##STR00424##
B and R.sup.4 are as described herein.
[0448] In embodiments, the compound has the formula:
##STR00425##
B and R.sup.4 are as described herein.
[0449] In embodiments, the compound has the formula:
##STR00426##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXVI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXVI), R.sup.100 is --CN.
[0450] In embodiments, the compound has the formula:
##STR00427##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0451] In embodiments, the compound has the formula:
##STR00428##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0452] In embodiments, the compound has the formula:
##STR00429##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXVII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXVII), R.sup.100 is --CN.
[0453] In embodiments, the compound has the formula:
##STR00430##
B and R.sup.4 are as described herein.
[0454] In embodiments, the compound has the formula:
##STR00431##
B and R.sup.4 are as described herein.
[0455] In embodiments, the compound has the formula:
##STR00432##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXVIII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXVIII), R.sup.100 is --CN.
[0456] In embodiments, the compound has the formula:
##STR00433##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0457] In embodiments, the compound has the formula:
##STR00434##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0458] In embodiments, the compound has the formula:
##STR00435##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXIX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXIX), R.sup.100 is --CN.
[0459] In embodiments, the compound has the formula:
##STR00436##
B and R.sup.4 are as described herein.
[0460] In embodiments, the compound has the formula:
##STR00437##
B and R.sup.4 are as described herein.
[0461] In embodiments, the compound has the formula:
##STR00438##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXX), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXX), R.sup.100 is --CN.
[0462] In embodiments, the compound has the formula:
##STR00439##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0463] In embodiments, the compound has the formula:
##STR00440##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0464] In embodiments, the compound has the formula:
##STR00441##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXXI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXXI), R.sup.100 is --CN.
[0465] In embodiments, the compound has the formula:
##STR00442##
B and R.sup.4 are as described herein.
[0466] In embodiments, the compound has the formula:
##STR00443##
B and R.sup.4 are as described herein.
[0467] In embodiments, the compound has the formula:
##STR00444##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXXII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXXII), R.sup.100 is --CN.
[0468] In embodiments, the compound has the formula:
##STR00445##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0469] In embodiments, the compound has the formula:
##STR00446##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0470] In embodiments, the compound has the formula:
##STR00447##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXXIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXXIII), R.sup.100 is --CN.
[0471] In embodiments, the compound has the formula:
##STR00448##
B and R.sup.4 are as described herein.
[0472] In embodiments, the compound has the formula:
##STR00449##
B and R.sup.4 are as described herein.
[0473] In embodiments, the compound has the formula:
##STR00450##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXXIV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXXIV), R.sup.100 is --CN.
[0474] In embodiments, the compound has the formula:
##STR00451##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0475] In embodiments, the compound has the formula:
##STR00452##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0476] In embodiments, the compound has the formula:
##STR00453##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXXV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXXV), R.sup.100 is --CN.
[0477] In embodiments, the compound has the formula:
##STR00454##
B and R.sup.4 are as described herein.
[0478] In embodiments, the compound has the formula:
##STR00455##
B and R.sup.4 are as described herein.
[0479] In embodiments, the compound has the formula:
##STR00456##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXXVI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXXVI), R.sup.100 is --CN.
[0480] In embodiments, the compound has the formula:
##STR00457##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0481] In embodiments, the compound has the formula:
##STR00458##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0482] In embodiments, the compound has the formula:
##STR00459##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXXVII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XXXVII), R.sup.100 is --CN.
[0483] In embodiments, the compound has the formula:
##STR00460##
B and R.sup.4 are as described herein.
[0484] In embodiments, the compound has the formula:
##STR00461##
B and R.sup.4 are as described herein.
[0485] In embodiments, the compound has the formula:
##STR00462##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XXXVIII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXXVIII), R.sup.100 is --CN.
[0486] In embodiments, the compound has the formula:
##STR00463##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0487] In embodiments, the compound has the formula:
##STR00464##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0488] In embodiments, the compound has the formula:
##STR00465##
B and R.sup.4 are as described herein. In embodiments of Formula
(XXXIX), R.sup.100 is and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XXXIX), R.sup.100 is --CN.
[0489] In embodiments, the compound has the formula:
##STR00466##
B and R.sup.4 are as described herein.
[0490] In embodiments, the compound has the formula:
##STR00467##
B and R.sup.4 are as described herein.
[0491] In embodiments, the compound has the formula:
##STR00468##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XL), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XL), R.sup.100 is --CN.
[0492] In embodiments, the compound has the formula:
##STR00469##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0493] In embodiments, the compound has the formula:
##STR00470##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0494] In embodiments, the compound has the formula:
##STR00471##
B and R.sup.4 are as described herein. In embodiments of Formula
(XLI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XLI), R.sup.100 is --CN.
[0495] In embodiments, the compound has the formula:
##STR00472##
and R.sup.4 are as described herein. In embodiments of Formula
(XLII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XLII), R.sup.100 is --CN.
[0496] In embodiments, the compound has the formula:
##STR00473##
B and R.sup.4 are as described herein.
[0497] In embodiments, the compound has the formula:
##STR00474##
B and R.sup.4 are as described herein.
[0498] In embodiments, the compound has the formula:
##STR00475##
B and R.sup.4 are as described herein.
[0499] In embodiments, the compound has the formula:
##STR00476##
B and R.sup.4 are as described herein.
[0500] In embodiments, the compound has the formula:
##STR00477##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XLIII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XLIII), R.sup.100 is --CN.
[0501] In embodiments, the compound has the formula:
##STR00478##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0502] In embodiments, the compound has the formula:
##STR00479##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0503] In embodiments, the compound has the formula:
##STR00480##
B and R.sup.4 are as described herein. In embodiments of Formula
(XLIV) R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein (e.g., unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments
of Formula (XLIV), R.sup.100 is --CN.
[0504] In embodiments, the compound has the formula:
##STR00481##
B and R.sup.4 are as described herein. In embodiments of Formula
(XLV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XLV), R.sup.100 is --CN.
[0505] In embodiments, the compound has the formula:
##STR00482##
B and R.sup.4 are as described herein.
[0506] In embodiments, the compound has the formula:
##STR00483##
B and R.sup.4 are as described herein.
[0507] In embodiments, the compound has the formula:
##STR00484##
B and R.sup.4 are as described herein.
[0508] In embodiments, the compound has the formula:
##STR00485##
B and R.sup.4 are as described herein.
[0509] In embodiments, the compound has the formula:
##STR00486##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XLVI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XLVI), R.sup.100 is --CN.
[0510] In embodiments, the compound has the formula:
##STR00487##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0511] In embodiments, the compound has the formula:
##STR00488##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0512] In embodiments, the compound has the formula:
##STR00489##
B and R.sup.4 are as described herein. In embodiments of Formula
(XLVII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XLVII), R.sup.100 is --CN.
[0513] In embodiments, the compound has the formula:
##STR00490##
B and R.sup.4 are as described herein. In embodiments of Formula
(XLVIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (XLVIII), R.sup.100 is --CN.
[0514] In embodiments, the compound has the formula:
##STR00491##
B and R.sup.4 are as described herein.
[0515] In embodiments, the compound has the formula:
##STR00492##
B and R.sup.4 are as described herein.
[0516] In embodiments, the compound has the formula:
##STR00493##
B and R.sup.4 are as described herein.
[0517] In embodiments, the compound has the formula:
##STR00494##
B and R.sup.4 are as described herein.
[0518] In embodiments, the compound has the formula:
##STR00495##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (XLIX) R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(XLIX), R.sup.100 is --CN.
[0519] In embodiments, the compound has the formula:
##STR00496##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0520] In embodiments, the compound has the formula:
##STR00497##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0521] In embodiments, the compound has the formula:
##STR00498##
B and R.sup.4 are as described herein. In embodiments of Formula
(L), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (L), R.sup.100 is --CN.
[0522] In embodiments, the compound has the formula:
##STR00499##
and R.sup.4 are as described herein. In embodiments of Formula
(LI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LI), R.sup.100 is --CN.
[0523] In embodiments, the compound has the formula:
##STR00500##
B and R.sup.4 are as described herein.
[0524] In embodiments, the compound has the formula:
##STR00501##
B and R.sup.4 are as described herein.
[0525] In embodiments, the compound has the formula:
##STR00502##
B and R.sup.4 are as described herein.
[0526] In embodiments, the compound has the formula:
##STR00503##
B and R.sup.4 are as described herein.
[0527] In embodiments, the compound has the formula:
##STR00504##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LII), R.sup.100 is --CN.
[0528] In embodiments, the compound has the formula:
##STR00505##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0529] In embodiments, the compound has the formula:
##STR00506##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0530] In embodiments, the compound has the formula:
##STR00507##
B and R.sup.4 are as described herein. In embodiments of Formula
(LIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LIII), R.sup.100 is --CN.
[0531] In embodiments, the compound has the formula:
##STR00508##
B and R.sup.4 are as described herein. In embodiments of Formula
(LIV), R.sup.100 is --SR.sup.102, and R.sup.11/2 is as described
herein. In embodiments of Formula (LIV), R.sup.100 is --CN.
[0532] In embodiments, the compound has the formula:
##STR00509##
B and R.sup.4 are as described herein.
[0533] In embodiments, the compound has the formula:
##STR00510##
B and R.sup.4 are as described herein.
[0534] In embodiments, the compound has the formula:
##STR00511##
B and R.sup.4 are as described herein.
[0535] In embodiments, the compound has the formula:
##STR00512##
B and R.sup.4 are as described herein.
[0536] In embodiments, the compound has the formula:
##STR00513##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LV), R.sup.100 is --CN.
[0537] In embodiments, the compound has the formula:
##STR00514##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0538] In embodiments, the compound has the formula:
##STR00515##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0539] In embodiments, the compound has the formula:
##STR00516##
B and R.sup.4 are as described herein. In embodiments of Formula
(LVI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LVI), R.sup.100 is --CN.
[0540] In embodiments, the compound has the formula:
##STR00517##
B and R.sup.4 are as described herein. In embodiments of Formula
(LVII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LVII), R.sup.100 is --CN.
[0541] In embodiments, the compound has the formula:
##STR00518##
B and R.sup.4 are as described herein.
[0542] In embodiments, the compound has the formula:
##STR00519##
B and R.sup.4 are as described herein.
[0543] In embodiments, the compound has the formula:
##STR00520##
B and R.sup.4 are as described herein.
[0544] In embodiments, the compound has the formula:
##STR00521##
B and R.sup.4 are as described herein.
[0545] In embodiments, the compound has the formula:
##STR00522##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LVIII) R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LVIII), R.sup.100 is --CN.
[0546] In embodiments, the compound has the formula:
##STR00523##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0547] In embodiments, the compound has the formula:
##STR00524##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0548] In embodiments, the compound has the formula:
##STR00525##
B and R.sup.4 are as described herein. In embodiments of Formula
(LIX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LIX), R.sup.100 is --CN.
[0549] In embodiments, the compound has the formula:
##STR00526##
B and R.sup.4 are as described herein. In embodiments of Formula
(LX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LX), R.sup.100 is --CN.
[0550] In embodiments, the compound has the formula:
##STR00527##
B and R.sup.4 are as described herein.
[0551] In embodiments, the compound has the formula:
##STR00528##
B and R.sup.4 are as described herein.
[0552] In embodiments, the compound has the formula:
##STR00529##
B and R.sup.4 are as described herein.
[0553] In embodiments, the compound has the formula:
##STR00530##
B and R.sup.4 are as described herein.
[0554] In embodiments, the compound has the formula:
##STR00531##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXI), R.sup.100 is --CN.
[0555] In embodiments, the compound has the formula:
##STR00532##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0556] In embodiments, the compound has the formula:
##STR00533##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0557] In embodiments, the compound has the formula:
##STR00534##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXII), R.sup.100 is --CN.
[0558] In embodiments, the compound has the formula:
##STR00535##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXIII), R.sup.100 is --CN.
[0559] In embodiments, the compound has the formula:
##STR00536##
B and R.sup.4 are as described herein.
[0560] In embodiments, the compound has the formula:
##STR00537##
B and R.sup.4 are as described herein.
[0561] In embodiments, the compound has the formula:
##STR00538##
B and R.sup.4 are as described herein.
[0562] In embodiments, the compound has the formula:
##STR00539##
B and R.sup.4 are as described herein.
[0563] In embodiments, the compound has the formula:
##STR00540##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXIV), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXIV), R.sup.100 is --CN.
[0564] In embodiments, the compound has the formula:
##STR00541##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0565] In embodiments, the compound has the formula:
##STR00542##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0566] In embodiments, the compound has the formula:
##STR00543##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXV), R.sup.100 is --CN.
[0567] In embodiments, the compound has the formula:
##STR00544##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXVI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXVI), R.sup.100 is --CN.
[0568] In embodiments, the compound has the formula:
##STR00545##
B and R.sup.4 are as described herein.
[0569] In embodiments, the compound has the formula:
##STR00546##
B and R.sup.4 are as described herein.
[0570] In embodiments, the compound has the formula:
##STR00547##
B and R.sup.4 are as described herein.
[0571] In embodiments, the compound has the formula:
##STR00548##
B and R.sup.4 are as described herein.
[0572] In embodiments, the compound has the formula:
##STR00549##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXVII) 00 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
usubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXVII), R.sup.100 is --CN.
[0573] In embodiments, the compound has the formula:
##STR00550##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0574] In embodiments, the compound has the formula:
##STR00551##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0575] In embodiments, the compound has the formula:
##STR00552##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXVIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXVIII), R.sup.100 is --CN.
[0576] In embodiments, the compound has the formula:
##STR00553##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXIX), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXIX), R.sup.100 is --CN.
[0577] In embodiments, the compound has the formula:
##STR00554##
B and R.sup.4 are as described herein.
[0578] In embodiments, the compound has the formula:
##STR00555##
B and R.sup.4 are as described herein.
[0579] In embodiments, the compound has the formula:
##STR00556##
B and R.sup.4 are as described herein.
[0580] In embodiments, the compound has the formula:
##STR00557##
B and R.sup.4 are as described herein.
[0581] In embodiments, the compound has the formula:
##STR00558##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXX), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXX), R.sup.100 is --CN.
[0582] In embodiments, the compound has the formula:
##STR00559##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0583] In embodiments, the compound has the formula:
##STR00560##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0584] In embodiments, the compound has the formula:
##STR00561##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXI), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXXI), R.sup.100 is --CN.
[0585] In embodiments, the compound has the formula:
##STR00562##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXXII), R.sup.100 is --CN.
[0586] In embodiments, the compound has the formula:
##STR00563##
B and R.sup.4 are as described herein.
[0587] In embodiments, the compound has the formula:
##STR00564##
B and R.sup.4 are as described herein.
[0588] In embodiments, the compound has the formula:
##STR00565##
B and R.sup.4 are as described herein.
[0589] In embodiments, the compound has the formula:
##STR00566##
B and R.sup.4 are as described herein.
[0590] In embodiments, the compound has the formula:
##STR00567##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXXIII), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXXIII), R.sup.100 is --CN.
[0591] In embodiments, the compound has the formula:
##STR00568##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0592] In embodiments, the compound has the formula:
##STR00569##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0593] In embodiments, the compound has the formula:
##STR00570##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXIV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXXIV), R.sup.100 is --CN.
[0594] In embodiments, the compound has the formula:
##STR00571##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXV), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXXV), R.sup.100 is --CN.
[0595] In embodiments, the compound has the formula:
##STR00572##
B and R.sup.4 are as described herein.
[0596] In embodiments, the compound has the formula:
##STR00573##
B and R.sup.4 are as described herein.
[0597] In embodiments, the compound has the formula:
##STR00574##
B and R.sup.4 are as described herein.
[0598] In embodiments, the compound has the formula:
##STR00575##
B and R.sup.4 are as described herein.
[0599] In embodiments, the compound has the formula:
##STR00576##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein. In embodiments of Formula (LXXVI), R.sup.100 is
--SR.sup.102, and R.sup.102 is as described herein (e.g.,
unsubstituted C.sub.1-C.sub.4 alkyl). In embodiments of Formula
(LXXVI), R.sup.100 is --CN.
[0600] In embodiments, the compound has the formula:
##STR00577##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0601] In embodiments, the compound has the formula:
##STR00578##
B, L.sup.101, L.sup.103, L.sup.104, L.sup.105, and R.sup.4 are as
described herein.
[0602] In embodiments, the compound has the formula:
##STR00579##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXVII), R.sup.100 is and R.sup.102 is as described herein. In
embodiments of Formula (LXXVII), R.sup.100 is --CN.
[0603] In embodiments, the compound has the formula:
##STR00580##
B and R.sup.4 are as described herein. In embodiments of Formula
(LXXVIII), R.sup.100 is --SR.sup.102, and R.sup.102 is as described
herein. In embodiments of Formula (LXXVIII), R.sup.100 is --CN.
[0604] In embodiments, the compound has the formula:
##STR00581##
B and R.sup.4 are as described herein.
[0605] In embodiments, the compound has the formula:
##STR00582##
B and R.sup.4 are as described herein.
[0606] In embodiments, the compound has the formula:
##STR00583##
B and R.sup.4 are as described herein.
[0607] In embodiments, the compound has the formula:
##STR00584##
B and R.sup.4 are as described herein.
[0608] In an aspect is provided a nucleic acid polymerase complex,
wherein the nucleic acid polymerase is bound (e.g., non-covalently
bound) to a compound described herein, including embodiments. In
another aspect is provided a modified nucleotide or nucleoside, the
nucleotide or nucleoside including a sugar moiety (e.g., a ribose
or deoxyribose sugar moiety) having a 3' --O-polymerase-compatible
cleavable moiety and a base (e.g., a purine or pyrimidine base)
linked via a covalent linker to a detectable moiety, wherein the
covalent linker includes a thio-trigger moiety having the
formula
##STR00585##
wherein R.sup.100 is --SR.sup.102 or --CN; and R.sup.102 and
R.sup.102a are as described herein, including embodiments. In
embodiments, the thio-trigger moiety has the formula:
##STR00586##
[0609] In embodiments, the thio-trigger moiety has the formula:
##STR00587##
wherein R.sup.102 is as described herein, including in embodiments.
In embodiments, the thio-trigger moiety has the formula:
##STR00588##
In embodiments, the thio-trigger moiety has the formula:
##STR00589##
In embodiments, the thio-trigger moiety has the formula:
##STR00590##
In embodiments, the thio-trigger moiety has the formula.
##STR00591##
In embodiments, the thio-trigger moiety has the formula:
##STR00592##
In embodiments, the thio-trigger moiety has the formula:
##STR00593##
In embodiments, the thio-trigger moiety has the formula:
##STR00594##
In embodiments, the thio-trigger moiety has the formula:
##STR00595##
[0610] In embodiments, the nucleic acid polymerase is a Taq
polymerase, Therminator .gamma., 9.degree. N polymerase (exo-),
Therminator II, Therminator III, or Therminator IX. In embodiments,
the nucleic acid polymerase is Therminator .gamma.. In embodiments,
the nucleic acid polymerase is 9.degree. N polymerase (exo-). In
embodiments, the nucleic acid polymerase is Therminator II. In
embodiments, the nucleic acid polymerase is Therminator III. In
embodiments, the nucleic acid polymerase is Therminator IX. In
embodiments, the nucleic acid polymerase is a Taq polymerase. In
embodiments, the nucleic acid polymerase is a nucleic acid
polymerase. In embodiments, the nucleic acid polymerase is
9.degree. N and mutants thereof. In embodiments, the nucleic acid
polymerase is Phi29 and mutants thereof.
[0611] In an aspect is provided a compound having the formula:
##STR00596##
wherein L.sup.101, B, and R.sup.3A are as described herein,
including in embodiments. In embodiments, L.sup.1 is
##STR00597##
In embodiments, L.sup.1 is
##STR00598##
In embodiments, L.sup.1 is
##STR00599##
[0612] In embodiments, the compound is a compound described
herein.
[0613] Some embodiments disclosed herein relate to kits including a
labeled nucleoside or nucleotide including a linker between the
fluorophore and the nucleoside or nucleotide, wherein the linker
comprises a thio-trigger moiety as described herein.
[0614] In an aspect, provided herein are kits for use in accordance
with any of the methods disclosed herein, and including one or more
elements thereof. In embodiments, a kit includes labeled
nucleotides including four differently labeled nucleotides (e.g.,
compounds described herein). In embodiments, the kit further
includes instructions for use thereof. In embodiments, kits
described herein include a polymerase. In embodiments, the
polymerase is a DNA polymerase. In embodiments, the DNA polymerase
is a thermophilic nucleic acid polymerase. In embodiments, the DNA
polymerase is a modified archaeal DNA polymerase. In embodiments,
the kit includes a sequencing solution. In embodiments, the
sequencing solution include labeled nucleotides including four
differently labeled nucleotides, wherein the label identifies the
type of nucleotide. For example, each of an adenine nucleotide, or
analog thereof; a thymine nucleotide; a cytosine nucleotide, or
analog thereof; and a guanine nucleotide, or analog thereof may be
labeled with a different fluorescent label.
[0615] In embodiments, the sequencing solution includes a buffer
solution. Typically, the buffered solutions contemplated herein are
made from a weak acid and its conjugate base or a weak base and its
conjugate acid. For example, sodium acetate and acetic acid are
buffer agents that can be used to form an acetate buffer. Other
examples of buffer agents that can be used to make buffered
solutions include, but are not limited to, Tris, Tricine, HEPES,
TES, MOPS, MOPSO and PIPES. Additionally, other buffer agents that
can be used in enzyme reactions, hybridization reactions, and
detection reactions are well known in the art. In embodiments, the
buffered solution can include Tris. With respect to the embodiments
described herein, the pH of the buffered solution can be modulated
to permit any of the described reactions. In some embodiments, the
buffered solution can have a pH greater than pH 7.0, greater than
pH 7.5, greater than pH 8.0, greater than pH 8.5, greater than pH
9.0, greater than pH 9.5, greater than pH 10, greater than pH 10.5,
greater than pH 11.0, or greater than pH 11.5. In other
embodiments, the buffered solution can have a pH ranging, for
example, from about pH 6 to about pH 9, from about pH 8 to about pH
10, or from about pH 7 to about pH 9. In embodiments, the buffered
solution can comprise one or more divalent cations. Examples of
divalent cations can include, but are not limited to, Mg.sup.2+,
Mn.sup.2+, Zn.sup.2+, and Ca.sup.2+. In embodiments, the buffered
solution can contain one or more divalent cations at a
concentration sufficient to permit hybridization of a nucleic acid.
In some embodiments, a concentration can be more than about 1
.mu.M, more than about 2 .mu.M, more than about 5 .mu.M, more than
about 10 .mu.M, more than about 25 .mu.M, more than about 50 .mu.M,
more than about 75 .mu.M, more than about 100 .mu.M, more than
about 200 .mu.M, more than about 300 .mu.M, more than about 400
.mu.M, more than about 500 .mu.M, more than about 750 .mu.M, more
than about 1 mM, more than about 2 mM, more than about 5 mM, more
than about 10 mM, more than about 20 mM, more than about 30 mM,
more than about 40 mM, more than about 50 mM, more than about 60
mM, more than about 70 mM, more than about 80 mM, more than about
90 mM, more than about 100 mM, more than about 150 mM, more than
about 200 mM, more than about 250 mM, more than about 300 mM, more
than about 350 mM, more than about 400 mM, more than about 450 mM,
more than about 500 mM, more than about 550 mM, more than about 600
mM, more than about 650 mM, more than about 700 mM, more than about
750 mM, more than about 800 mM, more than about 850 mM, more than
about 900 mM, more than about 950 mM or more than about 1 M.
III. Methods of Use
[0616] In an aspect is provided a method for sequencing a nucleic
acid, including: (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different labeled
nucleoside analogues into a primer to create an extension strand,
wherein the primer is hybridized to the nucleic acid and wherein
each of the four different labeled nucleoside analogues include a
unique detectable label; and (ii) detecting the unique detectable
label of each incorporated nucleoside analogue, so as to thereby
identify each incorporated nucleoside analogue in the extension
strand, thereby sequencing the nucleic acid; wherein each of the
four different labeled nucleoside analogues is independently a
compound described herein.
[0617] In an aspect is provided a method for sequencing a nucleic
acid, including: (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different labeled
nucleoside analogues into a primer to create an extension strand,
wherein the primer is hybridized to the nucleic acid and wherein
each of the four different labeled nucleoside analogues include a
unique detectable label; and (ii) detecting the unique detectable
label of each incorporated nucleoside analogue, so as to thereby
identify each incorporated nucleoside analogue in the extension
strand, thereby sequencing the nucleic acid; wherein each of the
four different labeled nucleoside analogues is independently a
compound described herein, including in embodiments.
[0618] In an aspect is provided a method for sequencing a nucleic
acid, including: (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different labeled
nucleotide analogues into a primer to create an extension strand,
wherein the primer is hybridized to the nucleic acid and wherein
each of the four different labeled nucleotide analogues include a
unique detectable label; and (ii) detecting the unique detectable
label of each incorporated nucleotide analogue, so as to thereby
identify each incorporated nucleotide analogue in the extension
strand, thereby sequencing the nucleic acid; wherein each of the
four different labeled nucleotide analogues is independently a
compound described herein, including in embodiments.
[0619] In embodiments, the method further including, after each of
the incorporating steps, adding to the reaction vessel four
different unlabeled nucleotide analogues, wherein each of the four
different unlabeled nucleotide analogues are of the structure as
described herein, including embodiments, wherein in the first of
the four different unlabeled nucleotide analogues, B is a thymidine
or uridine hybridizing base; in the second of the four different
unlabeled nucleotide analogues, B is an adenosine hybridizing base;
in the third of the four different unlabeled nucleotide analogues,
B is a guanosine hybridizing base; and in the fourth of the four
different unlabeled nucleotide analogues, B is a cytosine
hybridizing base.
[0620] In embodiments, the method further including, after each of
the incorporating steps, adding to the reaction vessel four
different unlabeled nucleotide analogues, wherein each of the four
different unlabeled nucleotide analogues are of the structure as
described herein, including embodiments, wherein in the first of
the four different unlabeled nucleotide analogues, B is a thymidine
or uridine hybridizing base; in the second of the four different
unlabeled nucleotide analogues, B is an adenosine hybridizing base;
in the third of the four different unlabeled nucleotide analogues,
B is a guanosine hybridizing base; and in the fourth of the four
different unlabeled nucleotide analogues, B is a cytosine
hybridizing base. In embodiments, the primer is immobilized on a
substrate. In embodiments, the nucleic acid is immobilized on a
substrate. In embodiments, the sequencing methods are performed
with the primer arrayed on a solid substrate. Multiple nucleic
acids can be immobilized on the solid support through linker
molecules, or can be attached to particles, e.g., microspheres,
which can also be attached to a solid substrate. The solid
substrate is in the form of a chip, a bead, a well, a capillary
tube, a slide, a wafer, a filter, a fiber, a porous media, or a
column. This invention also provides the instant method, wherein
the solid substrate is gold, quartz, silica, plastic, glass,
diamond, silver, metal, or polypropylene. This invention also
provides the instant method, wherein the solid substrate is
porous.
[0621] In embodiments, the method includes performing a plurality
of sequencing cycles. In embodiments, the methods of sequencing a
template nucleic acid include a total number of sequencing cycles
of about 1 to about 100, or about 20 to about 50. In embodiments,
the total number of sequencing cycles is about 1, 2, 5, 10, 15, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 cycles. In
embodiments, the total number of sequencing cycles is about 50
cycles. In embodiments, the total number of sequencing cycles is
about 100 cycles. In embodiments, the total number of sequencing
cycles is about 150 cycles. In embodiments, the total number of
sequencing cycles is about 200 cycles. In embodiments, the total
number of sequencing cycle is greater than 50 cycles. In
embodiments, the total number of sequencing cycle is greater than
100 cycles. In embodiments, the total number of sequencing cycle is
greater than 150 cycles. In embodiments, the total number of
sequencing cycle is greater than 200 cycles.
[0622] In embodiments, the nucleic acid can include any nucleic
acid of interest. The nucleic acid can include DNA, RNA, peptide
nucleic acid, morpholino nucleic acid, locked nucleic acid, glycol
nucleic acid, threose nucleic acid, mixtures thereof, and hybrids
thereof. In embodiments, the nucleic acid is obtained from one or
more source organisms. As used herein the term "organism" is not
necessarily limited to a particular species of organism but can be
used to refer to the living or self replicating particle at any
level of classification, which comprises the template nucleic acid.
For example, the term "organism" can be used to refer collectively
to all of the species within the genus Salmonella or all of the
bacteria within the kingdom Eubacteria.
[0623] In some embodiments, the nucleic acid can include a selected
sequence or a portion of a larger sequence. In embodiments,
sequencing a portion of a nucleic acid or a fragment thereof can be
used to identify the source of the nucleic acid. With reference to
nucleic acids, polynucleotides and/or nucleotide sequences a
"portion," "fragment" or "region" can be at least 5 consecutive
nucleotides, at least 10 consecutive nucleotides, at least 15
consecutive nucleotides, at least 20 consecutive nucleotides, at
least 25 consecutive nucleotides, at least 50 consecutive
nucleotides or at least 100 consecutive nucleotides.
[0624] In embodiments, the methods of sequencing a nucleic acid
include a extending a polynucleotide by using a polymerase. In
embodiments, the polymerase is a DNA polymerase. In embodiments,
the DNA polymerase is a Pol I DNA polymerase, Pol II DNA
polymerase, Pol III DNA polymerase, Pol IV DNA polymerase, Pol V
DNA polymerase, Pol .beta. DNA polymerase, Pol .mu. DNA polymerase,
Pol .lamda. DNA polymerase, Pol .sigma. DNA polymerase, Pol .alpha.
DNA polymerase, Pol .delta. DNA polymerase, Pol .epsilon. DNA
polymerase, Pol .eta. DNA polymerase, Pol DNA polymerase, Pol
.kappa. DNA polymerase, Pol .zeta. DNA polymerase, Pol .gamma. DNA
polymerase, Pol .theta. DNA polymerase, Pol .upsilon. DNA
polymerase, or a thermophilic nucleic acid polymerase (e.g.,
Therminator .gamma., 9.degree. N polymerase (exo-), Therminator II,
Therminator III, or Therminator IX). In embodiments, the DNA
polymerase is a thermophilic nucleic acid polymerase. In
embodiments, the DNA polymerase is a modified archaeal DNA
polymerase.
[0625] In embodiments, the methods of sequencing a nucleic acid
include extending a complementary polynucleotide (e.g., a primer)
that is hybridized to the nucleic acid by incorporating a first
nucleotide. In embodiments, the method includes a buffer exchange
or wash step.
[0626] In embodiments, the methods of sequencing a template nucleic
acid include a sequencing solution. The sequencing solution
includes (a) an adenine nucleotide, or analog thereof; (b) (i) a
thymine nucleotide, or analog thereof, or (ii) a uracil nucleotide,
or analog thereof; (c) a cytosine nucleotide, or analog thereof;
and (d) a guanine nucleotide, or analog thereof.
[0627] In another aspect is provided a method of incorporating a
nucleoside analogue into a primer, the method including combining a
polymerase, a primer hybridized to nucleic acid template and a
nucleoside analogue within a reaction vessel and allowing the
polymerase to incorporate the nucleoside analogue into the primer
thereby forming an extended primer, wherein the nucleoside analogue
is a compound described herein, including embodiments.
[0628] In another aspect is provided a method of incorporating a
nucleotide analogue into a primer, the method including combining a
polymerase, a primer hybridized to nucleic acid template and a
nucleotide analogue within a reaction vessel and allowing the
polymerase to incorporate the nucleotide analogue into the primer
thereby forming an extended primer, wherein the nucleotide analogue
is a compound described herein, including embodiments.
[0629] In an aspect is provided a method for sequencing a nucleic
acid, including: incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different
compounds into a primer to create an extension strand, wherein the
primer is hybridized to the nucleic acid and wherein each of the
four different compounds includes a unique detectable label;
detecting the unique detectable label of each incorporated
compound, so as to thereby identify each incorporated compound in
the extension strand, thereby sequencing the nucleic acid; wherein
each of the four different compounds is independently a compound
described herein.
[0630] In an aspect is provided a method for sequencing a nucleic
acid, including: incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different
compounds into a primer to create an extension strand, wherein the
primer is hybridized to the nucleic acid and wherein each of the
four different compounds includes a unique detectable label;
detecting the unique detectable label of each incorporated
compound, so as to thereby identify each incorporated compound in
the extension strand, thereby sequencing the nucleic acid; wherein
each of the four different compounds is independently a compound
described herein, including in embodiments.
[0631] In an aspect is provided a method for sequencing a nucleic
acid, including:
[0632] incorporating in series with a nucleic acid polymerase,
within a reaction vessel, a compound into a primer to create an
extension strand, wherein the primer is hybridized to the nucleic
acid and wherein the compound includes a detectable label;
detecting the detectable label of the incorporated compound, so as
to thereby identify the incorporated compound in the extension
strand, thereby sequencing the nucleic acid; wherein the compound
is independently a compound described herein. In embodiments, the
method further including, after each of the incorporating steps,
adding to the reaction vessel four different unlabeled nucleotide
analogues, wherein each of the four different unlabeled nucleotide
analogues are of the structure as described herein, including
embodiments, wherein in the first of the four different unlabeled
nucleotide analogues, B is a thymidine or uridine hybridizing base;
in the second of the four different unlabeled nucleotide analogues,
B is an adenosine hybridizing base; in the third of the four
different unlabeled nucleotide analogues, B is a guanosine
hybridizing base; and in the fourth of the four different unlabeled
nucleotide analogues, B is a cytosine hybridizing base.
[0633] In an aspect is provided a method for sequencing a nucleic
acid, including: incorporating in series with a nucleic acid
polymerase, within a reaction vessel, a compound into a primer to
create an extension strand, wherein the primer is hybridized to the
nucleic acid and wherein the compound includes a detectable label;
detecting the detectable label of the incorporated compound, so as
to thereby identify the incorporated compound in the extension
strand, thereby sequencing the nucleic acid; wherein the compound
is independently a compound described herein, including in
embodiments. In embodiments, the method further including, after
each of the incorporating steps, adding to the reaction vessel four
different unlabeled nucleotide analogues, wherein each of the four
different unlabeled nucleotide analogues are of the structure as
described herein, including embodiments, wherein in the first of
the four different unlabeled nucleotide analogues, B is a thymidine
or uridine hybridizing base; in the second of the four different
unlabeled nucleotide analogues, B is an adenosine hybridizing base;
in the third of the four different unlabeled nucleotide analogues,
B is a guanosine hybridizing base; and in the fourth of the four
different unlabeled nucleotide analogues, B is a cytosine
hybridizing base.
[0634] In an aspect is provided a method of incorporating a
compound into a primer, the method including combining a
polymerase, a primer hybridized to nucleic acid template and the
compound within a reaction vessel and allowing the polymerase to
incorporate the compound into the primer thereby forming an
extended primer, wherein the compound is a compound described
herein.
[0635] In an aspect is provided a method of incorporating a
compound into a primer, the method including combining a
polymerase, a primer hybridized to nucleic acid template and the
compound within a reaction vessel and allowing the polymerase to
incorporate the compound into the primer thereby forming an
extended primer, wherein the compound is a compound described
herein, including in embodiments.
[0636] In an aspect is provided a nucleic acid polymerase complex
including a nucleic acid polymerase, wherein the nucleic acid
polymerase is bound to a compound described herein.
[0637] In an aspect is provided a nucleic acid polymerase complex
including a nucleic acid polymerase, wherein the nucleic acid
polymerase is bound (e.g., non-covalently bound) to a compound
described herein.
[0638] In embodiments, the nucleic acid polymerase is a
thermophilic nucleic acid polymerase. In embodiments, the nucleic
acid polymerase is 9.degree. N and mutants thereof. In embodiments,
the nucleic acid polymerase is Phi29 and mutants thereof. In
embodiments, the nucleic acid polymerase is a Pyrococcus abyssi
polymerase and mutants thereof.
[0639] In embodiments, the nucleic acid polymerase is a
thermophilic nucleic acid polymerase. In embodiments, the nucleic
acid polymerase is 9.degree. N and mutants thereof. In embodiments,
the nucleic acid polymerase is Phi29 and mutants thereof.
[0640] In embodiments, the method includes simultaneously
sequencing a plurality of different nucleic acids, including: a)
extending a plurality of priming DNA strands hybridized to template
DNAs, each of which includes one of the priming DNA strands, by
incorporating a labeled nucleotide; and b) identifying each labeled
nucleotide, so as to simultaneously sequence the plurality of
different nucleic acids. In embodiments, the labeled nucleotide is
a compound described herein.
[0641] In embodiments, the method includes simultaneously
sequencing a plurality of different nucleic acids, including: a)
extending a plurality of priming DNA strands hybridized to template
DNAs, each of which includes one of the priming DNA strands, by
incorporating a labeled nucleotide; and b) identifying each labeled
nucleotide, so as to simultaneously sequence the plurality of
different nucleic acids. In embodiments, the labeled nucleotide is
a compound described herein, including in embodiments.
[0642] In embodiments, the method further including, after the
incorporating, cleaving the linker (e.g., the thio-trigger
containing linker,
-(L.sup.101)-OC(SR.sup.100)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(-
L.sup.105)-) with a cleaving reagent (e.g., a water-soluble
phosphine, such as tris(hydroxypropyl)phosphine (THPP)). In
embodiments, the cleaving reagent is a reducing agent. In
embodiments, the cleaving agent is a phosphine containing agent. In
embodiments, the cleaving agent is a thiol containing agent. In
embodiments, the cleaving agent is di-mercaptopropane sulfonate
(DMPS). In embodiments, the cleaving reagent is
Tris-(2-carboxyethyl)phosphines trisodium salt (TCEP),
tris(hydroxypropyl)phosphine (THPP), guanidine, urea, cysteine,
2-mercaptoethylamine, or dithiothreitol (DTT). In embodiments, the
cleaving reagent is an acid, base, oxidizing agent, reducing agent,
Pd(0), tris-(2-carboxyethyl)phosphine, dilute nitrous acid,
fluoride, tris(3-hydroxypropyl)phosphine), sodium dithionite
(Na.sub.2S.sub.2O.sub.4), or hydrazine (N.sub.2H.sub.4). In
embodiments, the cleaving reagent is in a buffer. In embodiments,
the buffer includes an acetate buffer,
3-(N-morpholino)propanesulfonic acid (MOPS) buffer,
N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES) buffer,
phosphate-buffered saline (PBS) buffer,
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer,
N-(1,1-Dimethyl-2-hydroxyethyl)-3-amino-2-hydroxypropanesulfonic
acid (AMPSO) buffer, borate buffer (e.g., borate buffered saline,
sodium borate buffer, boric acid buffer),
2-Amino-2-methyl-1,3-propanediol (AMPD) buffer,
N-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acid (CAPSO) buffer,
2-Amino-2-methyl-1-propanol (AMP) buffer,
4-(Cyclohexylamino)-1-butanesulfonic acid (CABS) buffer,
glycine-NaOH buffer, N-Cyclohexyl-2-aminoethanesulfonic acid (CHES)
buffer, tris(hydroxymethyl)aminomethane (Tris) buffer, or a
N-cyclohexyl-3-aminopropanesulfonic acid (CAPS) buffer. In
embodiments, the buffer is a borate buffer. In embodiments, the
buffer is a CHES buffer.
[0643] In embodiments, the method further including, after the
incorporating, cleaving the linker (e.g., the thio-trigger
containing linker,
-(L.sup.101)-OC(SR.sup.100)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(-
L.sup.105)-) with a cleaving reagent (e.g., a water-soluble
phosphine, such as tris(hydroxypropyl)phosphine (THPP)). In
embodiments, the cleaving reagent is a reducing agent. In
embodiments, the cleaving agent is a phosphine containing agent. In
embodiments, the cleaving agent is a thiol containing agent. In
embodiments, the cleaving agent is di-mercaptopropane sulfonate
(DMPS). In embodiments, the cleaving reagent is
Tris-(2-carboxyethyl)phosphines trisodium salt (TCEP),
tris(hydroxypropyl)phosphine (THPP), guanidine, urea, cysteine,
2-mercaptoethylamine, or dithiothreitol (DTT). In embodiments, the
cleaving reagent is an acid, base, oxidizing agent, reducing agent,
Pd(0), tris-(2-carboxyethyl)phosphine, dilute nitrous acid,
fluoride, tris(3-hydroxypropyl)phosphine), sodium dithionite
(Na.sub.2S.sub.2O.sub.4), or hydrazine (N.sub.2H.sub.4). In
embodiments, the reducing agent is dithiothreitol (DTT), or a
phosphine reagent such as tris(2-carboxyethyl)phosphine (TCEP),
tris(hydroxymethyl)phosphine (THP), tris(3-hydroxypropyl)phosphine
(THPP), 1,3,5-triaza-7-phosphaadamantane (PTA),
1,4,7-triaza-9-phosphatricyclo[5.3.2.1]-tridecane (CAP),
proazaphosphatrane, trialkylphosphines, or aminophosphines. In
embodiments, the reducing agent is Na.sub.2S.sub.2O.sub.3,
Na.sub.2SO.sub.3, NaN.sub.3, EtNO.sub.2, CH.sub.2(CN).sub.2, or
NEt.sub.3. In embodiments, the reducing agent is a thiol-containing
agent, such as di-mercaptopropanesulfonate,
di-mercaptopropanephosphonate, di-mercaptopropanol, cysteine,
cysteamine, dithio-succinic acid, dithiothreitol (DTT),
dithiobutylamine,
meso-2,5-dimercapto-N,N,N',N'-tetramethyladipamide (DTA),
Bis(2-mercaptoethyl)sulfone (BMS), or N,N'-dimethyl,
N,N'-bis(mercaptoacetyl)-hydrazine (DMH). In embodiments, the
cleaving agent is a cleaving agent described in US 2017/0211134. In
embodiments, the cleaving reagent is in a buffer. In embodiments,
the buffer includes an acetate buffer,
3-(N-morpholino)propanesulfonic acid (MOPS) buffer,
N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES) buffer,
phosphate-buffered saline (PBS) buffer,
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer,
N-(1,1-Dimethyl-2-hydroxyethyl)-3-amino-2-hydroxypropanesulfonic
acid (AMPSO) buffer, borate buffer (e.g., borate buffered saline,
sodium borate buffer, boric acid buffer),
2-Amino-2-methyl-1,3-propanediol (AMPD) buffer,
N-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acid (CAPSO) buffer,
2-Amino-2-methyl-1-propanol (AMP) buffer,
4-(Cyclohexylamino)-1-butanesulfonic acid (CABS) buffer,
glycine-NaOH buffer, N-Cyclohexyl-2-aminoethanesulfonic acid (CHES)
buffer, tris(hydroxymethyl)aminomethane (Tris) buffer, or a
N-cyclohexyl-3-aminopropanesulfonic acid (CAPS) buffer. In
embodiments, the buffer is a borate buffer. In embodiments, the
buffer is a CHES buffer.
[0644] In embodiments, the method includes contacting the compound
(e.g., a compound described herein) with a reducing agent. In
embodiments, the method further including, after the incorporating,
cleaving the linker at about 55.degree. C. In embodiments, the
method further including, after the incorporating, cleaving the
linker at about 55.degree. C. to about 80.degree. C. In
embodiments, the method further including, after the incorporating,
cleaving the linker at about 60.degree. C. to about 70.degree. C.
In embodiments, the method further including, after the
incorporating, cleaving the linker at about 65.degree. C. to about
75.degree. C. In embodiments, the method further including, after
the incorporating, cleaving the linker at about 65.degree. C. In
embodiments, the method further including, after the incorporating,
cleaving the linker at about 55.degree. C., 56.degree. C.,
57.degree. C., 58.degree. C., 59.degree. C., 60.degree. C.,
61.degree. C., 62.degree. C., 63.degree. C., 64.degree. C.,
65.degree. C., 66.degree. C., 67.degree. C., 68.degree. C.,
69.degree. C., 70.degree. C., 71.degree. C., 72.degree. C.,
73.degree. C., 74.degree. C., 75.degree. C., 76.degree. C.,
77.degree. C., 78.degree. C., 79.degree. C., or about 80.degree. C.
In embodiments, the method further including, after the
incorporating, cleaving the linker at a pH at about 8.0 to 11.0. In
embodiments, the pH is 9.0 to 11.0. In embodiments, the pH is 9.5.
In embodiments, the pH is 10.0. In embodiments, the pH is 8.0, 8.5,
9.0, 9.5, 10.0, 10.5, or 11.0. In embodiments, the pH is between
9.0 and 11.0, and the temperature is about 60.degree. C. to about
70.degree. C.
[0645] In embodiments, the cleaving reagent cleaves both the linker
and the polymerase-compatible cleavable moiety simultaneously.
[0646] In embodiments, the cleaving reagent cleaves both the linker
and the polymerase-compatible cleavable moiety simultaneously. In
embodiments, the linker is cleaved prior to cleavage of the
polymerase-compatible cleavable moiety. In embodiments, the linker
is cleaved after to cleavage of the polymerase-compatible cleavable
moiety.
[0647] In embodiments, the thermophilic nucleic acid polymerase is
a Taq polymerase, Therminator .gamma., 9.degree. N polymerase
(exo-), Therminator II, Therminator III, or Therminator IX. In
embodiments, the thermophilic nucleic acid polymerase is
Therminator .gamma.. In embodiments, the thermophilic nucleic acid
polymerase is 9.degree. N polymerase (exo-). In embodiments, the
thermophilic nucleic acid polymerase is Therminator II. In
embodiments, the thermophilic nucleic acid polymerase is
Therminator III. In embodiments, the thermophilic nucleic acid
polymerase is Therminator IX. In embodiments, the thermophilic
nucleic acid polymerase is a Taq polymerase. In embodiments, the
nucleic acid polymerase is a thermophilic nucleic acid polymerase.
In embodiments, the nucleic acid polymerase is 9.degree. N and
mutants thereof. In embodiments, the nucleic acid polymerase is
Phi29 and mutants thereof. In embodiments, the polymerase is a
non-thermophilic nucleic acid polymerase.
[0648] In embodiments, chemical cleavage of a compound (e.g.,
cleavage of a polymerase-compatible cleavable moiety or cleavage of
the thio-trigger containing linker of a compound described herein)
described herein (e.g., in an aspect or embodiment) includes
contacting the compound with a reducing agent. In embodiments,
chemical cleavage of a (e.g., cleavage of a polymerase-compatible
cleavable moiety or cleavage of the thio-trigger containing linker
of a compound described herein) described herein (e.g., in an
aspect or embodiment) includes contacting the compound with THPP
(e.g., about 10 mM THPP, at least 10 mM THPP). In embodiments,
chemical cleavage of a compound (e.g., cleavage of a
polymerase-compatible cleavable moiety or cleavage of the
thio-trigger containing linker of a compound described herein)
described herein (e.g., in an aspect or embodiment) is performed at
about 55 degrees Celsius. In embodiments, chemical cleavage of a
compound (e.g., cleavage of a polymerase-compatible cleavable
moiety or cleavage of the thio-trigger containing linker of a
compound described herein) described herein (e.g., in an aspect or
embodiment) is performed at a temperature of at least 55 degrees
Celsius. In embodiments, chemical cleavage of a compound (e.g.,
cleavage of a polymerase-compatible cleavable moiety or cleavage of
the thio-trigger containing linker of a compound described herein)
described herein (e.g., in an aspect or embodiment) is performed at
about pH 9.5-10.0. In embodiments, chemical cleavage of a compound
(e.g., cleavage of a polymerase-compatible cleavable moiety or
cleavage of the thio-trigger containing linker of a compound
described herein) described herein (e.g., in an aspect or
embodiment) is performed at pH 9.5.
[0649] The methods and kits of the present disclosure may be
applied, mutatis mutandis, to the sequencing of RNA, or to
determining the identity of a ribonucleotide.
[0650] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
All publications, patents, and patent applications cited herein are
hereby incorporated by reference in their entirety for all
purposes.
IV. Embodiments
[0651] Embodiment P1. A compound having the formula:
##STR00600##
wherein, [0652] B is a divalent nucleobase; [0653] R.sup.1 is
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, a 5'-nucleoside protecting
group, monophosphate moiety, polyphosphate moiety, or nucleic acid
moiety; and [0654] R.sup.2 and R.sup.3 are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or a --O-polymerase-compatible cleavable moiety; [0655]
L.sup.101, L.sup.103, L.sup.104 , and L.sup.105 are independently a
bond, --NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--,
--NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0656] R.sup.100 is
--SR.sup.102 or --CN; [0657] R.sup.102 and R.sup.102a are
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; and [0658] R.sup.4 is a
detectable moiety.
[0659] Embodiment P2. The compound of embodiment P1, wherein
R.sup.3 is an --O-polymerase-compatible cleavable moiety.
[0660] Embodiment P3. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently
-(substituted or unsubstituted alkylene)-SS-(unsubstituted
alkyl).
[0661] Embodiment P4. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently
-(halo-substituted or unsubstituted C.sub.1-C.sub.3
alkylene)-SS-(unsubstituted C.sub.1-C.sub.4 alkyl).
[0662] Embodiment P5. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00601## ##STR00602## ##STR00603## ##STR00604##
[0663] Embodiment P6. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00605## ##STR00606## ##STR00607## ##STR00608##
[0664] Embodiment P7. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00609## ##STR00610## ##STR00611## ##STR00612##
[0665] Embodiment P8. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00613##
[0666] Embodiment P9. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00614##
[0667] Embodiment P10. The compound of embodiment P2, wherein the
-polymerase-compatible cleavable moiety is independently:
##STR00615##
[0668] Embodiment P11. The compound of one of embodiments P1 to
P10, wherein R.sup.2 is hydrogen.
[0669] Embodiment P12. The compound of one of embodiments P1 to
P10, wherein R.sup.2 is --OH.
[0670] Embodiment P13. The compound of one of embodiments P1 to
P10, wherein R.sup.2 is --O-polymerase-compatible cleavable
moiety.
[0671] Embodiment P14. The compound of one of embodiments P1 to
P13, wherein R.sup.1 is hydrogen.
[0672] Embodiment P15. The compound of one of embodiments P1 to
P13, wherein R.sup.1 is a monophosphate moiety.
[0673] Embodiment P16. The compound of one of embodiments P1 to
P13, wherein R.sup.1 is a polyphosphate moiety.
[0674] Embodiment P17. The compound of one of embodiments P1 to
P13, wherein R.sup.1 is a triphosphate moiety.
[0675] Embodiment P18. The compound of one of embodiments P1 to
P13, wherein R.sup.1 is a nucleic acid moiety.
[0676] Embodiment P19. The compound of one of embodiments P1 to
P18, wherein [0677] B is a divalent cytosine or a derivative
thereof, divalent guanine or a derivative thereof, divalent adenine
or a derivative thereof, divalent thymine or a derivative thereof,
divalent uracil or a derivative thereof, divalent hypoxanthine or a
derivative thereof, divalent xanthine or a derivative thereof,
divalent 7-methylguanine or a derivative thereof, divalent
5,6-dihydrouracil or a derivative thereof, divalent
5-methylcytosine or a derivative thereof, or divalent
5-hydroxymethylcytosine or a derivative thereof.
[0678] Embodiment P20. The compound of embodiment P19, wherein B
is
##STR00616##
[0679] Embodiment P21. The compound of one of embodiments P1 to
P20, wherein, R.sup.100 is --SR.sup.102.
[0680] Embodiment P22. The compound of one of embodiments P1 to
P21, wherein; L.sup.101, L.sup.103, L.sup.104 , and L.sup.105 are
independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0681] R.sup.102
and R.sup.102a are independently hydrogen or unsubstituted
alkyl.
[0682] Embodiment P23. The compound of one of embodiments P1 to
P21, wherein [0683] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0684] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0685] L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; [0686] L.sup.105 is
independently bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and [0687] R.sup.102 is unsubstituted
C.sub.1-C.sub.4 alkyl; and [0688] R.sup.102a is hydrogen or
unsubstituted methyl.
[0689] Embodiment P24. The compound of one of embodiments P1 to
P21, wherein [0690] L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; [0691] L.sup.104 is unsubstituted phenylene; and
[0692] R.sup.102 and R.sup.102a are independently hydrogen or
unsubstituted alkyl.
[0693] Embodiment P25. The compound of one of embodiments P1 to
P21, wherein [0694] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0695] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0696] L.sup.104 is independently an
unsubstituted phenylene; [0697] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
[0698] R.sup.102 is unsubstituted C.sub.1-C.sub.4 alkyl; and [0699]
R.sup.102a is hydrogen or unsubstituted methyl.
[0700] Embodiment P26. The compound of one of embodiments P1 to
P21, wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)--
(L.sup.105)- is
##STR00617## ##STR00618##
[0701] Embodiment P27. The compound of one of embodiments P1 to
P21, wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)--
(L.sup.105)- is
##STR00619## ##STR00620##
[0702] Embodiment P28. The compound of one of embodiments P1 to
P20, wherein R.sup.100 is --CN.
[0703] Embodiment P29. The compound of embodiment P28, wherein;
[0704] L.sup.101, L.sup.103, L.sup.104 , and L.sup.105 are
independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0705] R.sup.102a
is independently hydrogen or unsubstituted alkyl.
[0706] Embodiment P30. The compound of embodiment P28, wherein
[0707] L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0708] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0709] L.sup.104 is independently a bond, substituted or
unsubstituted 4 to 18 membered heteroalkylene, or substituted or
unsubstituted phenylene; [0710] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
[0711] R.sup.102a is hydrogen or unsubstituted methyl.
[0712] Embodiment P31. The compound of embodiment P28, wherein
[0713] L.sup.101, L.sup.103, and L.sup.105 are independently a
bond, --NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--,
--NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0714] L.sup.104 is
unsubstituted phenylene; and [0715] R.sup.102a is independently
hydrogen or unsubstituted alkyl.
[0716] Embodiment P32. The compound of embodiment P28, wherein
[0717] L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0718] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0719] L.sup.104 is independently an unsubstituted phenylene;
[0720] L.sup.105 is independently bond or substituted or
unsubstituted 4 to 18 membered heteroalkylene; and [0721]
R.sup.102a is hydrogen or unsubstituted methyl.
[0722] Embodiment P33. The compound of embodiment P28, wherein
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00621##
[0723] Embodiment P34. The compound of one of embodiments P1 to
P33, wherein R.sup.4 is a fluorescent dye moiety.
[0724] Embodiment P35. The compound of one of embodiments P1 to
P33, wherein R.sup.4 is
##STR00622##
[0725] Embodiment P36. A method for sequencing a nucleic acid,
comprising: [0726] (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different
compounds into a primer to create an extension strand, wherein said
primer is hybridized to said nucleic acid and wherein each of the
four different compounds comprises a unique detectable label;
[0727] (ii) detecting said unique detectable label of each
incorporated compound, so as to thereby identify each incorporated
compound in said extension strand, thereby sequencing the nucleic
acid; wherein each of said four different compounds is
independently a compound of one of embodiments P1 to P35.
[0728] Embodiment P37. A method of incorporating a compound into a
primer, the method comprising combining a polymerase, a primer
hybridized to nucleic acid template and the compound within a
reaction vessel and allowing said polymerase to incorporate said
compound into said primer thereby forming an extended primer,
wherein said compound is a compound of one of embodiments P1 to
P35.
[0729] Embodiment P38. A nucleic acid polymerase complex comprising
a nucleic acid polymerase, wherein said nucleic acid polymerase is
bound to a compound of one of embodiments P1 to P35.
[0730] Embodiment Q1. A compound having the formula:
##STR00623##
wherein, [0731] B is a divalent nucleobase; [0732] R.sup.1 is
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, a 5'-nucleoside protecting
group, monophosphate moiety, polyphosphate moiety, or nucleic acid
moiety; and [0733] R.sup.2 and R.sup.3 are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; [0734]
L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are independently a
bond, --NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--,
--NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0735] R.sup.100 is
--SR.sup.102 or --CN; [0736] R.sup.102 and R.sup.102a are
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; and [0737] R.sup.4 is a
detectable moiety.
[0738] Embodiment Q2. The compound of embodiment Q1, wherein
R.sup.3 is an --O-polymerase-compatible cleavable moiety.
[0739] Embodiment Q3. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is independently
(substituted or unsubstituted alkylene)-SS-(unsubstituted
alkyl).
[0740] Embodiment Q4. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is independently
(halo-substituted or unsubstituted C.sub.1-C.sub.3
alkylene)-SS-(unsubstituted C.sub.1-C.sub.4 alkyl).
[0741] Embodiment Q5. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00624## ##STR00625## ##STR00626## ##STR00627##
[0742] Embodiment Q6. The compound of one of embodiments Q1 to Q2,
wherein the -polymerase-compatible cleavable moiety is
independently:
##STR00628## ##STR00629## ##STR00630## ##STR00631##
[0743] Embodiment Q7. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00632## ##STR00633## ##STR00634## ##STR00635##
[0744] Embodiment Q8. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00636##
[0745] Embodiment Q9. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00637##
[0746] Embodiment Q10. The compound of one of embodiments Q1 to Q2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00638##
[0747] Embodiment Q11. The compound of one of embodiments Q1 to
Q10, wherein R.sup.2 is hydrogen.
[0748] Embodiment Q12. The compound of one of embodiments Q1 to
Q10, wherein R.sup.2 is --OH.
[0749] Embodiment Q13. The compound of one of embodiments Q1 to
Q10, wherein R.sup.2 is an --O-polymerase-compatible cleavable
moiety.
[0750] Embodiment Q14. The compound of one of embodiments Q1 to
Q13, wherein R.sup.1 is hydrogen.
[0751] Embodiment Q15. The compound of one of embodiments Q1 to
Q13, wherein R.sup.1 is a monophosphate moiety.
[0752] Embodiment Q16. The compound of one of embodiments Q1 to
Q13, wherein R.sup.1 is a polyphosphate moiety.
[0753] Embodiment Q17. The compound of one of embodiments Q1 to
Q13, wherein R.sup.1 is a triphosphate moiety.
[0754] Embodiment Q18. The compound of one of embodiments Q1 to
Q13, wherein R.sup.1 is a nucleic acid moiety.
[0755] Embodiment Q19. The compound of one of embodiments Q1 to
Q18, wherein [0756] B is a divalent cytosine or a derivative
thereof, divalent guanine or a derivative thereof, divalent adenine
or a derivative thereof, divalent thymine or a derivative thereof,
divalent uracil or a derivative thereof, divalent hypoxanthine or a
derivative thereof, divalent xanthine or a derivative thereof,
divalent 7-methylguanine or a derivative thereof, divalent
5,6-dihydrouracil or a derivative thereof, divalent
5-methylcytosine or a derivative thereof, or divalent
5-hydroxymethylcytosine or a derivative thereof.
[0757] Embodiment Q20. The compound of embodiment Q19, wherein B
is
##STR00639##
[0758] Embodiment Q21. The compound of one of embodiments Q1 to
Q20, wherein, R.sup.100 is --SR.sup.102.
[0759] Embodiment Q22. The compound of one of embodiments Q1 to
Q21, wherein; [0760] L.sup.101, L.sup.103, L.sup.104, and L.sup.105
are independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0761] R.sup.102
and R.sup.102a are independently hydrogen or unsubstituted
alkyl.
[0762] Embodiment Q23. The compound of one of embodiments Q1 to
Q21, wherein [0763] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0764] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0765] L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; [0766] L.sup.105 is
independently bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and [0767] R.sup.102 is unsubstituted
C.sub.1-C.sub.4 alkyl; and [0768] R.sup.102a is hydrogen or
unsubstituted methyl.
[0769] Embodiment Q24. The compound of one of embodiments Q1 to
Q21, wherein [0770] L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; [0771] L.sup.104 is unsubstituted phenylene; and
[0772] R.sup.102 and R.sup.102a are independently hydrogen or
unsubstituted alkyl.
[0773] Embodiment Q25. The compound of one of embodiments Q1 to
Q21, wherein [0774] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0775] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0776] L.sup.104 is independently an
unsubstituted phenylene; [0777] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
[0778] R.sup.102 is unsubstituted C.sub.1-C.sub.4 alkyl; and [0779]
R.sup.102a is hydrogen or unsubstituted methyl.
[0780] Embodiment Q26. The compound of one of embodiments Q1 to
Q21, wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)--
(L.sup.105)- is
##STR00640##
[0781] Embodiment Q27. The compound of one of embodiments Q1 to
Q21, wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)--
(L.sup.105)- is
##STR00641## ##STR00642##
[0782] Embodiment Q28. The compound of one of embodiments Q1 to
Q20, wherein R.sup.100 is --CN.
[0783] Embodiment Q29. The compound of embodiment Q28, wherein;
[0784] L.sup.101, L.sup.103, L.sup.104 , and L.sup.105 are
independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0785] R.sup.102a
is independently hydrogen or unsubstituted alkyl.
[0786] Embodiment Q30. The compound of embodiment Q28, wherein
[0787] L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0788] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0789] L.sup.104 is independently a bond, substituted or
unsubstituted 4 to 18 membered heteroalkylene, or substituted or
unsubstituted phenylene; [0790] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
[0791] R.sup.102a is hydrogen or unsubstituted methyl.
[0792] Embodiment Q31. The compound of embodiment Q28, wherein
[0793] L.sup.101, L.sup.103, and L.sup.105 are independently a
bond, --NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--,
--NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0794] L.sup.104 is
unsubstituted phenylene; and [0795] R.sup.102a is independently
hydrogen or unsubstituted alkyl.
[0796] Embodiment Q32. The compound of embodiment Q28, wherein
[0797] L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0798] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0799] L.sup.104 is independently an unsubstituted phenylene;
[0800] L.sup.105 is independently bond or substituted or
unsubstituted 4 to 18 membered heteroalkylene; and [0801]
R.sup.102a is hydrogen or unsubstituted methyl.
[0802] Embodiment Q33. The compound of embodiment Q28, wherein
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00643##
[0803] Embodiment Q34. The compound of one of embodiments Q1 to
Q33, wherein R.sup.4 is a fluorescent dye moiety.
[0804] Embodiment Q35. The compound of one of embodiments Q1 to
Q33, wherein R.sup.4 is
##STR00644##
[0805] Embodiment Q36. A method for sequencing a nucleic acid,
comprising: [0806] (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different
compounds into a primer to create an extension strand, wherein said
primer is hybridized to said nucleic acid and wherein each of the
four different compounds comprises a unique detectable label;
[0807] (ii) detecting said unique detectable label of each
incorporated compound, so as to thereby identify each incorporated
compound in said extension strand, thereby sequencing the nucleic
acid; wherein each of said four different compounds is
independently a compound of one of embodiments Q1 to Q35.
[0808] Embodiment Q37. A method of incorporating a compound into a
primer, the method comprising combining a polymerase, a primer
hybridized to nucleic acid template and the compound within a
reaction vessel and allowing said polymerase to incorporate said
compound into said primer thereby forming an extended primer,
wherein said compound is a compound of one of embodiments Q1 to
Q35.
[0809] Embodiment Q38. A nucleic acid polymerase complex comprising
a nucleic acid polymerase, wherein said nucleic acid polymerase is
bound to a compound of one of embodiments Q1 to Q35.
V. Additional Embodiments
[0810] Embodiment 1. A compound having the formula:
##STR00645##
wherein [0811] B is a divalent nucleobase; [0812] R.sup.1 is
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
substituted or unsubstituted heteroaryl, a 5'-nucleoside protecting
group, monophosphate moiety, polyphosphate moiety, or nucleic acid
moiety; and [0813] R.sup.2 and R.sup.3 are independently hydrogen,
halogen, --CCl.sub.3, --CBr.sub.3, --CF.sub.3, --CI.sub.3,
--CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2, --CHI.sub.2, --CH.sub.2Cl,
--CH.sub.2Br, --CH.sub.2F, --CH.sub.2I, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2, --NHC(O)NHNH.sub.2,
--NHC(O)NH.sub.2, --NHSO.sub.2H, --NHC(O)H, --NHC(O)OH, --NHOH,
--OCCl.sub.3, --OCF.sub.3, --OCBr.sub.3, --OCI.sub.3,
--OCHCl.sub.2, --OCHBr.sub.2, --OCHI.sub.2, --OCHF.sub.2,
--OCH.sub.2Cl, --OCH.sub.2Br, --OCH.sub.2I, --OCH.sub.2F,
--N.sub.3, --SF.sub.5, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, substituted or
unsubstituted heteroaryl; or a polymerase-compatible cleavable
moiety or an --O-polymerase-compatible cleavable moiety; [0814]
L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are independently a
bond, --NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--,
--NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or unsubstituted
alkylene, substituted or unsubstituted heteroalkylene, substituted
or unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0815] R.sup.100 is
--SR.sup.102 or --CN; [0816] R.sup.102 and R.sup.102a are
independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; and [0817] R.sup.4 is a
detectable moiety.
[0818] Embodiment 2. The compound of embodiment 1, wherein R.sup.3
is an --O-polymerase-compatible cleavable moiety.
[0819] Embodiment 3. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is independently
-(substituted or unsubstituted alkylene)-SS-(unsubstituted
alkyl).
[0820] Embodiment 4. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is independently
-(halo-substituted or unsubstituted C.sub.1-C.sub.3
alkylene)-SS-(unsubstituted C.sub.1-C.sub.4 alkyl).
[0821] Embodiment 5. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00646## ##STR00647## ##STR00648## ##STR00649##
[0822] Embodiment 6. The compound of one of embodiments 1 to 2,
wherein the -polymerase-compatible cleavable moiety is
independently:
##STR00650## ##STR00651## ##STR00652## ##STR00653##
[0823] Embodiment 7. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00654## ##STR00655## ##STR00656## ##STR00657##
[0824] Embodiment 8. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00658##
[0825] Embodiment 9. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00659##
[0826] Embodiment 10. The compound of one of embodiments 1 to 2,
wherein the polymerase-compatible cleavable moiety is
independently:
##STR00660##
[0827] Embodiment 11. The compound of one of embodiments 1 to 10,
wherein R.sup.2 is hydrogen.
[0828] Embodiment 12. The compound of one of embodiments 1 to 10,
wherein R.sup.2 is --OH.
[0829] Embodiment 13. The compound of one of embodiments 1 to 10,
wherein R.sup.2 is an --O-polymerase-compatible cleavable
moiety.
[0830] Embodiment 14. The compound of one of embodiments 1 to 13,
wherein R.sup.1 is hydrogen.
[0831] Embodiment 15. The compound of one of embodiments 1 to 13,
wherein R.sup.1 is a monophosphate moiety.
[0832] Embodiment 16. The compound of one of embodiments 1 to 13,
wherein R.sup.1 is a polyphosphate moiety.
[0833] Embodiment 17. The compound of one of embodiments 1 to 13,
wherein R.sup.1 is a triphosphate moiety.
[0834] Embodiment 18. The compound of one of embodiments 1 to 13,
wherein R.sup.1 is a nucleic acid moiety.
[0835] Embodiment 19. The compound of one of embodiments 1 to 18,
wherein [0836] B is a divalent cytosine or a derivative thereof,
divalent guanine or a derivative thereof, divalent adenine or a
derivative thereof, divalent thymine or a derivative thereof,
divalent uracil or a derivative thereof, divalent hypoxanthine or a
derivative thereof, divalent xanthine or a derivative thereof,
divalent 7-methylguanine or a derivative thereof, divalent
5,6-dihydrouracil or a derivative thereof, divalent
5-methylcytosine or a derivative thereof, or divalent
5-hydroxymethylcytosine or a derivative thereof.
[0837] Embodiment 20. The compound of embodiment 19, wherein B
is
##STR00661##
[0838] Embodiment 21. The compound of one of embodiments 1 to 20,
wherein, R.sup.100 is --SR.sup.102.
[0839] Embodiment 22. The compound of one of embodiments 1 to 21,
wherein; [0840] L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are
independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0841] R.sup.102
and R.sup.102a are independently hydrogen or unsubstituted
alkyl.
[0842] Embodiment 23. The compound of one of embodiments 1 to 21,
wherein [0843] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0844] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0845] L.sup.104 is independently a bond,
substituted or unsubstituted 4 to 18 membered heteroalkylene, or
substituted or unsubstituted phenylene; [0846] L.sup.105 is
independently bond or substituted or unsubstituted 4 to 18 membered
heteroalkylene; and [0847] R.sup.102 is unsubstituted
C.sub.1-C.sub.4 alkyl; and [0848] R.sup.102a is hydrogen or
unsubstituted methyl.
[0849] Embodiment 24. The compound of one of embodiments 1 to 21,
wherein [0850] L.sup.101, L.sup.103, and L.sup.105 are
independently a bond, --NH--, --O--, --C(O)--, --C(O)NH--,
--NHC(O)--, --NHC(O)NH--, --C(O)O--, --OC(O)--, substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, or substituted or unsubstituted
heteroarylene; [0851] L.sup.104 is unsubstituted phenylene; and
[0852] R.sup.102 and R.sup.102a are independently hydrogen or
unsubstituted alkyl.
[0853] Embodiment 25. The compound of one of embodiments 1 to 21,
wherein [0854] L.sup.101 is independently a substituted or
unsubstituted C.sub.1-C.sub.4 alkylene or substituted or
unsubstituted 8 to 20 membered heteroalkylene; [0855] L.sup.103 is
independently a bond or substituted or unsubstituted 2 to 10
membered heteroalkylene; [0856] L.sup.104 is independently an
unsubstituted phenylene; [0857] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene;
[0858] R.sup.102 is unsubstituted C.sub.1-C.sub.4 alkyl; and [0859]
R.sup.102a is hydrogen or unsubstituted methyl.
[0860] Embodiment 26. The compound of one of embodiments 1 to 21,
wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00662## ##STR00663##
[0861] Embodiment 27. The compound of one of embodiments 1 to 21,
wherein
-(L.sup.101)-OC(SSR.sup.102)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.1-
05)- is
##STR00664## ##STR00665##
[0862] Embodiment 28. The compound of one of embodiments 1 to 20,
wherein R.sup.100 is --CN.
[0863] Embodiment 29. The compound of embodiment 28, wherein;
[0864] L.sup.101, L.sup.103, L.sup.104, and L.sup.105 are
independently a bond, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; and [0865] R.sup.102a
is independently hydrogen or unsubstituted alkyl.
[0866] Embodiment 30. The compound of embodiment 28, wherein [0867]
L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0868] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0869] L.sup.104 is independently a bond, substituted or
unsubstituted 4 to 18 membered heteroalkylene, or substituted or
unsubstituted phenylene; [0870] L.sup.105 is independently bond or
substituted or unsubstituted 4 to 18 membered heteroalkylene; and
[0871] R.sup.102a is hydrogen or unsubstituted methyl.
[0872] Embodiment 31. The compound of embodiment 28, wherein [0873]
L.sup.101, L.sup.103, and L.sup.105 are independently a bond,
--NH--, --O--, --C(O)--, --C(O)NH--, --NHC(O)--, --NHC(O)NH--,
--C(O)O--, --OC(O)--, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene, or
substituted or unsubstituted heteroarylene; [0874] L.sup.104 is
unsubstituted phenylene; and [0875] R.sup.102a is independently
hydrogen or unsubstituted alkyl.
[0876] Embodiment 32. The compound of embodiment 28, wherein [0877]
L.sup.101 is independently a substituted or unsubstituted
C.sub.1-C.sub.4 alkylene or substituted or unsubstituted 8 to 20
membered heteroalkylene; [0878] L.sup.103 is independently a bond
or substituted or unsubstituted 2 to 10 membered heteroalkylene;
[0879] L.sup.104 is independently an unsubstituted phenylene;
[0880] L.sup.105 is independently bond or substituted or
unsubstituted 4 to 18 membered heteroalkylene; and [0881]
R.sup.102a is hydrogen or unsubstituted methyl.
[0882] Embodiment 33. The compound of embodiment 28, wherein
-(L.sup.101)-OC(SCN)(R.sup.102a)-(L.sup.103)-(L.sup.104)-(L.sup.105)-
is
##STR00666##
[0883] Embodiment 34. The compound of one of embodiments 1 to 33,
wherein R.sup.4 is a fluorescent dye moiety.
[0884] Embodiment 35. The compound of one of embodiments 1 to 33,
wherein R.sup.4 is
##STR00667##
[0885] Embodiment 36. The compound of one of embodiments 1 to 35,
having the formula:
##STR00668##
wherein [0886] R.sup.3 is an --O-polymerase-compatible cleavable
moiety.
[0887] Embodiment 37. A method for sequencing a nucleic acid,
comprising: [0888] (i) incorporating in series with a nucleic acid
polymerase, within a reaction vessel, one of four different
compounds into a primer to create an extension strand, wherein said
primer is hybridized to said nucleic acid and wherein each of the
four different compounds comprises a unique detectable label;
[0889] (ii) detecting said unique detectable label of each
incorporated compound, so as to thereby identify each incorporated
compound in said extension strand, thereby sequencing the nucleic
acid; wherein each of said four different compounds is
independently a compound of one of embodiments 1 to 36.
[0890] Embodiment 38. A method of incorporating a compound into a
primer, the method comprising combining a polymerase, a primer
hybridized to nucleic acid template and the compound within a
reaction vessel and allowing said polymerase to incorporate said
compound into said primer thereby forming an extended primer,
wherein said compound is a compound of one of embodiments 1 to
36.
[0891] Embodiment 39. A nucleic acid polymerase complex comprising
a nucleic acid polymerase, wherein said nucleic acid polymerase is
bound to a compound of one of embodiments 1 to 36.
[0892] Embodiment 40. A modified nucleotide or nucleoside, the
nucleotide or nucleoside comprising a sugar moiety having a
3'-O-polymerase-compatible cleavable moiety and a base linked via a
covalent linker to a detectable moiety, wherein the covalent linker
includes a thio-trigger moiety having the formula
##STR00669##
wherein R.sup.100 is --SR.sup.102 or --CN: R.sup.102 and R.sup.102a
are independently hydrogen, halogen, --CCl.sub.3, --CBr.sub.3,
--CF.sub.3, --CI.sub.3, --CHCl.sub.2, --CHBr.sub.2, --CHF.sub.2,
--CHI.sub.2, --CH.sub.2Cl, --CH.sub.2Br, --CH.sub.2F, --CH.sub.2I,
--CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC(O)NHNH.sub.2, --NHC(O)NH.sub.2, --NHSO.sub.2H,
--NHC(O)H, --NHC(O)OH, --NHOH, --OCCl.sub.3, --OCF.sub.3,
--OCBr.sub.3, --OCI.sub.3, --OCHCl.sub.2, --OCHBr.sub.2,
--OCHI.sub.2, --OCHF.sub.2, --OCH.sub.2Cl, --OCH.sub.2Br,
--OCH.sub.2I, --OCH.sub.2F, --N.sub.3, --SF.sub.5, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl.
[0893] Embodiment 41. The modified nucleotide or nucleoside of
embodiment 40, wherein the thio-trigger moiety has the formula:
##STR00670##
[0894] Embodiment 42. The modified nucleotide or nucleoside of
embodiment 40, wherein the thio-trigger moiety has the formula
##STR00671##
[0895] Embodiment 43. The modified nucleotide or nucleoside of
embodiment 40, wherein the thio-trigger moiety has the formula
##STR00672##
[0896] Embodiment 44. The modified nucleotide or nucleoside of
embodiment 40, wherein the thio-trigger moiety has the formula
##STR00673##
EXAMPLES
Example 1. Synthesis of Labeled Nucleosides
[0897] DNA sequencing is a fundamental tool in biological and
medical research; it is an essential technology for the paradigm of
personalized precision medicine. Sanger sequencing, where the
sequence of a nucleic acid is determined by selective incorporation
and detection of dideoxynucleotides, enabled the mapping of the
first human reference genome. While this methodology is still
useful for validating newer sequencing technologies, efforts to
sequence and assemble genomes using the Sanger method are an
expensive and laborious undertaking, requiring specialized
equipment and expertise. Certain new sequencing methodologies make
use of simultaneously sequencing millions of fragments of nucleic
acids, resulting in a 50,000-fold drop in the costs associated with
sequencing.
[0898] Traditional sequencing-by-synthesis (SBS) methodologies
employ serial incorporation and detection of labeled nucleotide
analogues. For example, high-throughput SBS technology uses
cleavable fluorescent nucleotide reversible terminator (NRT)
sequencing chemistry. These cleavable fluorescent NRTs were
designed based on the following rationale: each of the four
nucleotides (A, C, G, T, and/or U) is modified by attaching a
unique cleavable fluorophore to the specific location of the
nucleobase and capping the 3'-OH group of the nucleotide sugar with
a small reversible moiety (also referred to herein as a reversible
terminator) so that they are still recognized by DNA polymerase as
substrates. The reversible terminator temporarily halts the
polymerase reaction after nucleotide incorporation while the
fluorophore signal is detected. After incorporation and signal
detection, the fluorophore and the reversible terminator are
cleaved to resume the polymerase reaction in the next cycle. A
balance needs to be found between efficient incorporation of the
labeled nucleotides, efficient cleavage to remove all the
incorporated labels, and efficient incorporation of the next
nucleotide. Described herein in are optimized nucleotide structures
and synthetic schemes that improve the performance of nucleotides
in Sequencing-by-Synthesis (SBS) cycles.
##STR00674## ##STR00675##
##STR00676## ##STR00677##
##STR00678## ##STR00679## ##STR00680##
##STR00681##
##STR00682##
##STR00683## ##STR00684##
##STR00685## ##STR00686##
##STR00687## ##STR00688##
##STR00689## ##STR00690##
##STR00691## ##STR00692##
##STR00693## ##STR00694##
##STR00695## ##STR00696##
##STR00697## ##STR00698##
##STR00699##
##STR00700##
##STR00701## ##STR00702##
##STR00703##
##STR00704## ##STR00705##
##STR00706##
##STR00707##
[0899] Preparation of T3a. T2a (1.0 g, 2.08 mmol) was suspended in
dichloromethane (4 mL) and ethyl vinyl ether (2 mL). Pyridinium
p-toluenesulfonate (26 mg, 0.1 mmol) was added and the reaction
mixture was stirred at ambient temperature. After 1 hour the
reaction mixture was clear, and the solvent was evaporated. The
residue was dissolved in ether (25 mL) and washed with 0.1 M
NaHCO.sub.3 (2.times.25 mL) followed by brine (25 mL) and dried
over magnesium sulfate.
[0900] The crude product was purified by chromatography on silica
gel eluting with dichloromethane/methanol (98:2) to afford T3a as a
white foam (0.92 g, 1.66 mmol, 80%). LCMS observed m/z 552
calculated m/z 552. .sup.1H NMR (500 MHz, CDCl.sub.3) .delta. 9.80
(q, J=3.0 Hz, 1H), 7.99 (br s, 1H), 7.67-7.64 (m, 4H), 7.48-7.39
(m, 7H), 6.37 (dd, J=8.0, 5.5 Hz, 1H), 4.58-4.57 (m, 1H), 4.05-3.96
(m, 2H), 3.88-3.85 (m, 1H), 2.40-2.36 (m, 1H), 2.24-2.17 (m, 1H),
2.21 (d, J=3.0 Hz, 3H), 1.65 (d, J=1.0 Hz, 3H), 1.21 (d, J=6.5 Hz,
6H), 1.09 (s, 9H).
[0901] Preparation of T4a and T5a. T3a (542 mg, 0.982 mmol) was
dissolved in anhydrous dichloromethane (4 mL) and cooled in an ice
bath. Collidine (583 .mu.L, 4.42 mmol) was added followed by
dropwise addition of trimethylsilyl triflate (533 .mu.L, 2.95
mmol). After stirring 30 min, 18-crown-6 (528 mg, 2 mmol) was added
followed by potassium p-toluenethiosulfonate (452 mg, 2 mmol). The
reaction mixture was warmed to room temperature and stirred for 30
min. Sodium thiomethoxide (210 mg, 3 mmol) was added and the
reaction mixture was stirred at room temperature for 1 hour. The
reaction mixture was added directly to a silica gel column and
eluted with dichloromethane/methanol (97:3). The product was
further purified by reverse phase HPLC eluting with
acetonitrile/water 60:40 to 98:2 over 40 min. The fraction eluting
between 23 and 27 minutes contained a mixture of T4a and T5a (209
mg, 36%). LCMS observed m/z 586 calculated m/z 586.
[0902] Preparation of T6a and T7a. A mixture of T4a and T5a (209
mg, 0.357 mmol) was dissolved in anhydrous tetrahydrofuran (2 mL).
Tetrabutylammonium fluoride (0.536 mL, 1 M in THF) was added and
the reaction mixture was left to sit for 1 hour at room
temperature. The tetrahydrofuran was evaporated, and the crude
product was triturated with ethyl ether (3.times.10 mL) and then
purified by reverse phase HPLC eluting with acetonitrile/water
(20:80 to 30:70 over 40 min). The fraction eluting between 22 and
26 minutes contained a mixture of T6a and T7a (81 mg, 0.233 mmol,
65%). LCMS observed m/z 348 calculated m/z 348. .sup.1H NMR (500
MHz, CDCl.sub.3) .delta. 9.28 (br s, 2H), 7.45 (d, J=1.5 Hz, 1H),
7.36 (d, J=1.0 Hz, 1H), 6.16-6.13 (m, 2H), 4.73 (q, J=6.0 Hz, 1H),
4.69 (q, J=6.0 Hz, 1H), 4.10-4.09 (m, 1H), 4.06-4.04 (m, 1H),
3.94-3.90 (m, 2H), 3.83-3.75 (m, 2H), 3.03 (br s, 1H), 2.85 (br s,
1H), 2.429 (s, 1H), 2.425(s, 1H), 2.41-2.38 (m, 4H), 1.89 (s, 3H),
1.88 (s, 3H), 1.62 (d, J=6.0 Hz, 3H), 1.61 (d, J=6.0 Hz, 3H).
.sup.13C NMR (125 MHz, CDCl3) .delta. 164.1, 150.7, 137.1, 136.9,
111.3, 87.2, 86.7, 86.2, 86.0, 85.5, 85.0, 77.4, 76.9, 62.9, 62.4,
38.3, 37.2, 24.7, 24.6, 22.9, 22.8, 12.7.
[0903] Preparation of T8a and T9a. A solution of
2-chloro-4-H-1,3,2-benzodioxaphosphorin-4-one (44 mg, 0.216 mmol)
in anhydrous acetonitrile (0.12 mL) was added dropwise to a
solution of tributylammonium pyrophosphate (158 mg, 0.287 mmol) in
anhydrous tributylamine (137 .mu.L, 0.575 mmol) and anhydrous
acetonitrile (0.3 mL). After stirring for 20 min at room
temperature the solution was transferred to a solution of T6a and
T7a (25 mg, 72 .mu.mol) in anhydrous acetonitrile (0.2 mL). The
reaction mixture was stirred for 30 minutes and then iodine
solution (1 mL, 50 mM in 9:1 pyridine/water) was added. After 30
minutes water (1 mL) was added and the reaction mixture was stirred
for 1 hour. The reaction mixture was concentrated to near dryness
and the residue was triturated with ether (3.times.5 mL). The crude
product was purified by reverse phase HPLC eluting with
acetonitrile/50 mM TEAB (2:98 to 30:70 over 40 min). The fraction
eluting at 22 minutes contained T8a (5 .mu.mol, 7%) and the
fraction eluting at 24 minutes contained T9a (4.4 .mu.mol, 6%).
LCMS observed m/z 587 calculated m/z 587.
[0904] Experimental Procedures for Thio-Trigger Containing
Linker
##STR00708##
Sodium iodide (1.5 g, 10.0 mmol) and potassium carbonate (6.9 g, 50
mmol) were added to a stirred solution of ethyl 3-hydroxybenzoate
(4.15 g, 25 mmol), 2-bromomethyl-1,3-dioxolane (10.4 mL, 100 mmol)
in DMF (15 mL) and was heated to 120.degree. C. The progress of the
reaction was monitored by HPLC (100 mM TEAA/MeCN, 60% to 100% over
15 min, hold for 5 min at 100%). The reaction mixture was cooled to
room temperature when the amount of ethyl-3-hydroxybenzoate was
less than 5%. The suspension was filtered and washed with ether
(2.times.50 mL). The combined filtrates were washed with water
(3.times.50 mL) and brine (50 mL), dried over sodium sulfate and
concentrated in vacuo. The crude product was purified by silica gel
chromatography (hexanes/ethyl acetate, 80:20) to obtain the desired
compound, ethyl 3-((1,3-dioxolan-2-yl)methoxy)benzoate as colorless
clear liquid (5.57 g, 88%). .sup.1H NMR (500 MHz, DMSO) .delta.
7.59-7.52 (m, 1H), 7.48-7.39 (m, 2H), 7.25 (ddd, J=8.3, 2.7, 1.0
Hz, 1H), 5.22 (t, J=3.9 Hz, 1H), 4.35-4.25 (m, 2H), 4.07 (d, J=3.9
Hz, 2H), 4.01-3.91 (m, 2H), 3.86 (ddd, J=15.2, 9.1, 5.6 Hz, 2H),
1.31 (q, J=7.2 Hz, 3H); MS: calc'd for
[C.sub.13H.sub.16O.sub.5+Na]: 275.1, found 275.3.
##STR00709##
[0905] 2,4,6-Collidine (2.38 mmol, 3.0 equiv.) was added to a
stirred solution of ethyl 3-((1,3-dioxolan-2-yl)methoxy)benzoate
(0.2 g, 0.79 mmol) in DCM (0.1 M) at 0.degree. C. under Ar
atmosphere followed by the addition of trimethylsilyl triflate
(1.59 mmol, 2.0 equiv.). The mixture was stirred at the same
temperature until the disappearance of an acetal on TLC and
formation of highly polar compound was observed, after which
potassium thiotosylate (1.59 mmol, 2.0 equiv.) and 18-crown-6 (1.59
mmol, 2.0 equiv.) were added to the reaction mixture. Disappearance
of the polar component was confirmed by TLC, after which tent-
butyl thiol (1.59 mmol, 2.0 equiv.) was added. The reaction mixture
was loaded on to silica gel column upon completion of the reaction
and the desired product, ethyl
3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)benzoate was
eluted with 20% ethyl acetate and hexanes mixture as a colorless
oil (235.6 mg, 63% yield). .sup.1H NMR (500 MHz, DMSO) .delta. 7.57
(dd, J=6.6, 1.2 Hz, 1H), 7.51-7.42 (m, 2H), 7.27 (ddd, J=8.2, 2.7,
0.8 Hz, 1H), 4.92 (t, J=5.4 Hz, 1H), 4.69 (t, J=5.4 Hz, 1H),
4.35-4.25 (m, 4H), 3.89-3.80 (m, 1H), 3.61-3.49 (m, 3H), 1.37-1.28
(m, 12H). MS: calc'd for [C.sub.17H.sub.26O.sub.5S.sub.2+Na]:
397.1, found 397.3.
##STR00710##
[0906] Sodium hydroxide (0.7 mL, 2 M) was added to a stirred
solution of ethyl
3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)benzoate
(131 mg, 0.35 mmol) in 1:1 methanol (0.33 mL) and THF (0.33 mL)
mixture. The solution was initially heterogeneous but became
homogenous after 1 hour of stirring. The reaction progress was
monitored by HPLC (100 mM TEAA/MeCN, 60% to 100% over 15 min, hold
for 5 min at 100%). Upon completion, the reaction mixture was
concentrated and HCl (1 M, 1.382 mL) was added dropwise with
stirring until the milky swirl persisted. The aqueous suspension
was extracted with DCM (3.times.15 mL) and the extracts were dried
over sodium sulfate. The crude product was purified using silica
gel chromatography (50% ethyl acetate:hexanes) and
3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)benzoic acid
was obtained as a colorless oil (87 mg, 72% yield). .sup.1H NMR
(500 MHz, DMSO) .delta. 13.00 (s, 1H), 7.58-7.52 (m, 1H), 7.47 (dt,
J=11.9, 6.1 Hz, 1H), 7.42 (t, J=7.9 Hz, 1H), 7.21-7.19 (m, 1H),
4.92 (t, J=5.4 Hz, 1H), 4.69 (s, 1H), 4.34-4.24 (m, 2H), 3.88-3.82
(m, 1H), 3.61-3.50 (m, 3H), 1.35-1.26 (m, 9H). MS: calc'd for
[C.sub.15H.sub.22O.sub.5S.sub.2+Na]: 369.1, found 369.2.
##STR00711##
[0907] To a mixture of
3-(2-(tent-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)benzoic acid
(43 mg, 0.124 mmol), N-(2-aminoethyl)-2,2,2-trifluoroacetamide
(28.6 mg, 0.148 mmol, 1.2 equiv.), 4-N,N-dimethylaminopyridine (4.5
mg, 0.037 mmol, 0.3 equiv.) in DCM (0.2 mL, 0.6 M) at 0.degree. C.,
was added N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide
hydrochloride (33 mg, 0.174 mmol, 1.4 equiv.) in DCM dropwise. The
reaction was stirred at room temperature until the disappearance of
the starting material as monitored by HPLC (100 mM TEAA/MeCN, 60%
to 100% over 15 min, hold for 5 min at 100%). The reaction mixture
was diluted with water and extracted with ethyl acetate (3.times.15
mL) and dried over sodium sulfate. The crude was purified by silica
gel chromatography (60% ethyl acetate: hexanes) and
3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)-N-(2-(2,2,2-t-
rifluoroacetamido)ethyl)benzamide was obtained as colorless liquid
(38 mg, 63.3% yield). .sup.1H NMR (500 MHz, DMSO) .delta. 9.49 (d,
J=5.5 Hz, 1H), 8.59 (t, J=5.5 Hz, 1H), 7.40 (dq, J=22.8, 7.7 Hz,
3H), 7.12 (dd, J=8.0, 1.6 Hz, 1H), 4.92 (t, J=5.4 Hz, 1H), 4.70 (t,
J=5.3 Hz, 1H), 4.35-4.19 (m, 2H), 3.87 (dt, J=9.6, 4.3 Hz, 1H),
3.62-3.50 (m, 3H), 3.43-3.33 (m, 4H), 1.31 (s, 9H). MS: calc'd for
[C.sub.19H.sub.27F.sub.3N.sub.2O.sub.5S.sub.2+Na]: 507.1, found
507.2.
##STR00712##
[0908] To a stirred solution of
3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)-N-(2-(2,2,2-trifl-
uoroacetamido)ethyl)benzamide (55 mg, 0.115 mmol) in methanol (0.5
mL), potassium carbonate (45.5 mg, 0.329 mmol, 2.9 equiv.) was
added. The reaction progress was monitored by HPLC (100 mM
TEAA/MeCN, 60% to 100% over 15 min, hold for 5 min at 100%) and
upon completion, the reaction mixture was diluted with water and
extracted with ethyl acetate (3.times.5 mL). The organic fractions
were collected, dried over sodium sulfate and purified by HPLC to
obtain
N-(2-aminoethyl)-3-(2-(tert-butyldisulfaneyl)-2-(2-hydroxyethoxy)ethoxy)b-
enzamide as colorless liquid. .sup.1H NMR (500 MHz, DMSO) .delta.
8.43 (d, J=5.0 Hz, 1H), 7.45 (t, J=5.8 Hz, 2H), 7.37 (t, J=7.8 Hz,
1H), 7.11 (dd, J=7.8, 2.1 Hz, 1H), 4.92 (t, J=5.3 Hz, 1H), 4.71 (s,
1H), 4.28 (d, J=5.9 Hz, 2H), 3.87 (dt, J=9.4, 4.2 Hz, 1H),
3.63-3.50 (m, 3H), 3.32-3.22 (m, 4H), 2.71 (t, J=6.5 Hz, 2H), 1.31
(s, 9H). MS: calc'd for [C.sub.17H.sub.28N.sub.2O.sub.4S.sub.2+H]:
389.2, found 389.4.
##STR00713##
[0909] Experimental Procedures for Thio-Trigger Containing
Linker
##STR00714##
[0910] 2,4,6-Collidine (0.59 mmol, 3.0 equiv.) was added to a
stirred solution of ethyl 3-((1,3-dioxolan-2-yl)methoxy)benzoate
(0.05 g, 0.79 mmol) in DCM (0.1 M) at 0.degree. C. under Ar
atmosphere followed by the addition of trimethylsilyl triflate (0.4
mmol, 2.0 equiv.). The mixture was stirred at the same temperature
until the disappearance of an acetal on TLC and formation of highly
polar compound was observed, after which a solution of potassium
thiocyanate (0.99 mmol, 5.0 equiv.) and 18-crown-6 (0.99 mmol, 5.0
equiv.) in acetone (0.2 mL) was added to it. Disappearance of the
polar component was confirmed by TLC. The product formation was
confirmed by mass analysis, MS: calc'd for
[C.sub.14H.sub.17NO.sub.5S--H].sup.-: 311.0, found 310.0.
TABLE-US-00001 TABLE 1 Detectable moieties to be used in selected
embodiments. Nucleoside/nucleotide Dye .lamda.max abbreviation name
(nm) dC Atto 532 532 dC Atto Rho 6G 535 dC R6G 534 dC Tet 521 dT
Atto Rho 11 572 dT Atto 565 564 dT Alexa Fluor 568 578 dT dTamra
578 dA Alexa Fluor 647 650 dA Atto 647N 644 dA Janelia Fluor 646
646 dG Alexa Fluor 680 682 dG Alexa Fluor 700 696 dG CF680R 680
Example 2. Thio-Trigger Containing Linkers
[0911] In the context of nucleic acid sequencing reactions it is
desirable to increase the rate of nucleotide incorporation during
sequencing by synthesis and eliminate any potential side reactions
so that the efficiency of the sequencing method can be
improved.
[0912] The compounds described herein utilize a covalent linker
between the base moiety (e.g., a purine or pyrimidine base) of the
nucleoside or nucleotide and the detectable label. Often in
sequencing by synthesis (SBS) techniques, the detectable label is
removed by breaking apart, or cleaving, the linker. The use of a
cleavable linker ensures that the label can, if required, be
removed after detection, avoiding any interfering signal with any
labelled nucleotide incorporated subsequently. Suitable linkers can
be adapted from standard chemical blocking groups, as disclosed in
Greene & Wuts, Protective Groups in Organic Synthesis, John
Wiley & Sons and in Guillier et al. (Chem. Rev. 100:2092-2157,
2000).
[0913] For example, a linker used in SBS methodologies is a
disulfide linker (referred to herein as an SS linker) having the
formula:
##STR00715##
wherein the SS linker is linear (i.e., continuous) within the
linker. Upon exposure to a reducing agent, the intermediate forms a
reactive thiol capable of interacting with the polymerase or other
reactive moieties and decreasing the efficiency. In contrast,
certain compounds described herein include a thio-trigger
containing linker, which forms non-reactive products and cleaves
approximately 5.times. faster than the SS linker under similar
conditions. Additionally, in embodiments, the thio-trigger
containing linker and the polymerase-compatible cleavable moiety
are cleaved simultaneously under the given reaction conditions
(e.g., cleaved under the same reaction conditions but not
necessarily at the exact same time or rate). In embodiments,
modifying the reaction conditions (e.g., elevating the temperature
to 65.degree. C., increasing the pH) results in faster
cleavage.
##STR00716##
[0914] Minimal scar nucleotides. Following detecting and
identifying the incorporated nucleotide (e.g., the nucleotide as
described herein), the linker can be cleaved thus allowing the
fluorophore to be removed. Cleavage may result in a "scar" moiety
located on each of the detected nucleotides which may negatively
impact incorporation of the subsequent nucleotide. Minimizing the
scar length can improve sequencing results by allowing for more
efficient nucleotide incorporation.
* * * * *