U.S. patent application number 16/371031 was filed with the patent office on 2019-07-25 for microarray having a base cleavable linker.
This patent application is currently assigned to CustomArray, Inc.. The applicant listed for this patent is CustomArray, Inc.. Invention is credited to Hetian Gao, Karl Maurer, Dominic Suciu.
Application Number | 20190227060 16/371031 |
Document ID | / |
Family ID | 37884647 |
Filed Date | 2019-07-25 |
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United States Patent
Application |
20190227060 |
Kind Code |
A1 |
Maurer; Karl ; et
al. |
July 25, 2019 |
MICROARRAY HAVING A BASE CLEAVABLE LINKER
Abstract
There is disclosed a microarray having base cleavable linkers
and a process of making the microarray. The microarray has a solid
surface with known locations, each having reactive hydroxyl groups.
The density of the known locations is greater than approximately
100 locations per square centimeter. Optionally, oligomers are
synthesized in situ onto the cleavable linkers and subsequently
cleaved using a cleaving base. Optionally, the oligomers are
cleaved and recovered as a pool of oligomers.
Inventors: |
Maurer; Karl; (Everett,
WA) ; Suciu; Dominic; (Edmonds, WA) ; Gao;
Hetian; (Fremont, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
CustomArray, Inc. |
Bothwell |
WA |
US |
|
|
Assignee: |
CustomArray, Inc.
Bothwell
WA
|
Family ID: |
37884647 |
Appl. No.: |
16/371031 |
Filed: |
March 31, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15990487 |
May 25, 2018 |
10261075 |
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16371031 |
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12387115 |
Apr 27, 2009 |
9983204 |
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15990487 |
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11361160 |
Feb 24, 2006 |
7541314 |
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12387115 |
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11229757 |
Sep 19, 2005 |
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11361160 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01J 2219/00653
20130101; C40B 50/18 20130101; B01J 2219/00454 20130101; B01J
2219/00713 20130101; B01J 2219/00608 20130101; B01J 2219/00722
20130101; B01J 19/0046 20130101; C12Q 1/6837 20130101; G01N
33/54353 20130101; C12Q 1/6837 20130101; C12Q 2525/197 20130101;
C12Q 2527/125 20130101 |
International
Class: |
G01N 33/543 20060101
G01N033/543; C12Q 1/6837 20060101 C12Q001/6837; C40B 50/18 20060101
C40B050/18; B01J 19/00 20060101 B01J019/00 |
Claims
1. A compound of formula: ##STR00027## where `MA` is a microarray
with a plurality of electronically addressable electrodes, where
the microarray includes a surface with a plurality of hydroxyl
reactive group associated with the plurality of electronically
addressable electrodes, where the Compound is attached through one
or more of the plurality of hydroxyl reactive groups in a plurality
of known locations, where `Base` of the compound denotes one of
adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U)
on the 5' hydroxyl of the Compound, where `Remainder of
Oligonucleotide Strand` of the Compound denotes one or more
oligonucleotides, where the Compound is susceptible to cleavage by
introducing a base to generate a 3' phosphate nucleoside species
including the one or more oligonucleotides.
2. The compound of claim 1, where the one or more oligonucleotides
is selected from the group consisting of DNA, RNA and combinations
thereof.
3. The compound of claim 1, where the one or more oligonucleotides
are synthesized in situ by a method selected from the group
consisting of (a) printing reagents via ink jet or other printing
technology and using regular phosphoramidite chemistry, (b)
maskless photo-generated acid controlled synthesis and using
regular phosphoramidite chemistry, (c) mask-directed parallel
synthesis using photo-cleavage of photolabile protecting groups,
and (d) maskless parallel synthesis using photo-cleavage of
photolabile protecting groups and digital photolithography.
4. The compound of claim 1, where the cleaving base is selected
from the group consisting of ammonium hydroxide, electrochemically
generated base, sodium hydroxide, potassium hydroxide, methylamine,
and ethylamine and combinations thereof.
5. The compound of claim 1, where the Compound is synthesized with
a sulfonate amidite.
6. The compound of claim 5, where the sulfonyl amidite moiety is
2-[2-(4,4'-dimethoxytrityloxy)ethylsulfonyl)ethyl-(2-cyanoethyl)-(N,N-dii-
-sopropyl)-phosphoramidite.
7. The compound of claim 1, where a porous reaction layer is
attached to the known locations to provides the one or more of the
plurality of hydroxyl reactive groups in the plurality of known
locations.
8. The compound of claim 1, where a Spacer having a reactive
hydroxyl groups is bound to the one or more of the plurality of
hydroxyl reactive groups in the plurality of known locations.
9. The compound of claim 8, where a sulfonyl amidite moiety is
bound to the reactive hydroxyl groups of the Spacer.
10. The compound of claim 8, where the spacer is approximately a
one-mer to a thirty five-mer.
11. The compound of claim 10, where a porous reaction layer
provides the one or more of the plurality of hydroxyl reactive
groups in the plurality of known locations.
12. The compound of claim 1, where the porous reaction layer
comprises a chemical species or mixture of chemical species
selected from the group consisting of a monosaccharide, a
disaccharide, and a trisaccharides.
13. The compound of claim 12, where the monosaccharide is selected
from the group consisting of allose, altrose, arabinose,
deoxyribose, erythrose, fructose, galactose, glucose, gulose,
idose, lyxose, mannose, psicose, L-rhamnose, ribose, ribulose,
sedoheptulose, D-sorbitol, sorbose, sylulose, tagatose, talose,
threose, xylulose, and xylose.
14. The compound of claim 12, where the disaccharide is selected
from the group consisting of amylose, cellobiose, lactose, maltose,
melibiose, palatinose, sucrose, and trehalose.
15. The compound of claim 12, where the triaccharide is selected
from the group consisting of raffinose and melezitose.
Description
PRIORITY CLAIM
[0001] This patent application is a continuation of (1) U.S. patent
application Ser. No. 15/990,487, filed May 25, 2018 which is a
continuation of (2) U.S. patent application Ser. No. 12/387,115,
filed Apr. 27, 2009 which issued May 29, 2018 as U.S. Pat. No.
9,983,204; which is a continuation of (3) U.S. patent application
Ser. No. 11/361,160, filed Feb. 24, 2006, which issued Jun. 2, 2009
as U.S. Pat. No. 7,541,314; and (2) is also a continuation of (4)
U.S. patent application Ser. No. 11/229,757, filed Sep. 19, 2005
(abandoned Dec. 14, 2010), wherein applications (1)-(4) are hereby
incorporated by reference in their entireties for all purposes.
REFERENCE TO A "SEQUENCE LISTING," A TABLE, OR A COMPUTER PROGRAM
LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE
[0002] The Sequence Listing written in file CUST-01606US2_ST25.TXT,
created May 21, 2018, 781 bytes, machine format IBM-PC, MS-Windows
operating system, is hereby incorporated by reference.
TECHNICAL FIELD
[0003] Disclosed herein are microarrays having base cleavable
linker moieties attached at known locations on the microarray.
Further disclosed is a process to make the microarrays having the
base cleavable linkers attached at known locations. Further
disclosed are oligomers synthesized in situ onto the base cleavable
linkers. Further disclosed is cleaving the oligomers from the
microarray to provide a pool of oligomers.
BACKGROUND
[0004] Microarray preparation methods for synthetic oligomers,
including oligonucleotides (oligos) include the following: (i)
spotting a solution on a prepared flat or substantially planar
surface using spotting robots; (ii) in situ synthesis by printing
reagents via ink jet or other computer printing technology and
using standard phosphoramidite chemistry; (iii) in situ parallel
synthesis using electrochemically generated acid for removal of
protecting groups and using standard phosphoramidite chemistry;
(iv) in situ synthesis using maskless photo-generated acid for
removal of protecting groups and using regular phosphoramidite
chemistry; (v) mask-directed in situ parallel synthesis using
photo-cleavage of photolabile protecting groups (PLPG) and standard
phosphoramidite chemistry; (vi) maskless in situ parallel synthesis
using PLPG and digital photolithography and standard
phosphoramidite chemistry; and (vii) electric field
attraction/repulsion for depositing fully formed oligos onto known
locations.
[0005] Photolithographic techniques for in situ oligo synthesis are
disclosed in Fodor et al. U.S. Pat. No. 5,445,934 and the
additional patents claiming priority thereto, all of which are
incorporated by reference herein. Electric field
attraction/repulsion microarrays are disclosed in Hollis et al.
U.S. Pat. No. 5,653,939 and Heller et al. U.S. Pat. No. 5,929,208,
both of which are incorporated by reference herein. An electrode
microarray for in situ oligo synthesis using electrochemical
deblocking is disclosed in Montgomery U.S. Pat. Nos. 6,093,302;
6,280,595, and 6,444,111 (Montgomery I, II, and III respectively),
all of which are incorporated by reference herein. Another and
materially different electrode array (not a microarray) for in situ
oligo synthesis on surfaces separate and apart from electrodes
using electrochemical deblocking is disclosed in Southern U.S. Pat.
No. 5,667,667, which is incorporated by reference herein. A review
of oligo microarray synthesis is provided by: Gao et al.,
Biopolymers 2004, 73:579.
[0006] U.S. patent application Ser. No. 10/243,367, filed 12 Sep.
2002 (Oleinikov) discloses a process for assembling a
polynucleotide from a plurality of oligonucleotides. The claimed
process provides a plurality of oligonucleotide sequences that are
synthesized in situ or spotted on a microarray device. The
plurality of oligonucleotide sequences is attached to a solid or
porous surface of the microarray device. The oligonucleotide
sequences are cleaved at a cleavable linker site to form a soluble
mixture of oligonucleotides. The cleavable linker is a chemical
composition having a succinate moiety bound to a nucleotide moiety
such that cleavage produces a 3'-hydroxy nucleotide.
[0007] The succinate moiety disclosed in Oleinikov as a cleavable
linker is bound to the solid or porous surface through an ester
linkage by reacting the succinate moieties with the solid or porous
surface. In general, formation of an ester linkage to an organic
hydroxyl on a solid surface using a succinate is relatively
difficult and often results in relatively low yield. Additionally,
the reaction conditions require a relatively long period of time at
relatively high temperature. Increasing yield would increase
oligonucleotide density and provide more efficient production of
oligonucleotides on a microarray. Oligonucleotides cleaved from the
microarray disclosed in Oleinikov have a three prime hydroxyl,
which may limit the use of such oligonucleotides or result in the
need for an additional step to modify the three-prime hydroxyl.
Disclosed herein are embodiments that provide oligonucleotides
having three-prime functionality that is different from a three
prime hydroxyl of Oleinikov, of which different functionality
expands the use of such oligonucleotides. Further disclosed herein
are embodiments that address the problems in Oleinikov of low yield
and hence low oligonucleotide density at a location on a microarray
by providing alternative cleavable linker chemistry, which is more
reactive to hydroxyl groups on a microarray. Further disclosed
herein are embodiments that address the limitations of Oleinikov
with respect to attachment of oligonucleotides having a three-prime
hydroxyl to a solid or porous surface by providing different
three-prime chemistry.
SUMMARY
[0008] Disclosed herein is a process for forming a microarray
having base cleavable sulfonyl linkers. The process comprises
providing an array having known locations having a plurality of
hydroxyl groups. The array comprises a surface or a matrix
proximate to the surface, wherein the density of the known
locations is greater than approximately 100 per square centimeter.
The process further comprises bonding one or a plurality of
sulfonyl amidite containing reagents to the hydroxyl groups at the
known locations to form a plurality of cleavable linkers bonded to
the known locations. The cleavable linkers comprise a hydroxyl
moiety and a base-labile cleaving moiety. A phosphorous-oxygen bond
is formed between phosphorous of the sulfonyl amidite containing
reagent and oxygen of the hydroxyl groups.
[0009] Further disclosed herein is a process for forming a
microarray having base cleavable sulfonyl linkers. The process
comprises providing an array device having a plurality of known
locations, each having a plurality of hydroxyl groups. The density
of the known locations is greater than approximately 100 per square
centimeter. The process further comprises bonding a plurality of
sulfonyl amidite moieties to the hydroxyl groups to form a
plurality of cleavable linkers attached to the array device at each
known location. The cleavable linkers comprise a linker hydroxyl
moiety and a base-labile cleaving moiety. A phosphorous-oxygen bond
is formed between phosphorous of the sulfonyl amidite moieties and
oxygen of the hydroxyl groups. The process further comprises
synthesizing a plurality of oligomers onto the linker hydroxyl
moieties.
[0010] Further disclosed herein is a process for forming a
microarray having base cleavable sulfonyl linkers. The process
comprises providing an array device having a plurality of known
locations, each having a plurality of hydroxyl groups. The density
of the plurality of known locations is greater than approximately
100 per square centimeter. The process further comprises bonding a
plurality of sulfonyl amidite moieties to the hydroxyl groups to
form a plurality of cleavable linkers bonded to the known
locations. The cleavable linkers comprise a linker hydroxyl moiety
and a base-labile cleaving moiety. A phosphorous-oxygen bond is
formed between phosphorous of the sulfonyl amidite moieties and
oxygen of the hydroxyl groups. The process further comprises
synthesizing a plurality of oligomers covalently bound to the
linker hydroxyl moiety. The process further comprises cleaving the
oligomers from the known locations at the base-labile cleaving
moiety using a cleaving base. The oligomers are recoverable. The
oligomers comprising DNA and RNA have a 3' phosphate after cleaving
from the solid surface.
[0011] Further disclosed herein is a process for forming a pool of
oligomers produced by providing an array having known locations
having a plurality of hydroxyl groups. The array comprises a
surface or a matrix proximate to the surface. The density of the
known locations is greater than approximately 100 per square
centimeter. The process further comprises bonding a plurality of
sulfonyl amidite moieties to the hydroxyl groups to form a
plurality of cleavable linkers bonded to the known locations. The
cleavable linkers comprise a linker hydroxyl moiety and a
base-labile cleaving moiety. A phosphorous-oxygen bond is formed
between phosphorous of the sulfonyl amidite moieties and oxygen of
the hydroxyl groups. The process further comprises synthesizing a
plurality of oligomers covalently bound to the linker hydroxyl
moiety. The process further comprises cleaving the oligomers from
the known locations at the base-labile cleaving moiety using a
cleaving base. The oligomers comprise DNA and RNA and have a 3'
phosphate after cleaving from the solid surface. The oligomers are
oligonucleotides having a 3' phosphate. The pool comprises more
than approximately 100 different oligonucleotides.
[0012] Further disclosed herein is a microarray having base
cleavable sulfonyl linkers. The microarray comprises an array
device having a plurality of known locations where each location
has a plurality of reacted hydroxyl groups. The density of the
plurality of known locations is greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reacted sulfonyl amidite moieties bonded to the plurality of
reacted hydroxyl groups to form a plurality of cleavable linkers
attached to the plurality of known locations. The cleavable linkers
have a linker hydroxyl group and a base-labile cleaving site. A
phosphorous-oxygen bond is between phosphorous of the reacted
sulfonyl amidite moieties and oxygen of the reacted hydroxyl
groups.
[0013] Further disclosed herein is a microarray having base
cleavable sulfonyl linkers. The microarray comprises an array
device having a plurality of known locations where each location
has a plurality of reacted hydroxyl groups. The density of the
plurality of known locations is greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reacted sulfonyl amidite moieties bonded to the plurality of
reacted hydroxyl groups to form a plurality of cleavable linkers
attached to the plurality of known locations. The cleavable linkers
have a linker hydroxyl group and a base-labile cleaving site. A
phosphorous-oxygen bond is between phosphorous of the reacted
sulfonyl amidite moieties and oxygen of the reacted hydroxyl
groups. The microarray further comprises oligomers bonded to the
linker hydroxyl groups.
[0014] Further disclosed herein is a process for forming a
microarray having cleavable succinate linkers. The process
comprises providing a solid surface having free hydroxyl groups at
known locations. The density of the known locations is greater than
approximately 100 locations per square centimeter. The process
further comprises bonding a linker moiety to the hydroxyl groups.
The linker moiety comprises free amine group and a hydroxyl bonding
group. The process further comprises bonding a succinate-containing
moiety having free carboxyl groups to the free amine groups to form
cleavable linkers attached to the known locations. The
succinate-containing moieties comprise a sugar having both a
nucleotide base group and a succinate group bonded to the sugar.
The cleavable linkers have a base-labile cleaving site on the
succinate group and a reactable hydroxyl group on the sugar
group.
[0015] Further disclosed herein is a microarray having base
cleavable succinate linkers. The microarray comprises a solid
surface having known locations and reactive hydroxyl groups. The
known locations have a density greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reactive amino amidite moieties bonded to the reactive hydroxyl
groups on the solid surface. The reactive amino moieties comprise
an amine group and a hydroxyl bonding group. The hydroxyl bonding
group is bonded to the reactive hydroxyl groups at the known
locations. The microarray further comprises a plurality of reactive
succinate moieties bonded to the amine groups. The reactive
succinate moieties comprise a sugar group bonded to the succinate
group and to a base group bonded. In an alternative embodiment,
microarray further comprises oligomers bonded onto the reactable
hydroxyl groups. In one or more embodiments, the sugar group is
ribose and the base group is selected from the group consisting of
adenine, guanine, cytosine, and uracyl, or the sugar group is
deoxyribose and the base group is selected from the group
consisting of adenine, guanine, cytosine, and thymine.
[0016] Further disclosed herein is a process of forming a
microarray having base cleavable phosphoramidite linkers. The
process comprises providing a microarray having a surface with a
plurality of known locations on the surface. Each location has a
plurality of hydroxyl groups, and the density of the known
locations is greater than approximately 100 per square centimeter
on the surface. The process further comprises bonding a plurality
of base cleavable phosphoramidite linkers to the plurality of
hydroxyl groups directly or by using an intermediate chemical
moiety attached to the hydroxyl groups to form a plurality of
cleavable linkers at the plurality of known locations. The
cleavable linkers each have a linker hydroxyl group and a
base-labile cleaving site. The linker hydroxyl group is protected
by a protecting group, and the base-labile cleaving site is an
ether linkage. Optionally, the process further comprises
synthesizing oligomers onto the linker hydroxyl groups to provide a
microarray of oligomers. The protecting group is removed from the
linker hydroxyl groups before synthesizing the oligomers, and the
oligomers at the known locations, as between different known
locations, are different or the same. Optionally, the process
further comprises cleaving at the base-labile cleaving site the
oligomers from the surface using a cleaving base to provide a pool
of cleaved oligomers.
[0017] Further disclosed herein is a pool of oligomers produced
according to one or more of the processes disclosed herein, wherein
the oligomers are oligonucleotides having a 3' phosphate, wherein
the pool comprises more than approximately 100 different
oligonucleotides. Further disclosed herein is a pool of oligomers
produced according to one or more of the processes disclosed
herein, wherein the oligomers are oligonucleotides having a 3'
hydroxyl, wherein the pool comprises more than approximately 100
different oligonucleotides.
[0018] Further disclosed herein is a microarray having base
cleavable linkers. The microarray comprises a microarray having a
surface with a plurality of known locations on the surface, wherein
each location has a plurality of hydroxyl groups, wherein the
density of the known locations is greater than approximately 100
per square centimeter on the surface. The microarray further
comprises a plurality of base cleavable linkers bonded to the
plurality of hydroxyl groups to form a plurality of cleavable
linkers at the plurality of known locations, wherein the cleavable
linkers each have a linker hydroxyl group and a base-labile
cleaving site.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] FIGS. 1A and 1B are a schematic of a cross section of a
microarray device showing one known location undergoing a sequence
of steps for the bonding of a cleavable linker, an oligonucleotide
to the linker, and then removal of the oligonucleotide by cleaving
the linker using a base.
[0020] FIG. 2 is a schematic of a sulfonyl amidite used to form a
cleavable linker on a micro array.
[0021] FIG. 3 is an image of a gel from a gel electrophoresis of
oligonucleotides recovered from three different microarrays having
the cleavable sulfonyl linker.
[0022] FIG. 4 shows an image of a portion of the microarray after
exposure to the fluorescently labeled oligonucleotide. There are
four different areas, A, B, C, and D, shown in the figure. In areas
A, B, and C, oligonucleotides were synthesized with and without a
cleavable linker. As can be seen in the figure, the microarray
locations having the cleavable linker between the oligonucleotide
and the microarray are dark, indicating little or no hybridizable
oligonucleotide remained after cleaving. In contrast, those
locations that did not have the cleavable linker between the
oligonucleotide and the microarray are brighter, which indicates
that the oligonucleotide remained on the microarray. In area D,
some electrodes had cleavable linker while others did not; however,
no oligonucleotides were synthesized so that the entire area
appears dark.
[0023] FIGS. 5A and 5B are schematics showing the construction of
the microarray of the present invention.
[0024] FIG. 6 provides exemplary compounds used to construct the
microarray of the present invention.
[0025] FIG. 7 provides an image of the results from gel
electrophoresis of DNA strands that were amplified by PCR. The
image shows recovery of the three different DNA strands from a
microarray after cleaving the strands from a cleavable linker. The
DNA strands were synthesized in situ using electrochemical
synthesis on the cleavable linker attached to the microarray.
DETAILED DESCRIPTION
[0026] Generally, nomenclature for chemical groups as used herein
follows the recommendations of "The International Union for Pure
and Applied Chemistry", Principles of Chemical Nomenclature: a
Guide to IUPAC Recommendations, Leigh, G. J.; Favre, H. A. and
Metanomski, W. V., Blackwell Science, 1998, the disclosure of which
is incorporated by reference herein. Formation of substituted
structures is limited by atom valence requirements.
[0027] "Oligomer" means a molecule of intermediate relative
molecular mass, the structure of which essentially comprises a
small plurality of units derived, actually or conceptually, from
molecules of lower relative molecular mass. A molecule is regarded
as having an intermediate relative molecular mass if it has
properties which do vary significantly with the removal of one or a
few of the units. If a part or the whole of the molecule has an
intermediate relative molecular mass and essentially comprises a
small plurality of units derived, actually or conceptually, from
molecules of lower relative molecular mass, it may be described as
oligomeric, or by oligomer used adjectivally. Oligomers are
typically comprised of a monomer.
[0028] The term "co-oligomer" means an oligomer derived from more
than one species of monomer. The term oligomer includes
co-oligomers. A single stranded DNA molecule consisting of any
combination of deoxyadenylate (A), deoxyguanylate (G),
deoxycytidylate (C), and deoxythymidylate (T) units is an
oligomer.
[0029] The term "monomer" means a molecule that can undergo
polymerization thereby contributing constitutional units to the
essential structure of a macromolecule such as an oligomer,
co-oligomer, polymer, or co-polymer. Examples of monomers for
oligonucleotides include A, C, G, T, adenylate, guanylate,
cytidylate, and uridylate. Monomers for other oligomers, including
polypeptides, include amino acids, vinyl chloride, and other
vinyls.
[0030] The term "polymer" means a substance composed of
macromolecules, which is a molecule of high relative molecular
mass, the structure of which essentially comprises the multiple
repetition of units derived, actually or conceptually, from
molecules of low relative molecular mass. In many cases, especially
for synthetic polymers, a molecule can be regarded as having a high
relative molecular mass if the addition or removal of one or a few
of the units has a negligible effect on the molecular properties.
This statement fails in the case of certain macromolecules for
which the properties may be critically dependent on fine details of
the molecular structure. If a part or the whole of the molecule has
a high relative molecular mass and essentially comprises the
multiple repetition of units derived, actually or conceptually,
from molecules of low relative molecular mass, it may be described
as either macromolecular or polymeric, or by polymer used
adjectivally.
[0031] The term "copolymer" means a polymer derived from more than
one species of monomer. Copolymers that are obtained by
copolymerization of two monomer species are sometimes termed
biopolymers, those obtained from three monomers terpolymers, those
obtained from four monomers quaterpolymers, etc. The term polymer
includes co-polymers.
[0032] The term "polyethylene glycol" (PEG) means an organic
chemical having a chain consisting of the common repeating ethylene
glycol unit [--CH.sub.2--CH.sub.2--O--].sub.n. PEG's are typically
long chain organic polymers that are flexible, hydrophilic,
enzymatically stable, and biologically inert, but they do not have
an ionic charge in water. In general, PEG can be divided into two
categories. First, there is polymeric PEG having a molecular weight
ranging from 1000 to greater than 20,000. Second, there are
PEG-like chains having a molecular weight that is less than 1000.
Polymeric PEG has been used in bioconjugates, and numerous reviews
have described the attachment of this linker moiety to various
molecules. PEG has been used as a linker, where the short PEG-like
linkers can be classified into two types, the
homo-[X--(CH.sub.2--CH.sub.2--O)--X and heterobifunctional
[X--(CH.sub.2--CH.sub.2--O).sub.n]--Y spacers.
[0033] The term "PEG derivative" means an ethylene glycol
derivative having the common repeating unit of PEG. Examples of PEG
derivatives include, but are not limited to, diethylene glycol
(DEG), tetraethylene glycol (TEG), polyethylene glycol having
primary amino groups, di(ethylene glycol) mono allyl ether,
di(ethylene glycol) mono tosylate, tri(ethylene glycol) mono allyl
ether, tri(ethylene glycol) mono tosylate, tri(ethylene glycol)
mono benzyl ether, tri(ethylene glycol) mono trityl ether,
tri(ethylene glycol) mono chloro mono methyl ether, tri(ethylene
glycol) mono tosyl mono allyl ether, tri(ethylene glycol) mono
allyl mono methyl ether, tetra(ethlyne glycol) mono allyl ether,
tetra(ethylene glycol) mono methyl ether, tetra(ethylene glycol)
mono tosyl mono allyl ether, tetra(ethylene glycol) mono tosylate,
tetra(ethylene glycol) mono benzyl ether, tetra(ethylene glycol)
mono trityl ether, tetra(ethylene glycol) mono 1-hexenyl ether,
tetra(ethylene glycol) mono 1-heptenyl ether, tetra(ethylene
glycol) mono 1-octenyl ether, tetra(ethylene glycol) mono 1-decenyl
ether, tetra(ethylene glycol) mono 1-undecenyl ether,
penta(ethylene glycol) mono methyl ether, penta(ethylene glycol)
mono allyl mono methyl ether, penta(ethylene glycol) mono tosyl
mono methyl ether, penta(ethylene glycol) mono tosyl mono allyl
ether, hexa(ethylene glycol) mono allyl ether, hexa(ethylene
glycol) mono methyl ether, hexa(ethylene glycol) mono benzyl ether,
hexa(ethylene glycol) mono trityl ether, hexa(ethylene glycol) mono
1-hexenyl ether, hexa(ethylene glycol) mono 1-heptenyl ether,
hexa(ethylene glycol) mono 1-octenyl ether, hexa(ethylene glycol)
mono 1-decenyl ether, hexa(ethylene glycol) mono 1-undecenyl ether,
hexa(ethylene glycol) mono 4-benzophenonyl mono 1-undecenyl ether,
hepta(ethylene glycol) mono allyl ether, hepta(ethylene glycol)
mono methyl ether, hepta(ethylene glycol) mono tosyl mono methyl
ether, hepta(ethylene glycol) monoallyl mono methyl ether,
octa(ethylene glycol) mono allyl ether, octa(ethylene glycol) mono
tosylate, octa(ethylene glycol) mono tosyl mono allyl ether,
undeca(ethylene glycol) mono methyl ether, undeca(ethylene glycol)
mono allyl mono methyl ether, undeca(ethylene glycol) mono tosyl
mono methyl ether, undeca(ethylene glycol) mono allyl ether,
octadeca(ethylene glycol) mono allyl ether, octa(ethylene glycol),
deca(ethylene glycol), dodeca(ethylene glycol), tetradeca(ethylene
glycol), hexadeca(ethylene glycol), octadeca(ethylene glycol),
benzophenone-4-hexa(ethylene glycol) allyl ether,
benzophenone-4-hexa(ethylene glycol) hexenyl ether,
benzophenone-4-hexa(ethylene glycol) octenyl ether,
benzophenone-4-hexa(ethylene glycol) decenyl ether,
benzophenone-4-hexa(ethylene glycol) undecenyl ether,
4-fluorobenzophenone-4'-hexa(ethylene glycol) allyl ether,
4-fluorobenzophenone-4'-hexa(ethylene glycol) undecenyl ether,
4-hydroxybenzophenone-4'-hexa(ethylene glycol) allyl ether,
4-hydroxybenzophenone-4'-hexa(ethylene glycol) undecenyl ether,
4-hydroxybenzophenone-4'-tetra(ethylene glycol) allyl ether,
4-hydroxybenzophenone-4'-tetra(ethylene glycol) undecenyl ether,
4-morpholinobenzophenone-4'-hexa(ethylene glycol) allyl ether,
4-morpholinobenzophenone-4'-hexa(ethylene glycol) undecenyl ether,
4-morpholinobenzophenone-4'-tetra(ethylene glycol) allyl ether, and
4-morpholinobenzophenone-4'-tetra(ethylene glycol) undecenyl
ether.
[0034] The term "polyethylene glycol having primary amino groups"
refers to polyethylene glycol having substituted primary amino
groups in place of the hydroxyl groups. Substitution can be up to
98% in commercial products ranging in molecular weight from 5,000
to 20,000 Da.
[0035] The term "alkyl" means a straight or branched chain alkyl
group containing up to approximately 20 but preferably up to 8
carbon atoms. Examples of alkyl groups include but are not limited
to the following: methyl, ethyl, n-propyl, isopropyl, n-butyl,
isobutyl, sec-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl,
tert-pentyl, isohexyl, n-hexyl, n-heptyl, and n-octyl. A
substituted alkyl has one or more hydrogen atoms substituted by
other groups or a carbon replaced by a divalent, trivalent, or
tetravalent group or atom. Although alkyls by definition have a
single radical, as used herein, alkyl includes groups that have
more than one radical to meet valence requirements for
substitution.
[0036] The term "alkenyl" means a straight or branched chain alkyl
group having at least one carbon-carbon double bond, and containing
up to approximately 20 but preferably up to 8 carbon atoms.
Examples of alkenyl groups include, but are not limited to, vinyl,
1-propenyl, 2-butenyl, 1,3-butadienyl, 2-pentenyl, 2,4-hexadienyl,
4-(ethyl)-1,3-hexadienyl, and 2-(methyl)-3-(propyl)-1,3-butadienyl.
A substituted alkenyl has one or more hydrogen atoms substituted by
other groups or a carbon replaced by a divalent, trivalent, or
tetravalent group or atom. Although alkenyls by definition have a
single radical, as used herein, alkenyl includes groups that have
more than one radical to meet valence requirements for
substitution.
[0037] The term "alkynyl" means a straight or branched chain alkyl
group having a single radical, having at least one carbon-carbon
triple bond, and containing up to approximately 20 but preferably
up to 8 carbon atoms. Examples of alkynyl groups include, but are
not limited to, the ethynyl, 1-propynyl, 2-propynyl, 1-butynyl,
2-butynyl, 3-butynyl, 4-pentynyl, 5-hexynyl, 6-heptynyl, 7-octynyl,
1-methyl-2-butynyl, 2-methyl-3-pentynyl, 4-ethyl-2-pentynyl, and
5,5-methyl-1,3-hexynyl. A substituted alkynyl has one or more
hydrogen atoms substituted by other groups or a carbon replaced by
a divalent, trivalent, or tetravalent group or atom. Although
alkynyls by definition have a single radical, as used herein,
alkynyl includes groups that have more than one radical to meet
valence requirements for substitution.
[0038] The term "cycloalkyl" means an alkyl group forming at least
one ring, wherein the ring has approximately 3 to 14 carbon atoms.
Examples of cycloalkyl groups include but are not limited to the
following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. A
substituted cycloalkyl has one or more hydrogen atoms substituted
by other groups or a carbon replaced by a divalent, trivalent, or
tetravalent group or atom. Although cycloalkyls by definition have
a single radical, as used herein, cycloalkyl includes groups that
have more than one radical to meet valence requirements for
substitution.
[0039] The term "cycloalkenyl" means an alkenyl group forming at
least one ring and having at least one carbon-carbon double bond
within the ring, wherein the ring has approximately 3 to 14 carbon
atoms. Examples of cycloalkenyl groups include, but are not limited
to, cyclopropenyl, cyclobutenyl, cyclopentenyl,
1,3-cyclopentadienyl, and cyclohexenyl. A substituted cycloalkenyl
has one or more hydrogens substituted by other groups or a carbon
replaced by a divalent, trivalent, or tetravalent group or atom.
Although cycloalkenyls by definition have a single radical, as used
herein, cycloalkenyl includes groups that have more than one
radical to meet valence requirements for substitution.
[0040] The term "cycloalkynyl" means an alkynyl group forming at
least one ring and having at least one carbon-carbon triple bond,
wherein the ring contains up to approximately 14 carbon atoms. A
group forming a ring having at least one triple bond and having at
least one double bond is a cycloalkynyl group. An example of a
cycloalkynyl group includes, but is not limited to, cyclooctyne. A
substituted cycloalkynyl has one or more hydrogen atoms substituted
by other groups. Although cycloalkynyls by definition have a single
radical, as used herein, cycloalkynyl includes groups that have
more than one radical to meet valence requirements for
substitution.
[0041] The term "aryl" means an aromatic carbon ring group having a
single radical and having approximately 4 to 20 carbon atoms.
Examples of aryl groups include, but are not limited to, phenyl,
naphthyl, and anthryl. A substituted aryl has one or more hydrogen
atoms substituted by other groups. Although aryls by definition
have a single radical, as used herein, aryl includes groups that
have more than one radical to meet valence requirements for
substitution. An aryl group can be a part of a fused ring structure
such as N-hydroxysuccinimide bonded to phenyl (benzene) to form
N-hydroxyphthalimide.
[0042] The term "hetero" when used in the context of chemical
groups, or "heteroatom" means an atom other than carbon or
hydrogen. Preferred examples of heteroatoms include oxygen,
nitrogen, phosphorous, sulfur, boron, silicon, and selenium.
[0043] The term "heterocyclic ring" means a ring structure having
at least one ring moiety having at least one heteroatom forming a
part of the ring, wherein the heterocyclic ring has approximately 4
to 20 atoms connected to form the ring structure. An example of a
heterocyclic ring having 6 atoms is pyridine with a single
hereroatom. Additional examples of heterocyclic ring structures
having a single radical include, but are not limited to, acridine,
carbazole, chromene, imidazole, furan, indole, quinoline, and
phosphinoline. Examples of heterocyclic ring structures include,
but are not limited to, aziridine, 1,3-dithiolane, 1,3-diazetidine,
and 1,4,2-oxazaphospholidine. Examples of heterocyclic ring
structures having a single radical include, but are not limited to,
fused aromatic and non-aromatic structures: 2H-furo[3,2-b]pyran,
5H-pyrido[2,3-d]-o-oxazine, 1H-pyrazolo[4,3-d]oxazole,
4H-imidazo[4,5-d]thiazole, selenazolo[5,4j]benzothiazole, and
cyclopenta[b]pyran. Heterocyclic rings can have one or more
radicals to meet valence requirements for substitution.
[0044] The term "polycyclic" or "polycyclic group" means a carbon
ring structure having more than one ring, wherein the polycyclic
group has approximately 4 to 20 carbons forming the ring structure
and has a single radical. Examples of polycyclic groups include,
but are not limited to, bicyclo[1.1.0]butane, bicyclo[5.2.0]nonane,
and tricycle[5.3.1.1]dodecane. Polycyclic groups can have one or
more radicals to meet valence requirements for substitution.
[0045] The term "halo" or "halogen" means fluorine, chlorine,
bromine, or iodine.
[0046] The term "heteroatom group" means one heteroatom or more
than one heteroatoms bound together and having two free valences
for forming a covalent bridge between two atoms. For example, the
oxy radical, --O-- can form a bridge between two methyls to form
CH.sub.3--O--CH.sub.3 (dimethyl ether) or can form a bridge between
two carbons to form an epoxy such as cis or trans
2,3-epoxybutane,
##STR00001##
As used herein and in contrast to the normal usage, the term
heteroatom group will be used to mean the replacement of groups in
an alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and
cycloalkynyl and not the formation of cyclic bridges, such as an
epoxy, unless the term cyclic bridge is used with the term
heteroatom group to denote the normal usage.
[0047] Examples of heteroatom groups, using the nomenclature for
hetero bridges (such as an epoxy bridge), include but are not
limited to the following: azimino (--N.dbd.N--HN--), azo
(--N.dbd.N--), biimino (--NH--NH--), epidioxy epidithio (--S--S--),
epithio (--S--), epithioximino (--S--0--NH--), epoxy (--0--),
epoxyimino (--0--NH--), epoxynitrilo N.dbd.), epoxythio (--0--S--),
epoxythioxy(--O--S--0--), furano (--CH.sub.20--), imino (--NH--) ,
and nitrilo (--N.dbd.). Examples of heteroatom groups using the
nomenclature for forming acyclic bridges include but are not
limited to the following: epoxy (--O--), epithio (--S--), episeleno
(--Se--), epidioxy epidithio (--S--S--), lambda.sup.4-sulfano
(--SH.sub.2--), epoxythio (--0--S--), epoxythioxy (--0--S--0--),
epoxyimino (--0--NH--), epimino (--NH--), diazano (--NH--NH--),
diazeno (--N.dbd.N--), triaz[1]eno (--N.dbd.N--NH--), phosphano
(--PH--), stannano (--SnH.sub.2--), epoxymethano (--O--CH.sub.2--),
epoxyethano (--O--CH.sub.2--CH.sub.2--), epoxyprop [1 ]eno
##STR00002##
[0048] The term "bridge" means a connection between one part of a
ring structure to another part of the ring structure by a
hydrocarbon bridge. Examples of bridges include but are not limited
to the following: methano, ethano, etheno, propano, butano,
2-buteno, and benzeno.
[0049] The term "hetero bridge" means a connection between one part
of a ring structure to another part of the ring structure by one or
more heteroatom groups, or a ring formed by a heterobridge
connecting one part of a linear structure to another part of the
linear structure, thus forming a ring.
[0050] The term "oxy" means the divalent radical --0--.
[0051] The term "oxo" means the divalent radical .dbd.O.
[0052] The term "carbonyl" means the group
##STR00003##
[0053] wherein the carbon has two radicals for bonding.
[0054] The term "amide" or "acylamino" means the group
##STR00004##
[0055] wherein the nitrogen has one single radical for bonding and
R is hydrogen or an unsubstituted or substituted alkyl, alkenyl,
alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic
ring, or polycyclic group.
[0056] The term "alkoxy" means the group --O--R, wherein the oxygen
has a single radical and R is hydrogen or an unsubstituted or
substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, or polycyclic group.
Examples of alkoxy groups where the R is an alkyl include but are
not limited to the following: methoxy, ethoxy, propoxy, butoxy,
pentoxy, hexoxy, heptoxy, octoxy, 1,1-dimethylethoxy,
1,1-dimethylpropoxy, 1,1-dimethylbutoxy, 1,1-dimethylpentoxy,
1-ethyl-l-methylbutoxy, 2,2-dimethylpropoxy, 2,2-dimethylbutoxy,
1-methyl-1-ethylpropoxy, 1,1-diethylpropoxy,
1,1,2-trimethylpropoxy, 1,1,2-trimethylbutoxy,
1,1,2,2-tetramethylpropoxy. Examples of alkoxy groups where the R
is an alkenyl group include but are not limited to the following:
ethenyloxy, 1-propenyloxy, 2-propenyloxy, 1-butenyloxy,
2-butenyloxy, 3-butenyloxy, 1-methyl-prop-2-enyloxy,
1,1-dimethyl-prop-2-enyloxy, 1,1,2-trimethyl-prop-2-enyloxy, and
1,1-dimethyl-but-2-enyloxy, 2-ethyl-1,3-dimethyl-but-l-enyloxy.
Examples of alkyloxy groups where the R is an alkynyl include but
are not limited to the following: ethynyloxy, 1-propynyloxy,
2-propynyloxy, 1-butynyloxy, 2-butynyloxy, 3-butynyloxy,
1-methyl-prop-2-ynyloxy, 1,1-dimethyl-prop-2-ynyloxy, and
1,1-dimethyl-but-2-ynyloxy, 3-ethyl-3-methyl-but-l-ynyloxy.
Examples of alkoxy groups where the R is an aryl group include but
are not limited to the following: phenoxy, 2-naphthyloxy, and
1-anthyloxy.
[0057] The term "acyl" means the group
##STR00005##
wherein the carbon has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group. Examples of acyl groups include but are not limited to the
following: acetyl, propionyl, butyryl, isobutyryl, valeryl,
isovaleryl, acryloyl, propioloyl, mathacryloyl, crotonoyl,
isocrotonoyl, benzoyl, and naphthoyl.
[0058] The term "acyloxy" means the group
##STR00006##
[0059] wherein the oxygen has a single radical and R is hydrogen or
an unsubstituted or substituted alkyl, alkenyl, alkynyl,
cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or
polycyclic group. Examples of acyloxy groups include but are not
limited to the following: acetoxy, ethylcarbonyloxy,
2-propenylcarbonyloxy, pentylcarbonyloxy, 1-hexynylcarbonyloxy,
benzoyloxy, cyclohexylcarbonyloxy, 2-naphthoyloxy,
3-cyclodecenylcarbonyloxy.
[0060] The term "oxycarbonyl" means the group
##STR00007##
[0061] wherein the carbon has a single radical and R is hydrogen or
an unsubstituted or substituted alkyl, alkenyl, alkynyl,
cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or
polycyclic group. Examples of oxycarbonyl groups include but are
not limited to the following: methoxycarbonyl, ethoxycarbonyl,
isopropyloxycarbonyl, phenoxycarbonyl, and
cyclohexyloxycarbonyl.
[0062] The term "acyloxycarbonyl" means the group
##STR00008##
wherein the carbon has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0063] The term "alkoxycarbonyloxy" means the group
##STR00009##
wherein the oxygen has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0064] The term "carboxy" means the group --C(O)OH, wherein the
carbon has a single radical.
[0065] The term "imino" or "nitrene" means the group .dbd.N--R,
wherein the nitrogen has two radicals and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0066] The term "amino" means the group --NH2, where the nitrogen
has a single radical.
[0067] The term "secondary amino" means the group --NH--R, wherein
the nitrogen has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0068] The term "tertiary amino" means the group
##STR00010##
wherein the nitrogen has a single radical and R1 and R2 are
independently selected from the group consisting of unsubstituted
and substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, and polycyclic group.
[0069] The term "hydrazi" means the group --NH--NH--, wherein the
nitrogens have single radicals bound to the same atom. The term
"hydrazo" means the group --NH--NH--, wherein the nitrogens have
single radicals bound to the different atoms.
[0070] The term "hydrazine" means the group NH.sub.2--NH--, wherein
the nitrogen has a single radical.
[0071] The term "hydrazone" means the group NH.sub.2--N.dbd.,
wherein the nitrogen has two radicals.
[0072] The term "hydroxyimino" means the group HO--N.dbd., wherein
the nitrogen has two radicals.
[0073] The term "alkoxyimino" means the group R--O--N.dbd., wherein
the nitrogen has two radicals and R is an unsubstituted or
substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, or polycyclic group.
[0074] The term "azido" means the group N.sub.3--, wherein the
nitrogen has one radical.
[0075] The term "azoxy" means the group --N(O).dbd.N--, wherein the
nitrogens have one radical.
[0076] The term "alkazoxy" means the group R--N(O).dbd.N--, wherein
the nitrogen has one radical and R is hydrogen or an unsubstituted
or substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, or polycyclic group.
Azoxybenzene is an example compound.
[0077] The term "cyano" means the group --CN. The term "isocyano"
means the group --NC. The term "cyanato" means the group --OCN. The
term "isocyanato" means the group --NCO. The term "fulminato" means
the group --ONC. The term "thiocyanato" means the group --SCN. The
term "isothiocyanato" means the group --NCS. The term
"selenocyanato" means the group --SeCN. The term "isoselenocyanato"
means the group --NCSe.
[0078] The term "carboxyamido" or "acylamino" means the group
##STR00011##
wherein the nitrogen has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0079] The term "acylimino" means the group
##STR00012##
wherein the nitrogen has two radicals and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0080] The term "nitroso" means the group O.dbd.N--, wherein the
nitrogen has a single radical.
[0081] The term "aminooxy" means the group --O--NH.sub.2, wherein
the oxygen has a single radical.
[0082] The term "carxoimidioy" means the group
##STR00013##
wherein the carbon has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0083] The term "hydrazonoyl" means the group
##STR00014##
wherein the carbon has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0084] The term "hydroximoyl" or "oxime" means the group
##STR00015##
wherein the carbon has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group.
[0085] The term "hydrazine" means the group
##STR00016##
[0086] wherein the nitrogen has a single radical and R is hydrogen
or an unsubstituted or substituted alkyl, alkenyl, alkynyl,
cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or
polycyclic group.
[0087] The term "amidino" means the group
##STR00017##
wherein the carbon has a single radical.
[0088] The term "sulfide" means the group --S--R, wherein the
sulfur has a single radical and R is hydrogen or an unsubstituted
or substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, or polycyclic group.
[0089] The term "thiol" means the group --S--, wherein the sulfur
has two radicals. Hydrothiol means --SH.
[0090] The term "thioacyl" means the group --C(S)--R, wherein the
carbon has a single radical and R is hydrogen or an unsubstituted
or substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, or polycyclic group.
[0091] The term "sulfoxide" means the group
##STR00018##
wherein the sulfur has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group. The term "thiosulfoxide" means the substitution of sulfur
for oxygen in sulfoxide; the term includes substitution for an
oxygen bound between the sulfur and the R group when the first
carbon of the R group has been substituted by an oxy group and when
the sulfoxide is bound to a sulfur atom on another group.
[0092] The term "sulfone" means the group
##STR00019##
wherein the sulfur has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group. The term "thiosulfone" means substitution of sulfur for
oxygen in one or two locations in sulfone; the term includes
substitution for an oxygen bound between the sulfur and the R group
when the first carbon of the R group has been substituted by an oxy
group and when the sulfone is bound to a sulfur atom on another
group.
[0093] The term "sulfate" means the group
##STR00020##
wherein the oxygen has a single radical and R is hydrogen or an
unsubstituted or substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, or polycyclic
group. The term "thiosulfate" means substitution of sulfur for
oxygen in one, two, three, or four locations in sulfate.
[0094] The term "phosphoric acid ester" means the group
R.sup.1R.sup.2PO.sub.4--, wherein the oxygen has a single radical
and R.sup.1 is selected from the group consisting of hydrogen and
unsubstituted and substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, and polycyclic
group, and R.sup.2 is selected from the group consisting of
unsubstituted and substituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, and polycyclic
group.
[0095] The term "substituted" or "substitution," in the context of
chemical species, means independently selected from the group
consisting of (1) the replacement of a hydrogen on at least one
carbon by a monovalent radical, (2) the replacement of two
hydrogens on at least one carbon by a divalent radical, (3) the
replacement of three hydrogens on at least one terminal carbon
(methyl group) by a trivalent radical, (4) the replacement of at
least one carbon and the associated hydrogens (e.g., methylene
group) by a divalent, trivalent, or tetravalent radical, and (5)
combinations thereof. Meeting valence requirements restricts
substitution. Substitution occurs on alkyl, alkenyl, alkynyl,
cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring,
and polycyclic groups, providing substituted alkyl, substituted
alkenyl, substituted alkynyl, substituted cycloalkyl, substituted
cycloalkenyl, substituted cycloalkynyl, substituted aryl group,
substituted heterocyclic ring, and substituted polycyclic
groups.
[0096] The groups that are substituted on an alkyl, alkenyl,
alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heterocyclic
ring, and polycyclic groups are independently selected from the
group consisting of alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, polycyclic
group, halo, heteroatom group, oxy, oxo, carbonyl, amide, alkoxy,
acyl, acyloxy, oxycarbonyl, acyloxycarbonyl, alkoxycarbonyloxy,
carboxy, imino, amino, secondary amino, tertiary amino, hydrazi,
hydrazino, hydrazono, hydroxyimino, azido, azoxy, alkazoxy, cyano,
isocyano, cyanato, isocyanato, thiocyanato, fulminato,
isothiocyanato, isoselenocyanato, selenocyanato, carboxyamido,
acylimino, nitroso, aminooxy, carboximidoyl, hydrazonoyl, oxime,
acylhydrazino, amidino, sulfide, thiol, sulfoxide, thiosulfoxide,
sulfone, thiosulfone, sulfate, thio sulfate, hydroxyl, formyl,
hydroxyperoxy, hydroperoxy, peroxy acid, carbamoyl, trimethyl
silyl, nitrilo, nitro, aci-nitro, nitroso, semicarbazono, oxamoyl,
pentazolyl, seleno, thiooxi, sulfamoyl, sulfenamoyl, sulfeno,
sulfinamoyl, sulfino, sulfinyl, sulfo, sulfoamino, sulfonato,
sulfonyl, sulfonyldioxy, hydrothiol, tetrazolyl, thiocarbamoyl,
thiocarbazono, thiocarbodiazono, thiocarbonohydrazido,
thiocarbonyl, thiocarboxy, thiocyanato, thioformyl, thioacyl,
thiosemicarbazido, thiosulfino, thiosulfo, thioureido, thioxo,
triazano, triazeno, triazinyl, trithio, trithiosulfo, sulfinimidic
acid, sulfonimidic acid, sulfinohydrazonic acid, sulfonohydrazonic
acid, sulfinohydroximic acid, sulfonohydroximic acid, and
phosphoric acid ester, and combinations thereof.
[0097] As an example of a substitution, replacement of one hydrogen
atom on ethane by a hydroxyl provides ethanol, and replacement of
two hydrogens by an oxo on the middle carbon of propane provides
acetone (dimethyl ketone.) As a further example, replacement the
middle carbon (the methenyl group) of propane by the oxy radical
(--O--) provides dimethyl ether (CH.sub.3--O--OCH.sub.3.) As a
further example, replacement of one hydrogen atom on benzene by a
phenyl group provides biphenyl.
[0098] As provided above, heteroatom groups can be substituted
inside an alkyl, alkenyl, or alkylnyl group for a methylene group
(:CH.sub.2) thus forming a linear or branched substituted structure
rather than a ring or can be substituted for a methylene inside of
a cycloalkyl, cycloalkenyl, or cycloalkynyl ring thus forming a
heterocyclic ring. As a further example, nitrilo (--N.dbd.) can be
substituted on benzene for one of the carbons and associated
hydrogen to provide pyridine, or an oxy radical can be substituted
to provide pyran.
[0099] The term "unsubstituted" means that no hydrogen or carbon
has been replaced on an alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, or aryl group.
[0100] The term "linker" means a molecule having one end attached
or capable of attaching to a solid surface and the other end having
a reactive group that is attached or capable of attaching to a
chemical species of interest such as a small molecule, an oligomer,
or a polymer. A linker may already be bound to a solid surface
and/or may already have a chemical species of interest bound to its
reactive group. A linker may have a protective group attached to
its reactive group, where the protective group is chemically or
electrochemically removable. A linker may comprise more than one
molecule, where the molecules are covalently joined in situ to form
the linker having the desired reactive group projecting away from a
solid surface.
[0101] The term "spacer" or "linker moiety" means a molecule having
one end attached or capable of attaching to the reactive group of a
linker or porous reaction layer and the other end having a reactive
group that is attached or capable of attaching to a chemical
species of interest such as a small molecule, an oligomer, or a
polymer. A spacer may already be bound to a linker or a porous
reaction layer and/or may already have a chemical species of
interest bound to its reactive group. A spacer may have a
protective group attached to its reactive group, where the
protective group is chemically or electrochemically removable. A
spacer may be formed in situ on a linker or porous reaction layer.
A spacer may be formed and then attached to a linker already
attached to a solid surface or attached to a porous reaction layer
on the solid surface. A spacer may be externally synthesized on a
chemical species of interest followed by attachment to a linker
already attached to a solid surface or attached to a porous
reaction layer on the solid surface. A chemical species of interest
may be attached to a spacer that is attached to a linker where the
entire structure is then attached to a solid surface at a reactive
sight on the solid surface. The purpose of a spacer is to extend
the distance between a molecule of interest and a solid
surface.
[0102] The term "combination linker and spacer" means a linker
having both the properties of a linker and a spacer. A combination
linker and spacer may be synthesized in situ or synthesized
externally and attached to a solid surface.
[0103] The term "coating" means a thin layer of material that is
chemically and/or physically bound to a solid surface. A coating
may be attached to a solid surface by mechanical interlocking as
well as by van der Waals forces (dispersion forces and dipole
forces), electron donor-acceptor interactions, metallic
coordination/complexation, covalent bonding, or a combination of
the aforementioned. A coating can provide a reactive group for
direct attachment of a chemical species of interest, attachment of
a linker, or attachment of a combination linker and spacer. A
coating can be polymerized and/or cross-linked in situ.
[0104] The term "reactive" or "reaction" as used in reactive or
reaction coating or reactive or reaction layer means that there is
a chemical species or bound group within the layer that is capable
of forming a covalent bond for attachment of a linker, spacer, or
other chemical species to the layer or coating.
[0105] The term "porous" as used in porous reactive layer or
coating means that there are non-uniformities within the layer or
coating to allow molecular species to diffuse into and through the
layer or coating.
[0106] The term "adsorption" or "adsorbed" means a chemical
attachment by van der Waals forces (dispersion forces and dipole
forces), electron donor-acceptor interactions, or metallic
coordination/complexation, or a combination of the aforementioned
forces. After adsorption, a species may covalently bind to a
surface, depending on the surface, the species, and the
environmental conditions.
[0107] The term "microarray" refers to, in general, planer surface
having specific spots that are usually arranged in a column and row
format, wherein each spot can be used for some type of chemical or
biochemical analysis, synthesis, or method. The spots on a
microarray are typically smaller than 100 micrometers. The term
"electrode microarray" refers to a microarray of electrodes,
wherein the electrodes are the specific spots on the
microarray.
[0108] The term "synthesis quality" refers to, in general, the
average degree of similarity between a desired or designed chemical
or biochemical species and the species actually synthesized. The
term can refer to other issues in a synthesis such as the effect of
a layer or coating on the synthesis quality achieved.
[0109] The term "salvation" means a chemical process in which
solvent molecules and molecules or ions of a solute combine to form
a compound, wherein the compound is generally a loosely bound
complex held together by van der Waals forces (dispersion forces
and dipole forces), acid-base interactions (electron donor acceptor
interactions), ionic interaction, or metal complex interactions but
not covalent bonds. In water, the pH of the water can affect
solvation of dissociable species such as acids and bases. In
addition, the concentration of salts as well as the charge on salts
can affect salvation.
[0110] The term "agarose" means any commercially available agarose.
Agarose is a polysaccharide biopolymer and is usually obtained from
seaweed. Agarose has a relatively large number of hydroxyl groups,
which provide for high water solubility. Agarose is available
commercially in a wide range of molecular weights and
properties.
[0111] The term "controlled pore glass" means any commercially
available controlled pore glass material suitable for coating
purposes. In general, controlled pore glass (CPG) is an inorganic
glass material having a high surface area owing to a large amount
of void space.
[0112] The term "monosaccharide" means one sugar molecule unlinked
to any other sugars. Examples of monosaccharides include allose,
altrose, arabinose, deoxyribose, erythrose, fructose (D-Levulose),
galactose, glucose, gulose, idose, lyxose, mannose, psicose,
ribose, ribulose, sedoheptulose, D-sorbitol, sorbose, sylulose,
L-rhamnose (6-Deoxy-L-mannose), tagatose, talose, threose,
xylulose, and xylose.
[0113] The term "disaccharide" means two sugars linked together to
form one molecule. Examples of disaccharides include amylo se,
cellobiose (4-.beta.-D-glucopyranosyl-D-glucopyranose), lactose,
maltose (4-O-.alpha.-D-glucopyranosyl-D-glucose), melibiose
(6-O-.alpha.-D-Galactopyranosyl-D-glucose), palatinose
(6-O-.alpha.-D-Glucopyranosyl-D-fructose), sucrose, and trehalose
(a-D-Glucopyranosyl-.alpha.-D-glucopyranoside).
[0114] The term "trisaccharide" means three sugars linked together
to form one molecule. Examples of a trisaccharides include
raffinose
(6-O-.alpha.-D-Galactopyranosyl-D-glucopyranosyl-.beta.-D-fructofuranosid-
-e) and melezitose
(O-.alpha.-D-glucopyranosyl-(1.fwdarw.3)-.beta.-D-fructofurano
syl-.alpha.--D-glucopyranoside).
[0115] The term "polysaccharide" means more than three sugars
linked together to form one molecule, but more accurately means a
sugar-based polymer or oligomer. Examples of polysaccharides
include inulin, dextran, starches, and cellulose. Dextran is a
polymer composed of glucose subunits (mers.)
[0116] The term "linker hydroxyl group" means a hydroxyl group on a
linker moiety, wherein the hydroxyl group is initially protected by
a protecting group such as MMT or DMT. After deprotection, the
hydroxyl group becomes reactable. For example, after deprotection,
a phosphoramidite may be bonded to the linker hydroxyl group to
form a synthetic oligonucleotide.
[0117] Disclosed herein is a process for forming a microarray
having base cleavable sulfonyl linkers. The process comprises
providing an array having known locations having a plurality of
hydroxyl groups. The array comprises a surface or a matrix
proximate to the surface, wherein the density of the known
locations is greater than approximately 100 per square centimeter.
The process further comprises bonding one or a plurality of
sulfonyl amidite containing reagents to the hydroxyl groups at the
known locations to form a plurality of cleavable linkers bonded to
the known locations. The cleavable linkers comprise a hydroxyl
moiety and a base-labile cleaving moiety. A phosphorous-oxygen bond
is formed between phosphorous of the sulfonyl amidite containing
reagent and oxygen of the hydroxyl groups.
[0118] Further disclosed herein is a process for forming a
microarray having base cleavable sulfonyl linkers. The process
comprises providing an array device having a plurality of known
locations, each having a plurality of hydroxyl groups. The density
of the known locations is greater than approximately 100 per square
centimeter. The process further comprises bonding a plurality of
sulfonyl amidite moieties to the hydroxyl groups to form a
plurality of cleavable linkers attached to the array device at each
known location. The cleavable linkers comprise a linker hydroxyl
moiety and a base-labile cleaving moiety. A phosphorous-oxygen bond
is formed between phosphorous of the sulfonyl amidite moieties and
oxygen of the hydroxyl groups. The process further comprises
synthesizing a plurality of oligomers onto the linker hydroxyl
moieties.
[0119] Further disclosed herein is a process for forming a
microarray having base cleavable sulfonyl linkers. The process
comprises providing an array device having a plurality of known
locations, each having a plurality of hydroxyl groups. The density
of the plurality of known locations is greater than approximately
100 per square centimeter. The process further comprises bonding a
plurality of sulfonyl amidite moieties to the hydroxyl groups to
form a plurality of cleavable linkers bonded to the known
locations. The cleavable linkers comprise a linker hydroxyl moiety
and a base-labile cleaving moiety. A phosphorous-oxygen bond is
formed between phosphorous of the sulfonyl amidite moieties and
oxygen of the hydroxyl groups. The process further comprises
synthesizing a plurality of oligomers covalently bound to the
linker hydroxyl moiety. The process further comprises cleaving the
oligomers from the known locations at the base-labile cleaving
moiety using a cleaving base. The oligomers are recoverable. The
oligomers comprising DNA and RNA have a 3' phosphate after cleaving
from the solid surface.
[0120] In one or more embodiments, the cleaving base is selected
from the group consisting of ammonium hydroxide, electrochemically
generated base, sodium hydroxide, potassium hydroxide, methylamine,
and ethylamine and combinations thereof.
[0121] Further disclosed herein is a process for forming a pool of
oligomers produced by providing an array having known locations
having a plurality of hydroxyl groups. The array comprises a
surface or a matrix proximate to the surface. The density of the
known locations is greater than approximately 100 per square
centimeter. The process further comprises bonding a plurality of
sulfonyl amidite moieties to the hydroxyl groups to form a
plurality of cleavable linkers bonded to the known locations. The
cleavable linkers comprise a linker hydroxyl moiety and a
base-labile cleaving moiety. A phosphorous-oxygen bond is formed
between phosphorous of the sulfonyl amidite moieties and oxygen of
the hydroxyl groups. The process further comprises synthesizing a
plurality of oligomers covalently bound to the linker hydroxyl
moiety. The process further comprises cleaving the oligomers from
the known locations at the base-labile cleaving moiety using a
cleaving base. The oligomers comprise DNA and RNA and have a 3'
phosphate after cleaving from the solid surface. The oligomers are
oligonucleotides having a 3' phosphate. The pool comprises more
than approximately 100 different oligonucleotides.
[0122] Further disclosed herein is a microarray having base
cleavable sulfonyl linkers. The microarray comprises an array
device having a plurality of known locations where each location
has a plurality of reacted hydroxyl groups. The density of the
plurality of known locations is greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reacted sulfonyl amidite moieties bonded to the plurality of
reacted hydroxyl groups to form a plurality of cleavable linkers
attached to the plurality of known locations. The cleavable linkers
have a linker hydroxyl group and a base-labile cleaving site. A
phosphorous-oxygen bond is between phosphorous of the reacted
sulfonyl amidite moieties and oxygen of the reacted hydroxyl
groups.
[0123] Further disclosed herein is a microarray having base
cleavable sulfonyl linkers. The microarray comprises an array
device having a plurality of known locations where each location
has a plurality of reacted hydroxyl groups. The density of the
plurality of known locations is greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reacted sulfonyl amidite moieties bonded to the plurality of
reacted hydroxyl groups to form a plurality of cleavable linkers
attached to the plurality of known locations. The cleavable linkers
have a linker hydroxyl group and a base-labile cleaving site. A
phosphorous-oxygen bond is between phosphorous of the reacted
sulfonyl amidite moieties and oxygen of the reacted hydroxyl
groups. The microarray further comprises oligomers bonded to the
linker hydroxyl groups.
[0124] Further disclosed herein is a process for forming a
microarray having cleavable succinate linkers. The process
comprises providing a solid surface having free hydroxyl groups at
known locations. The density of the known locations is greater than
approximately 100 locations per square centimeter. The process
further comprises bonding a linker moiety to the hydroxyl groups.
The linker moiety comprises free amine group and a hydroxyl bonding
group. The process further comprises bonding a succinate-containing
moiety having free carboxyl groups to the free amine groups to form
cleavable linkers attached to the known locations. The
succinate-containing moieties comprise a sugar having both a
nucleotide base group and a succinate group bonded to the sugar.
The cleavable linkers have a base-labile cleaving site on the
succinate group and a reactable hydroxyl group on the sugar group.
In one or more embodiments, the sugar moiety has one or a plurality
of free hydroxyl groups. In another embodiment, the process further
comprises synthesizing oligomers, such as oligonucleotides,
attached to free hydroxyl groups of the sugar moiety. In another
embodiment, the process further comprises cleaving oligomers at the
base-labile cleaving site from the known location using a cleaving
base, whereby the oligomers are recoverable.
[0125] Further disclosed herein is a microarray having base
cleavable succinate linkers. The microarray comprises a solid
surface having known locations and reactive hydroxyl groups. The
known locations have a density greater than approximately 100 per
square centimeter. The microarray further comprises a plurality of
reactive amino amidite moieties bonded to the reactive hydroxyl
groups on the solid surface. The reactive amino moieties comprise
an amine group and a hydroxyl bonding group. The hydroxyl bonding
group is bonded to the reactive hydroxyl groups at the known
locations. The microarray further comprises a plurality of reactive
succinate moieties bonded to the amine groups. The reactive
succinate moieties comprise a sugar group bonded to the succinate
group and to a base group bonded. In an alternative embodiment,
microarray further comprises oligomers bonded onto the reactable
hydroxyl groups. In one or more embodiments, the sugar group is
ribose and the base group is selected from the group consisting of
adenine, guanine, cytosine, and uracyl, or the sugar group is
deoxyribose and the base group is selected from the group
consisting of adenine, guanine, cytosine, and thymine.
[0126] Further disclosed herein is a process of forming a
microarray having base cleavable phosphoramidite linkers. The
process comprises providing a microarray having a surface with a
plurality of known locations on the surface. Each location has a
plurality of hydroxyl groups, and the density of the known
locations is greater than approximately 100 per square centimeter
on the surface. The process further comprises bonding a plurality
of base cleavable phosphoramidite linkers to the plurality of
hydroxyl groups directly or by using an intermediate chemical
moiety attached to the hydroxyl groups to form a plurality of
cleavable linkers at the plurality of known locations. The
cleavable linkers each have a linker hydroxyl group and a
base-labile cleaving site. The linker hydroxyl group is protected
by a protecting group, and the base-labile cleaving site is an
ether linkage.
[0127] Further disclosed herein is a process of forming a
microarray having base cleavable phosphoramidite linkers. The
process comprises providing a microarray having a surface with a
plurality of known locations on the surface. Each location has a
plurality of hydroxyl groups, and the density of the known
locations is greater than approximately 100 per square centimeter
on the surface. The process further comprises bonding a plurality
of base cleavable phosphoramidite linkers to the plurality of
hydroxyl groups directly or by using an intermediate chemical
moiety attached to the hydroxyl groups to form a plurality of
cleavable linkers at the plurality of known locations. The
cleavable linkers each have a linker hydroxyl group and a
base-labile cleaving site. The linker hydroxyl group is protected
by a protecting group, and the base-labile cleaving site is an
ether linkage. The process further comprises synthesizing oligomers
onto the linker hydroxyl groups to provide a microarray of
oligomers. The protecting group is removed from the linker hydroxyl
groups before synthesizing the oligomers, and the oligomers at the
known locations, as between different known locations, are
different or the same.
[0128] Further disclosed herein is a process of forming a
microarray having base cleavable phosphoramidite linkers. The
process comprises providing a microarray having a surface with a
plurality of known locations on the surface. Each location has a
plurality of hydroxyl groups, and the density of the known
locations is greater than approximately 100 per square centimeter
on the surface. The process further comprises bonding a plurality
of base cleavable phosphoramidite linkers to the plurality of
hydroxyl groups directly or by using an intermediate chemical
moiety attached to the hydroxyl groups to form a plurality of
cleavable linkers at the plurality of known locations. The
cleavable linkers each have a linker hydroxyl group and a
base-labile cleaving site. The linker hydroxyl group is protected
by a protecting group, and the base-labile cleaving site is an
ether linkage. The process further comprises synthesizing oligomers
onto the linker hydroxyl groups to provide a microarray of
oligomers. The protecting group is removed from the linker hydroxyl
groups before synthesizing the oligomers, and the oligomers at the
known locations, as between different known locations, are
different or the same. The process further comprises cleaving at
the base-labile cleaving site the oligomers from the surface using
a cleaving base to provide a pool of cleaved oligomers.
[0129] Further disclosed herein is a pool of oligomers produced
according to one or more of the processes disclosed herein, wherein
the oligomers are oligonucleotides having a 3' phosphate, wherein
the pool comprises more than approximately 100 different
oligonucleotides. Further disclosed herein is a pool of oligomers
produced according to one or more of the processes disclosed
herein, wherein the oligomers are oligonucleotides having a 3'
hydroxyl, wherein the pool comprises more than approximately 100
different oligonucleotides.
[0130] In one or more embodiments, the oligomers are selected from
the group consisting of DNA, RNA, and polypeptides, and
combinations thereof. In one or more embodiments, the cleaving base
is selected from the group consisting of chemical base, ammonium
hydroxide, electrochemically generated base, sodium hydroxide,
potassium hydroxide, methylamine, and ethylamine and combinations
thereof. In one or more embodiments, the oligomers are synthesized
in situ using electrochemical synthesis. In one or more
embodiments, the oligomers are synthesized in situ by a method
selected from the group consisting of (i) printing reagents via ink
jet or other printing technology and using regular phosphoramidite
chemistry, (ii) maskless photo-generated acid controlled synthesis
and using regular phosphoramidite chemistry, (iii) mask-directed
parallel synthesis using photo-cleavage of photolabile protecting
groups, and (iv) maskless parallel synthesis using photo-cleavage
of photolabile protecting groups and digital photolithography.
[0131] Further disclosed herein is a microarray having base
cleavable linkers. The microarray comprises a microarray having a
surface with a plurality of known locations on the surface, wherein
each location has a plurality of hydroxyl groups, wherein the
density of the known locations is greater than approximately 100
per square centimeter on the surface. The microarray further
comprises a plurality of base cleavable linkers bonded to the
plurality of hydroxyl groups to form a plurality of cleavable
linkers at the plurality of known locations, wherein the cleavable
linkers each have a linker hydroxyl group and a base-labile
cleaving site.
[0132] In one or more embodiments, the surface has electrodes and
each of the known locations are associated with one of the
electrodes, wherein the electrodes are electronically addressable.
In one or more embodiments, the known locations are on the same
surface as the electrodes, on an opposing surface to the
electrodes, or on an overlayer over the electrodes.
[0133] In one or more embodiments, the array comprises electrodes
and each of the known locations has an electrode, wherein the
electrodes are electronically addressable. In one or more
embodiments, the known locations are on the same surface as the
electrodes, on an opposing surface to the electrodes, or on an
overlayer over the electrodes. An example of an electrode
microarray is a CombiMatrix CustomArray..TM.. 12K, which has over
12,000 electrodes and an electrode density of approximately 17,778
electrodes per square centimeter.
[0134] In one or more embodiments, the oligomers are selected from
the group consisting of DNA, RNA, and polypeptide, and combinations
thereof.
[0135] In one or more embodiments, the oligomers are synthesized in
situ using electrochemical synthesis. In one or more embodiments,
the oligomers are synthesized in situ by a method selected from the
group consisting of (i) printing reagents via ink jet or other
printing technology and using regular phosphoramidite chemistry,
(ii) maskless photo-generated acid controlled synthesis and using
regular phosphoramidite chemistry, (iii) mask-directed parallel
synthesis using photo-cleavage of photolabile protecting groups,
and (iv) maskless parallel synthesis using photo-cleavage of
photolabile protecting groups and digital photolithography.
[0136] In one or more embodiments, the array is glass having a
silane linking agent having organic hydroxyl groups, wherein the
organic hydroxyl groups are the hydroxyl groups of the known
locations. Preferably, the silane linking agent is a chemical
selected from the group consisting of hydroxymethyltriethoxysilane,
N-(3-triethoxysilylpropyl)gluconamide,
N-(3-triethoxysilylpropyl)-4-hydroxybutyramide,
1-trimethoxysilyl-3-propanol, 1-trimethoxysilyl-2,3-propanediol,
1-triethoxysilyl-3-propanol, 1-triethoxysilyl-2,3-propanediol,
1-trimethoxysilyl-2-ethanol, triethoxysilyl-2-ethanol,
trimethoxysilyl-11-undecanol, and triethoxysilyl-11-undecanol and
combinations thereof.
[0137] In one or more embodiments, the sulfonyl amidite moiety is
2-[2-(4,4'-dimethoxytrityloxy)ethylsulfonyl)ethyl-(2-cyanoethyl)-(N,N-dii-
-sopropyl)-phosphoramidite.
[0138] In one or more embodiments, spacers having reactive hydroxyl
groups are bound to the hydroxyl moieties, wherein the sulfonyl
amidite moieties are bound to the reactive hydroxyl groups of the
spacers. Preferably, the spacer is selected from the group
consisting of DNA, RNA, polyethylene glycol, and polypeptides, and
combinations thereof. Preferably, the spacer is approximately 1 to
35 mers.
[0139] In one or more embodiments, a porous reaction layer attached
to the known locations provides the hydroxyl groups, wherein the
porous reaction layer comprises a chemical species or mixture of
chemical specie, wherein the chemical species is selected from the
group consisting of monosaccharides, disaccharides, trisaccharides,
polyethylene glycol, polyethylene glycol derivative,
N-hydroxysuccinimide, formula I, formula II, formula III, formula
IV, formula V, formula VI, formula VII, and combinations thereof,
wherein formula I is
##STR00021##
formula II is
##STR00022##
formula III is HOR.sup.4(OR.sup.5).sub.mR.sup.9 formula IV is
##STR00023##
formula V is
##STR00024##
formula VI is
##STR00025##
and formula VII is
##STR00026##
wherein in each formula m is an integer from 1 to 4; R.sup.1,
R.sup.2; R.sup.7, and R.sup.8 are independently selected from the
group consisting of hydrogen, and substituted and unsubstituted
alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl,
aryl, heterocyclic ring, and polycyclic group, and halo, amide,
alkoxy, acyl, acyloxy, oxycarbonyl, acyloxycarbonyl,
alkoxycarbonyloxy, carboxy, amino, secondary amino, tertiary amino,
hydrazino, azido, alkazoxy, cyano, isocyano, cyanato, isocyanato,
thiocyanato, fulminato, isothiocyanato, isoselenocyanato,
selenocyanato, carboxyamido, acylimino, nitroso, aminooxy,
carboximidoyl, hydrazonoyl, oxime, acylhydrazino, amidino, sulfide,
sulfoxide, thiosulfoxide, sulfone, thiosulfone, sulfate, thio
sulfate, hydroxyl, formyl, hydroxyperoxy, hydroperoxy, peroxy acid,
carbamoyl, trimethyl silyl, nitro, nitroso, oxamoyl, pentazolyl,
sulfamoyl, sulfenamoyl, sulfeno, sulfinamoyl, sulfino, sulfo,
sulfoamino, hydrothiol, tetrazolyl, thiocarbamoyl, thiocarbazono,
thiocarbodiazono, thiocarbonohydrazido, thiocarboxy, thioformyl,
thioacyl, thiocyanato, thiosemicarbazido, thiosulfino, thiosulfo,
thioureido, triazano, triazeno, triazinyl, trithiosulfo,
sulfinimidic acid, sulfonimidic acid, sulfinohydrazonic acid,
sulfonohydrazonic acid, sulfinohydroximic acid, sulfonohydroximic
acid, and phosphoric acid ester; R.sup.3 is selected from the group
consisting of heteroatom group, carbonyl, and substituted and
unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,
cycloalkynyl, aryl, heterocyclic ring, and polycyclic group;
R.sup.4 and R.sup.5 are independently selected from the group
consisting of methylene, ethylene, propylene, butylene, pentylene,
and hexylene; R.sup.6 forming a ring structure with two carbons of
succinimide and is selected from the group consisting of
substituted and unsubstituted alkyl, alkenyl, alkynyl, cycloalkyl,
cycloalkenyl, cycloalkynyl, aryl, heterocyclic ring, and polycyclic
group; and R.sup.9 is selected from the group consisting of amino
and hydroxyl.
[0140] In one or more embodiments, the monosaccharide is selected
from the group consisting of allose, altrose, arabinose,
deoxyribose, erythrose, fructose, galactose, glucose, gulose,
idose, lyxose, mannose, psicose, L-rhamnose, ribose, ribulose,
sedoheptulose, D-sorbitol, sorbose, sylulose, tagatose, talose,
threose, xylulose, and xylose. In one or more embodiments, the
disaccharide is selected from the group consisting of amylose,
cellobiose, lactose, maltose, melibiose, palatinose, sucrose, and
trehalose. In one or more embodiments, the trisaccharide is
selected from the group consisting of raffinose and melezitose.
[0141] In one or more embodiments, the polyethylene glycol
derivative is selected from the group consisting of diethylene
glycol, tetraethylene glycol, polyethylene glycol having primary
amino groups, 2-(2-aminoethoxy) ethanol, ethanol amine, di(ethylene
glycol) mono allyl ether, di(ethylene glycol) mono tosylate,
tri(ethylene glycol) mono allyl ether, tri(ethylene glycol) mono
tosylate, tri(ethylene glycol) mono benzyl ether, tri(ethylene
glycol) mono trityl ether, tri(ethylene glycol) mono chloro mono
methyl ether, tri(ethylene glycol) mono tosyl mono allyl ether,
tri(ethylene glycol) mono allyl mono methyl ether, tetra(ethlyne
glycol) mono allyl ether, tetra(ethylene glycol) mono methyl ether,
tetra(ethylene glycol) mono tosyl mono allyl ether, tetra(ethylene
glycol) mono tosylate, tetra(ethylene glycol) mono benzyl ether,
tetra(ethylene glycol) mono trityl ether, tetra(ethylene glycol)
mono 1-hexenyl ether, tetra(ethylene glycol) mono 1-heptenyl ether,
tetra(ethylene glycol) mono 1-octenyl ether, tetra(ethylene glycol)
mono 1-decenyl ether, tetra(ethylene glycol) mono 1-undecenyl
ether, penta(ethylene glycol) mono methyl ether, penta(ethylene
glycol) mono allyl mono methyl ether, penta(ethylene glycol) mono
tosyl mono methyl ether, penta(ethylene glycol) mono tosyl mono
allyl ether, hexa(ethylene glycol) mono allyl ether, hexa(ethylene
glycol) mono methyl ether, hexa(ethylene glycol) mono benzyl ether,
hexa(ethylene glycol) mono trityl ether, hexa(ethylene glycol) mono
1-hexenyl ether, hexa(ethylene glycol) mono 1-heptenyl ether,
hexa(ethylene glycol) mono 1-octenyl ether, hexa(ethylene glycol)
mono 1-decenyl ether, hexa(ethylene glycol) mono 1-undecenyl ether,
hexa(ethylene glycol) mono 4-benzophenonyl mono 1-undecenyl ether,
hepta(ethylene glycol) mono allyl ether, hepta(ethylene glycol)
mono methyl ether, hepta(ethylene glycol) mono tosyl mono methyl
ether, hepta(ethylene glycol) monoallyl mono methyl ether,
octa(ethylene glycol) mono allyl ether, octa(ethylene glycol) mono
tosylate, octa(ethylene glycol) mono tosyl mono allyl ether,
undeca(ethylene glycol) mono methyl ether, undeca(ethylene glycol)
mono allyl mono methyl ether, undeca(ethylene glycol) mono tosyl
mono methyl ether, undeca(ethylene glycol) mono allyl ether,
octadeca(ethylene glycol) mono allyl ether, octa(ethylene glycol),
deca(ethylene glycol), dodeca(ethylene glycol), tetradeca(ethylene
glycol), hexadeca(ethylene glycol), octadeca(ethylene glycol),
benzophenone-4-hexa(ethylene glycol) allyl ether,
benzophenone-4-hexa(ethylene glycol) hexenyl ether,
benzophenone-4-hexa(ethylene glycol) octenyl ether,
benzophenone-4-hexa(ethylene glycol) decenyl ether,
benzophenone-4-hexa(ethylene glycol) undecenyl ether,
4-fluorobenzophenone-4'-hexa(ethylene glycol) allyl ether,
4-fluorobenzophenone-4'-hexa(ethylene glycol) undecenyl ether,
4-hydroxybenzophenone-4-hexa(ethylene glycol) allyl ether,
4-hydroxybenzophenone-4-hexa(ethylene glycol) undecenyl ether,
4-hydroxybenzophenone-4'-tetra(ethylene glycol) allyl ether,
4-hydroxybenzophenone-4'-tetra(ethylene glycol) undecenyl ether,
4-morpholinobenzophenone-4'-hexa(ethylene glycol) allyl ether,
4-morpholinobenzophenone-4'-hexa(ethylene glycol) undecenyl ether,
4-morpholinobenzophenone-4'-tetra(ethylene glycol) allyl ether, and
4-morpholinobenzophenone-4'-tetra(ethylene glycol) undecenyl ether.
Preferably, the polyethylene glycol has a molecular weight of
approximately 1,000 to 20,000.
[0142] In one or more embodiments, the sugar group is ribose and
the nucleotide base group is selected from the group consisting of
adenine, guanine, cytosine, and uracyl, or the sugar group is
deoxyribose and the base group is selected from the group
consisting of adenine, guanine, cytosine, and thymine.
[0143] In one or more embodiments, the cleaving base is selected
from the group consisting of ammonium hydroxide, electrochemically
generated base, sodium hydroxide, potassium hydroxide, methylamine,
and ethylamine and combinations thereof, whereby the oligomers
comprising DNA and RNA have a 3' hydroxyl after cleaving from the
solid surface.
[0144] In one or more embodiments, the amino moiety is selected
from the group consisting of aminopropyltrimethoxysilane,
aminopropyltriethoxysilane, aminopropylmethyldiethoxysilane,
aminopropylmethyldiethoxysilane hydrozylate,
m-aminophenyltrimethoxysilane, phenylaminopropyltrimethoxysilane,
1,1,2,4-tetramethyl-1-sila-2-azacyclopentane,
aminoethylaminopropyltrimethoxysilane,
aminoethylaminopropyltrimethoxysilane,
aminoethylaminopropyltriethoxysilane,
aminoethylaminopropylmethyldimethoxysilane,
aminoethylaminopropyltrimethoxysilane hydrolyzate,
aminoethylaminoisobutylmethyldimethoxysilane,
aminoethylaminoisobutylmethyldimethoxysilane,
aminoethylaminoisobutylmethyldimethoxysilane hydrolyzate,
trimethoxysilylpropyldiethylenetriamine,
vinylbenzylethylenediaminepropyltrimethoxysilane monohydrochloride,
vinylbenzylethylenediaminepropyltrimethoxysilane,
benzylethylenediaminepropyltrimethoxysilane monohydrochloride,
benzylethylenediaminepropyltrimethoxysilane, and
allylethylenediaminepropyltrimethoxysilane monohydrochloride, and
combinations thereof.
[0145] In one or more embodiments, the amino moieties are an amino
amidite moiety selected from the group consisting of
3-(trifluoroacetylamino)propyl-(2-cyanoethyl)-N,N-diisopropyl)-phosphoram-
-idite,
2-[2-(4-monomethoxytrityl)aminoethoxy]ethyl-(2-cyanoethyl)-N,N-dii-
s-opropyl)-phosphoramidite,
6-(4-monomethoxytritylamino)hexyl-(2-cyanoethyl)-N,N-diisopropyl)-phospho-
ramidite,
12-(4-monomethoxytritylamino)dodecyl-(2-cyanoethyl)-N,N-diisopro-
-pyl)-phosphoramidite, and
6-(trifluoroacetylamino)hexyl-(2-cyanoethyl)-N,N-diisopropyl)-phosphorami-
dite, and combinations thereof.
[0146] In one or more embodiments, the succinate moieties are
selected from a salt of a chemical selected from the group
consisting of
5'dimethoxytrityl-N-benzoyl-2'-deoxycytidine-3'-O-succinate,
5'dimethyoxytrityl-N-isobutyryl-2'-deoxyguanosine-3'-O- succinate,
5'-dimethoxytrityl-thymidine-3'-O-succinate, and
5'-dimethoxytrityl-N-benzoyl-2'-deoxyadeno sine-3'-Osuccinate, and
combinations thereof. Preferably the salt is a pyridium salt of the
succinate moieties.
[0147] FIGS. 1A and 1B provide a sequence of drawings that show a
process of making the microarrays recited In one or more
embodiments; the figures are not drawn to scale. The figures show a
cross-section of only one of the plurality of known locations,
preferably located on a solid surface of the microarray.
Preferably, the density of the plurality of known locations is
greater than 100 per square centimeter and can be approximately
1,000 to approximately 1,000,000 locations per square centimeter or
even higher. The first step in FIG. 1A shows the hydroxyl groups
before reaction. The hydroxyl groups are preferably accessible for
chemical reactions thereto. The second step of FIG. 1A shows the
sulfonyl amidite moieties attached to the hydroxyl groups through a
phosphorous-oxygen bond between the phosphorous of the sulfonyl
amidite moieties and the oxygen of the hydroxyl groups. A sulfonyl
amidite moiety is shown in FIG. 2. To attach the sulfonyl amidite
moiety, a mixture of activator and the amidite is made and applied
to the microarray. Preferably, the activator is tetrazole at a
concentration of about 0.45 molar before mixing. More preferably,
the activator is 5-ethylthio-1H-tetrazole at a concentration of
about 0.25 molar before mixing. Preferably, the activator is in
acetonitrile. Preferably, the concentration of the amidite is 100
millimolar before mixing. Preferably, the mixture is a one to one
mixture by volume. Preferably, the reaction of the amidite proceeds
for about 1 to 30 minutes, and more preferably the reaction
proceeds for about 5 minutes. After reaction, the hydroxyl groups
are referred to as reacted hydroxyl groups. The phosphorous is
oxidized from phosphorous III to V according to standard
phosphoramidite synthesis. Preferably, the oxidation is performed
using Ox-T solution and the reaction proceeds for about 10 to 60
seconds, and more preferably the reaction proceeds for about 30
seconds. The hydroxyl groups that are not reacted are capped. The
protecting group on the oxygen of the sulfonyl amidite moieties is
removed using acidic reagent. Preferably, acidic reagent is
generated electrochemically while being confined by scavenging
agents or buffers, natural diffusion, and the porous reaction
layer, which partially physically limits diffusion. The protecting
group is preferably dimethoxytrityl (DMT) although, generally, any
acid-labile protecting group will work such as those disclosed in
Montgomery I, II, or III. The resulting structure forms cleavable
linkers attached to the microarray at known locations. The cleaving
point is shown in the last step of FIG. 1A. FIG. 1B shows an
oligonucleotide cleaved from the microarray and having a three
prime phosphate.
[0148] FIG. 1A shows the attachment of the oligomers after
synthesis onto the deprotected hydroxyl of the sulfonyl amidite
moieties. Preferably, the oligomers are selected from the group
consisting of DNA, RNA, and polypeptide, and combinations thereof.
FIGS. 1A and 1B show the oligomers as oligonucleotides. More
preferably, the oligomers are DNA. Preferably, the oligomers are
synthesized in situ using electrochemical synthesis.
Electrochemical synthesis of DNA or RNA uses standard
phosphoramidite synthesis and electrochemical deblocking, which is
electrochemical generation of acid for deprotection of each unit of
a DNA or RNA strand. Electrochemical deblocking involves turning on
an electrode to generate acidic conditions at the electrode
sufficient to remove the protecting group only at that electrode.
The acidic reagent may be confined as disclosed previously for
removing DMT on a sulfonyl amidite and as disclosed in the
Montgomery patents. Removal of the protecting group allows addition
of the next unit (mer). Optionally, the oligomers are synthesized
in situ by a method selected from the group consisting of (i)
printing reagents via ink jet or other printing technology and
using regular phosphoramidite chemistry, (ii) maskless
photo-generated acid controlled synthesis and using regular
phosphoramidite chemistry, (iii) mask-directed parallel synthesis
using photo-cleavage of photolabile protecting groups, and (iv)
maskless parallel synthesis using photo-cleavage of photolabile
protecting groups and digital photolithography.
[0149] Preferably, the cleaving base is selected from the group
consisting of ammonium hydroxide, electrochemically generated base,
sodium hydroxide, potassium hydroxide, methylamine, and ethylamine
and combinations thereof. More preferably, the cleaving base is
concentrated ammonium hydroxide, the reaction temperature is about
65.degree. C., and the reaction time is about four to six hours.
During exposure to the cleaving base, cleaving occurs as well as
deprotection of oligonucleotides synthesized on the cleavable
linker. To recover oligonucleotides cleaved from a microarray, the
microarray is preferably place on ice for about 10 minutes, and if
ammonium hydroxide is used, a vacuum evaporator is used to remove
the ammonium hydroxide from the oligonucleotides. The
oligonucleotides may be re-suspended into solution and cleaned to
remove impurities.
[0150] Preferably, each of the known locations is associated with
an electrode to form an electrode array, wherein the electrodes are
electronically addressable. An example of an electrode microarray
is a CombiMatrix CustomArray..TM.. 12 k, which has over 12,000
electrodes and an electrode density of approximately 17,778
electrodes per square centimeter. Preferably, the known locations
are on the same surface as the electrodes, on an opposing surface
to the electrodes, or on an overlayer over the electrodes.
[0151] Optionally, the array comprises a surface that is glass
without a silane linking agent or with a silane linking agent.
Preferably, the silane linking agent has organic hydroxyl groups
that are the hydroxyl groups of the known locations. Preferably,
the silane linking agent is a chemical selected from the group
consisting of hydroxymethyltriethoxysilane,
N-(3-triethoxysilylpropyl)gluconamide,
N-(3-triethoxysilylpropyl)-4-hydroxybutyramide,
1-trimethoxysilyl-3-propanol, 1-trimethoxysilyl-2,3-propanediol,
1-triethoxysilyl-3-propanol, 1-triethoxysilyl-2,3-propanediol,
1-trimethoxysilyl-2-ethanol, triethoxysilyl-2-ethanol,
trimethoxysilyl-11-undecanol, and triethoxysilyl-11-undecanol and
combinations thereof.
[0152] Preferably, the sulfonyl amidite moiety is
2-[2-(4,4'-dimethoxytrityloxy)ethylsulfonyl)
ethyl-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite. Optionally,
spacers having reactive hydroxyl groups are bound to the hydroxyl
groups of the known locations, wherein the sulfonyl amidite
moieties are bound to the reactive hydroxyl groups of the spacers.
Preferably, the spacer is selected from the group consisting of
DNA, RNA, polyethylene glycol, and polypeptides, and combinations
thereof. Preferably, the spacer is approximately 1 to 35 mers. More
preferably, the spacer is a 10-T (SEQ ID NO:1), although A, C, G,
or U may be used in the spacer. The T-spacer is convenient because
of a lack of a protecting group on the base. An oligonucleotide
space may be synthesized using electrochemical synthesis or one of
the other methods suitable for oligonucleotide synthesis on a
microarray. Final deprotection of an oligonucleotide linker may be
accomplished by using electrochemical generation of acid or by
exposure to acidic solution such as Deblock-T solution, which is 3%
trichloroacetic acid in dichloromethane.
[0153] FIGS. 5A and 5B provide a schematic of the construction of a
microarray for one or more of the embodiments. The microarray has a
solid surface with known locations that have hydroxyl groups. The
hydroxyl groups are shown in FIG. 5A in the first step as not
reacted; however, the second step shows the hydroxyl groups
reacted. The density of the known locations is greater than
approximately 100 locations per square centimeter. Density of the
known locations can be approximately 1,000 to 1,000,000 locations
per square centimeter. Only one known location with one hydroxyl is
shown. Amino moieties are attached to the hydroxyl groups. The
attachment is through a phosphorous-oxygen bond between the
phosphorous of amino amidite moieties and the oxygen of the
hydroxyl groups as shown in the second step of FIG. 5A. Generally,
the hydroxyl groups are referred to as reacted hydroxyl groups
after attachment of the amino moieties. The amino moieties have an
amine group and a hydroxyl reactive group. The hydroxyl reactive
group bonds to the hydroxyl groups at the known locations.
[0154] The succinate moieties are attached to the amino moieties
through amide bonds as shown in the last step in FIG. 5A. Prior to
attachment of the succinate, the microarray is capped to cap
unreacted hydroxyl groups followed by deprotection to remove the
protecting group on the amine. The protecting group is preferably
monomethoxytrityl (MMT) although, generally, any acid-labile
protecting group will work such as those disclosed in Montgomery I,
II, or III, including dimethoxytrityl (DMT). The resulting
structure forms cleavable linkers attached to the microarray. The
cleaving point is shown in FIG. 5B. Oligomers are attached to the
cleavable linkers as shown in FIG. 5B. If the oligomers are DNA or
RNA and cleaved from the microarray, the resulting oligonucleotide
has a 3' hydroxyl. FIG. 5B provides an example structure on a
microarray. The succinate moieties have a succinate group bonded to
a sugar group and a base bonded to the sugar group.
[0155] The amine group on the amino amidite moiety is protected by
a protecting group. Generally, amino amidite moieties bonded to the
surface are referred to as reacted amino amidite moieties. Such
protection groups must be removed before a succinate moiety can be
reacted to form an amide linkage between the amino amidite and the
succinate moiety. The protecting groups are removed on an electrode
microarray by the generation of acidic protons at the locations
associated with an activated electrode. Alternatively, acidic
solution may be used. Alternatively, photolabile protecting groups
on the amine may be used such as those disclose in Fodor (cited
previously).
[0156] In one or more embodiments, succinate moieties reacted to
the amino amidite moieties are referred to as reacted succinate
moieties. In one or more embodiments, the salt is a pyridinium salt
as shown in FIG. 6, Compound B. Other salts of the succinate
moieties may be used such as triethyl ammonium salt (Pierce
Chemical Company), lutidine salt, or imidizole salt and salts
having the form HN(R1R2R3)+, wherein R1, R2, and R3 are alkyl
groups. HBTU/HOBT activation of the succinate moiety is a preferred
embodiment. Other procedures to activate the succinate can be used
and include use of a carbodiimide such as N,N'-dicyclohexyl
carbodiimide (DCC) or diisopropylcarbodiimide (DIC) both with or
without N-hydrooxybenzotriazole (HOBt) or by forming a symmetrical
anhydride. Use of other peptide coupling reagents such as
2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium
tetrafluoroborate (TBTU),
2-(5-norbornene-2,3-dicarboximido)-1,1,3,3-tetramethyluronium
tetrafluoroborate (TNTU),
O--(N-succinimidyl)-1,1,3,3-tetramethyluronium tetrafluoroborate
(TSTU),
benzotriazole-1-yl-oxy-tris-(dimethylamino)-phosphoniumhexafluorophasphat-
-e (BOP), benzotriazole-1-yl-oxy-tris-pyrrolidino-phosphonium
hexafluorophosphate (PyBOP), bromo-tris-pyrrolidino-phosphonium
hexafluorophosphate (PyBroP), or 1,1'-carbonyl-diimidazole
(CDI).
[0157] In one or more embodiments, oligomers are synthesized in
situ using electrochemical synthesis. Electrochemical synthesis of
DNA uses standard phosphoramidite chemistry coupled with
electrochemical deblocking of the protecting groups on the
synthesized DNA for the addition of each nucleotide contained in
the oligonucleotide. For attachment of the phosphoramidites, the
microarray has hydroxyl groups that allow attachment of the first
phosphoramidite. Electrochemical deblocking involves turning on an
electrode to generate acidic conditions that are sufficient to
remove the protecting group only at the active electrode. Buffer in
the solution used for deblocking and natural diffusion prevents
deblocking at non-activated electrodes. Removal of the protecting
groups allows addition of the next phosphoramidite.
EXAMPLE 1
[0158] In this example, a CombiMatrix CustomArray..TM.. 12 k
microarray was used to synthesize DNA attached to the microarray
through a 10-T (SEQ ID NO:1) spacer and a base-cleavable sulfonyl
linker. The microarray had approximately 12,000 platinum electrodes
on a solid surface having a porous reaction layer. Each electrode
was electronically addressable via computer control. The DNA was
electrochemically synthesized in situ onto known locations
associated with the electrodes on the microarray. The known
locations were on and within a porous reaction layer over the
electrodes. The porous reaction layer was composed of sucrose. The
electrochemical synthesis used phosphoramidite chemistry coupled
with electrochemical deblocking of the protecting groups on the
synthesized DNA for the addition of each subsequent nucleotide. For
bonding of the phosphoramidites, the microarray had reactive
hydroxyl groups provided by the sucrose. Electrochemical deblocking
involved turning on an electrode to generate acidic conditions at
the electrode that were sufficient to remove the protecting group
only at the active electrode. Buffer in the solution used for
deblocking and natural diffusion prevented deblocking at
non-activated electrodes. Removal of the protecting group allowed
addition of the next phosphoramidite.
[0159] The cleavable linker was at the end of the 10-T (SEQ ID
NO:1) linker/spacer. The microarray was prepared by electrochemical
synthesis of the 10-T (SEQ ID NO:1) linker on all locations on the
microarray. The final trityl on the 10-T linker was removed using
electrochemically-generated acid. After synthesis of the linker and
removal of the protecting groups on the linker, a solution having
sulfonyl amidite was coupled to selected locations. The sulfonyl
amidite was 2-[2-(4,4'-dimethoxytrityloxy)
ethylsulfonyl)ethyl-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite.
The coupling solution comprised a 1:1 mixture of activator solution
and 100 mM sulfonyl amidite solution in acetonitrile. The solution
was added to a reaction chamber of the microarray immediately after
mixing the components. Care was taken to prevent water
contamination during the coupling step. The coupling reaction
proceeded for 5 minutes. The reaction chamber was evacuated, and an
oxidation solution (Ox-T) was injected and allowed to react for 30
seconds to convert phosphorus III to phosphorus V. The reaction
chamber was then cleaned thoroughly with acetonitrile.
[0160] A pool of DNA was synthesized onto the cleavable linkers.
After synthesis, the microarray was placed in a custom chamber and
exposed to ammonium hydroxide at 65.degree. C. for 4-6 hours. The
chamber was designed to be able to withstand the pressures created
by heating the solution up to the temperature. During this step,
the oligonucleotides were cleaved from the microarray and
deprotected as the same time.
[0161] The microarray was placed on ice for about 10 minutes to
allow the ammonium hydroxide to cool to prevent the solution from
spraying out of the chamber because of the relatively higher
pressure inside the chamber. The ammonium hydroxide solution, which
contained the target oligonucleotides, was placed in a
65-microliter tube using a pipette. The ammonium hydroxide was
removed using a SpeedVac.RTM. vacuum system at a temperature of
about 65-85.degree. C. until dry, which took about 30 minutes to an
hour. The oligonucleotides were in the form of a pellet at the
bottom of the tube. The oligonucleotides were resuspended in a Tris
buffer solution and then cleaned using a Microspin.RTM. G-25 column
obtained from Amersham.
EXAMPLE 2
[0162] Thirteen microarrays were prepared according to Example 1
but with some exceptions. First, the microarrays had the same
oligonucleotide sequence synthesized on each electrode rather than
a pool of oligonucleotides. Additionally, six of the microarrays
had the sulfonyl cleavable linker, and seven of the microarrays did
not have the sulfonyl cleavable linker.
[0163] After synthesis of the oligonucleotides on the group of six
microarrays having the cleavable linker, each of those microarrays
was exposed to a concentrated ammonium hydroxide solution for four
hours at 65.degree. C. to remove the oligonucleotides. The
oligonucleotides from each microarray were recovered and amplified
using PCR. The oligonucleotide recovery was quantified using
quantitative PCR, which used SYBR I as the fluorescent
intercalating dye. The fluorescence intensity (FI) was monitored
during PCR and plotted against the number of PCR cycles. The FI for
each reaction was normalized to the highest FI value. For each
reaction, the FI value at 50% of the maximum FI value was
calculated for each microarray, and the corresponding number of PCR
cycles was obtained by interpolation. The average number of PCR
cycles to reach 50% FI value for the group six microarrays was
about 11 cycles.
[0164] For the group of seven microarrays without the cleavable
linker, each of those microarrays was exposed to different
treatments in an attempt to remove the oligonucleotides for
comparison to the cleavable linker microarrays. The treatments
included 1% hydrogen peroxide, 1% hydrogen peroxide plus 0.2 molar
sucrose, 0.1 molar hydrochloric acid, 0.4 molar hydrochloric acid,
concentrated ammonium hydroxide, and methylamine. The
oligonucleotides from each microarray were recovered and amplified
using PCR. The fluorescence intensity (FI) was monitored during PCR
and plotted against the number of PCR cycles. The FI was normalized
to the highest FI value. The FI value at 50% of the maximum FI
value was calculated for each microarray, and the corresponding
number of PCR cycles was obtained by interpolation. The range of
the number of PCR cycles to reach 50% FI value for the group seven
microarrays was from about 27 cycles to about 35 cycles.
Quantitative comparison of the recovery of oligonucleotides from
microarrays with and without the cleavable linkers using a standard
curve made from commercially synthesized oligonucleotides (of
identical sequence) revealed that the microarrays having the
cleavable linker yielded an increased recovery of approximately six
orders of magnitude over any other removal method we used.
EXAMPLE 3
[0165] In this example, three different electrode microarrays were
synthesized with each having different oligonucleotides ranging
from 66 to 80 base pairs. Each microarray was prepared as in
Example 1 except for the different oligonucleotides. After
synthesis, the microarrays were exposed to concentrated ammonium
hydroxide solution for four hours at 65.degree. C. to remove the
oligonucleotides. The oligonucleotides from each microarray were
recovered. The recovered oligonucleotides were amplified using PCR.
The amplified oligonucleotides were subjected to gel
electrophoresis. The gel was a 20% polyacrylamide gel. The
electrophoresis conditions were 200 volts for 90 minutes. The
expected PCR product was 66 to 80 base pairs. FIG. 3 shows an image
of the electrophoresis gel. Oligonucleotides 321/322 were from the
first microarray. Oligonucleotides 323/324 were from the second
microarray. Oligonucleotides 325/326 were from the third
microarray. The lanes having a positive sign are those where the
oligonucleotides were expected to be located. The lanes having a
negative sign are those where the oligonucleotides were not
expected to be located. Thus, the olignucleotideos were cleaved
from the microarray as expected.
EXAMPLE 4
[0166] In this example, a CombiMatrix CustomArray..TM.. 12K
microarray was used to synthesize oligonucleotides attached to the
microarray through a base-cleavable linker. The microarray had
approximately 12,000 platinum electrodes on a solid surface having
a porous reaction layer, wherein each electrode was electronically
addressable via computer control. The oligonucleotides were DNA and
were synthesized in situ using electrochemical synthesis at
locations associated with the electrodes on the microarray.
Electrochemical synthesis used standard phosphoramidite chemistry
coupled with electrochemical deblocking of the protecting groups on
the synthesized DNA for the addition of each nucleotide contained
in the oligonucleotide. For attachment of the phosphoramidites, the
microarray had organic reactive hydroxyl groups that allowed
attachment of the first phosphoramidite. Electrochemical deblocking
involved turning on an electrode to generate acidic conditions at
the electrode that were sufficient to remove the protecting group
only at the active electrode. Buffer in the solution used for
deblocking and natural diffusion prevented deblocking at
non-activated electrodes. Removal of the protecting group allowed
addition of the next phosphoramidite.
[0167] Some electrodes were used as controls while some electrodes
were used to synthesize the oligonucleotides. At the non-control
locations, a 15-unit deoxythymidylate (SEQ ID NO:2) spacer was
synthesized on the reactive hydroxyl groups. At some but not all
non-control locations, an amine amidite obtained from Glen Research
was attached to the 15-unit spacer. The specific amine amidite was
2-[2-(4-Monomethoxytrityl)aminoethoxy]ethyl-(2-cyanoethyl)-N,N-diisopropy-
-1)-phosphoramidite, catalog number 10-1905-xx (5'-Amino-Modifier
5.) The amine amidite had monomethoxytrityl (MMT) protecting groups
on the amine. The MMT protecting groups were removed using
electrochemical generation of acid by activating selected
electrodes.
[0168] After removal of the MMT protecting groups, the amine was
reacted to a T-succinate to form an amide linkage between the amine
groups and the succinate. The specific T-succinate used was
5'-dimethyloxytrityl-thymidine-3'-O-succinate (pyridium salt)
obtained from Transgenomic. (Alternatively, A, C, G, succinates
could have been used.) The solution to attach the T-succinate to
the amine was made by adding 330 milligrams of T-succinate, 150
milligrams of O-benzotriazol-1-yl-N,N,N',N'-tetramethyluronium
hexafluorophosphate (HBTU), and 60 milligrams of
N-hydroxybenztriazole (HOBT) to one milliliter dimethyl
formamide(DMF). To this solution, 225 microliters of
diisopropylethylamine (DIEPA) was added and the resulting mixture
was vortexed to dissolve the material (total mixing time 5-10 min)
prior to use.
[0169] To attach the T-succinate, the microarray was placed in a
manifold, rinsed with anhydrous DMF, and exposed to one-half of the
T-succinate coupling mixture for one hour at room temperature. The
microarray was washed in the manifold using different solvents
successively as follows: 5 milliliters of DMF, 5 milliliters of
methylene chloride, and 5 milliliter of DMF. The microarray was
exposed to the second half of the coupling mixture for one hour at
room temperature. After the completion of the second exposure to
the T-succinate reaction mixture, the microarray was washed again
using the same washing as above followed by methylene chloride (5
ml) and a stream of ethanol from a squirt bottle. After washing,
the microarray was ready for electrochemical synthesis. Synthesis
was done on a CombiMatrix bench top synthesizer, wherein
oligonucleotides of three different lengths (37, 42, and 47 bp)
were synthesized.
[0170] After the completion of electrochemical synthesis, the
synthetic oligonucleotides on the microarray were deprotected and
cleaved by exposure to concentrated ammonium hydroxide in a
pressurized cell at 65.degree. C. The concentration of ammonium
hydroxide was 28-30%. During this deprotection step, the cleavable
succinate linkage was cleaved thus releasing the synthetic
oligonucleotides. The oligonucleotides were isolated by evaporating
the ammonia solution and were subjected to amplification using
polymerase chain reaction (PCR). The oligonucleotides could be
amplified with one set of PCR primers due to the presence of primer
amplification sites at the ends of the oligonucleotides. The
oligonucleotides were dissolved in 75 microliters of Tris buffer at
95.degree. C. for 5 minutes.
[0171] To test if the nucleotides were released, a series of PCR
reactions were performed to determine if the oligonucleotides were
present in solution. PCR reaction products were run on a
non-denaturing polyacrylamide gel (20%) for 100 minutes at 200
volts. When the separation of the PCR products was complete, the
gel was stained with SYBR green II dye to visualize the PCR product
as shown in FIG. 7. Separation of the PCR product by gel
electrophoresis revealed that all three products (37, 42, and 47
bp) were present in approximately equal amounts and ran at the
calculated molecular weight. The novel linker allowed for the
release of oligonucleotides from the microarray surface.
[0172] At some locations on the array, the oligonucleotides
synthesized were attached without the cleavable linker. Thus,
oligonucleotides attached without the cleavable linker would be
expected to remain on the microarray after the ammonium hydroxide
reaction. To determine whether there were oligonucleotides
remaining on the microarray after the ammonium hydroxide reaction,
the microarray was exposed to complementary oligonucleotides having
a fluorescent label. FIG. 4 shows an image of a portion of the
microarray after exposure to the fluorescently labeled
oligonucleotide. There are four different areas, A, B, C, and D,
shown in the figure. In areas A, B, and C, oligos were synthesized
with and without the cleavable linker. As can be seen in the
figure, the microarray locations having the cleavable linker
between the oligonucleotide and the microarray are completely dark
or are mostly dark indicating little or no DNA remains after
cleaving. In contrast, those locations that did not have the
cleavable linker between the oligonucleotide and the microarray are
brighter, which indicates that the oligonucleotide remained on the
microarray. In area D, some electrodes had cleavable linker while
some did not; however, no oligo was synthesized so that the entire
area appears dark.
Sequence CWU 1
1
2110DNAArtificial SequenceSynthetic polynucleotide 1tttttttttt
10215DNAArtificial SequenceSynthetic polynucleotide 2tttttttttt
ttttt 15
* * * * *