U.S. patent number 7,045,609 [Application Number 10/265,645] was granted by the patent office on 2006-05-16 for hybrid oligonucleotide phosphorothioates.
This patent grant is currently assigned to University of Massachusetts Worcester. Invention is credited to Sudhir Agrawal, Valeri Metelev.
United States Patent |
7,045,609 |
Metelev , et al. |
May 16, 2006 |
Hybrid oligonucleotide phosphorothioates
Abstract
The invention provides hybrid oligonucleotides having
phosphorothioate or phosphorodithioate internucleotide linkages,
and both deoxyribonucleosides and ribonucleosides or 2'-substituted
ribonucleosides. Such hybrid oligonucleotides have superior
properties of duplex formation with RNA, nuclease resistance, and
RNase H activation.
Inventors: |
Metelev; Valeri (Moscow,
RU), Agrawal; Sudhir (Shrewsbury, MA) |
Assignee: |
University of Massachusetts
Worcester (Worcester, MA)
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Family
ID: |
27045055 |
Appl.
No.: |
10/265,645 |
Filed: |
October 8, 2002 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20030148980 A1 |
Aug 7, 2003 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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09886496 |
Jun 22, 2001 |
6683167 |
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09524368 |
Mar 14, 2000 |
6346614 |
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08476082 |
Jun 7, 1995 |
6143881 |
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07918239 |
Jul 23, 1992 |
5652355 |
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Current U.S.
Class: |
536/22.1;
435/6.1; 435/6.18; 536/23.1 |
Current CPC
Class: |
C07H
21/00 (20130101); C07H 21/04 (20130101); C12N
15/113 (20130101); C12N 15/1132 (20130101); F15B
13/0807 (20130101); C12N 2310/313 (20130101); C12N
2310/315 (20130101); C12N 2310/321 (20130101); C12N
2310/341 (20130101); C12N 2310/346 (20130101); C12N
2310/3521 (20130101) |
Current International
Class: |
C07H
21/00 (20060101); C07H 21/02 (20060101); C12Q
1/68 (20060101) |
Field of
Search: |
;435/6
;536/22.1,23.1 |
References Cited
[Referenced By]
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Nov 1989 |
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Nov 1989 |
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EP |
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Mar 1998 |
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EP |
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03240795 |
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Oct 1991 |
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JP |
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WO 89/05358 |
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Jun 1989 |
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WO |
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WO 90/15814 |
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WO |
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WO 91/06556 |
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WO |
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WO |
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WO |
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WO |
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WO 92/07065 |
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Apr 1992 |
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WO |
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WO 92/20697 |
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Nov 1992 |
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WO |
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WO 93/12121 |
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Jul 1993 |
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WO |
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Primary Examiner: Riley; Jezia
Attorney, Agent or Firm: Wilmer Cutler Pickering Hale and
Dorr LLP
Parent Case Text
RELATED APPLICATIONS
This application is a continuation of patent application Ser. No.
09/886,496, filed Jun. 22, 2001 now U.S. Pat. No. 6,683,167, which
is a continuation of patent application Ser. No. 09/524,368, filed
Mar. 14, 2000 (now U.S. Pat. No. 6,346,614), which is a
continuation of patent application Ser. No. 08/476,082, filed Jun.
7, 1995 (now U.S. Pat. No. 6,143,881), which is a continuation of
patent application Ser. No. 07/918,239 filed Jul. 23, 1992 (now
U.S. Pat. No. 5,652,355), each of which is incorporated in its
entirety by
Claims
We claim:
1. An oligonucleotide comprising a deoxyribonucleotide, a
2'-substituted ribonucleotide, and a phosphorothioate or a
phosphorodithioate internucleotide linkage.
2. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises at least four contiguous deoxyribonucleotides.
3. The oligonucleotide of claim 1, wherein the 2'-substituted
ribonucleotide is a 2'--O--C.sub.1-6 alkyl ribonucleotide, a
2'--O-aryl ribonucleotide, a 2'--O-allyl ribonucleotide, a 2'-halo
ribonucleotide or a 2'-amino ribonucleotide.
4. The oligonucleotide of claim 3, wherein the 2'--O-C.sub.1-6
alkyl ribonucleotide, the 2'--O-aryl ribonucleotide, or the
2'--O-allyl ribonucleotide is substituted with one or more
substituents selected from the group consisting of halo, hydroxy,
trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl,
carboxyalkyl and amino.
5. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises at least two contiguous 2'-substituted
ribonucleotides.
6. The oligonucleotide of claim 1, wherein the oligonucleotide
further comprises a ribonucleotide.
7. The oligonucleotide of claim 6, wherein the oligonucleotide
comprises at least two contiguous ribonucleotides.
8. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises a phosphorothioate and a phosphorodithioate
intemucleotide linkage.
9. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises from 2 to 50 nucleotides.
10. The oligonucleotide of claim 1, wherein the oligonucleotide has
a sequence selected from the group consisting of SEQ ID NOS. 2
6.
11. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises a sequence that is complementary to a nucleic acid
sequence from a virus, a pathogenic organism or a cellular
gene.
12. The oligonucleotide of claim 11, wherein the virus is selected
from the group consisting of AIDS, oral herpes, genital herpes,
papilloma warts, influenza, foot and mouth disease, yellow fever,
chicken pox, shingles, adult T-cell leukemia and hepatitis.
13. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises a sequence that inhibits the expression of a protein in a
male or female that is necessary for fertility.
14. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises a sequence that inhibits the expression of a protein
formed in Alzheimer's disease.
15. The oligonucleotide of claim 1, wherein the oligonucleotide
comprises a sequence that inhibits the expression of a protein in a
parasite that causes a disease selected from the group consisting
of amebiasis, Chegas' disease, toxoplasmosis, pneumocytosis,
giardiasis, cryptoporidiosis, trichomoniasis, malaria, ascariasis,
filariasis, trichinosia, and schistosomiasis.
16. The oligonucleotide of claim 1 or 6, wherein the
oligonucleotide has 6 or more nucleotides that are either a
ribonucleotide or a 2'-substituted ribonucleotide.
Description
BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to synthetic oligonucleotides that are useful
for studies of gene expression and in the antisense oligonucleotide
therapeutic approach. More particularly, the invention relates to
synthetic oligonucleotides that have improved qualities for such
applications resulting from modifications in the sugar phosphate
backbone of the oligonucleotides.
2. Summary of the Related Art
The potential for the development of an antisense oligonucleotide
therapeutic approach was first suggested in three articles
published in 1977 and 1978. Paterson et al., Proc. Natl. Acad. Sci.
USA 74: 4370 4374 (1977) discloses that cell-free translation of
mRNA can be inhibited by the binding of an oligonucleotide
complementary to the mRNA. Zamecnik and Stephenson, Proc. Natl.
Acad. Sci. USA 75: 280 284 and 285 288 (1978) discloses that a
13-mer synthetic oligonucleotide that is complementary to a part of
the Rous sarcoma virus (RSV) genome inhibits RSV replication in
infected chicken fibroblasts and inhibits RSV-mediated
transformation of primary chick fibroblasts into malignant sarcoma
cells.
These early indications that synthetic oligonucleotides can be used
to inhibit virus propagation and neoplasia have been followed by
the use of synthetic oligonucleotides to inhibit a wide variety of
viruses. Goodchild et al., U.S. Pat. No. 4,806,463 (the teachings
of which are hereby incorporated by reference) discloses inhibition
of human immunodeficiency virus (HIV) by synthetic
oligodeoxynucleotides complementary to various regions of the HIV
genome. Leiter et al., Proc. Natl. Acad. Sci. USA 87: 3430 3434
(1990) discloses inhibition of influenza virus by synthetic
oligonucleotides. Agris et al. Biochemistry 25: 6268 6275 (1986)
discloses the use of synthetic oligonucleotides to inhibit
vesicular stomatitis virus (VSV). Gao et al., Antimicrob. Agents
Chem. 34 808 812 (1990) discloses inhibition of herpes simplex
virus by synthetic oligonucleotides. Birg et al., Nucleic Acids
Res. 18: 2901 2908 (1990) discloses inhibition of simian virus
(SV40) by synthetic oligonucleotides. Storey et al., Nucleic Acids
Res. 19: 4109 4114 (1991) discloses inhibition of human papilloma
virus (HPV) by synthetic oligonucleotides. The use of synthetic
oligonucleotides and their analogs as antiviral agents has recently
been extensively reviewed by Agrawal, Trends in Biotech 10: 152 158
(1992).
In addition, synthetic oligonucleotides have been used to inhibit a
variety of non-viral pathogens, as well as to selectively inhibit
the expression of certain cellular genes. Thus, the utility of
synthetic oligonucleotides as agents to inhibit virus propagation,
propagation of non-viral pathogens and selective expression of
cellular genes has been well established. However, there is a need
for improved oligonucicotides that have greater efficacy in
inhibiting such viruses, pathogens and selective gene expression.
Various investigators have attempted to meet this need by preparing
and testing oligonucleotides having modifications in their
internucleoside linkages. Several investigations have shown that
such modified oligonucleotides are more effective than their
unmodified counterparts. Sarin et al., Proc. Natl. Acad. Sci. USA
85: 7448 7451 (1988) teaches that oligodeoxynucleoside
methylphosphonates are more active as inhibitors of HIV-1 than
conventional oligodeoxynucieotides. Agrawal et al., Proc. Natl.
Acad. Sci. USA 85: 7079 7083 (1988) teaches that oligonucleotide
phosphorothioates and certain oligonucleotide phosphoramidates are
more effective at inhibiting HIV-1 than conventional
oligodeoxynucleotides. Agrawal et al., Proc. Natl. Acad. Sci. USA
86: 7790 7794 (1989) discloses the advantage of oligonucleotide
phosphorothioates in inhibiting HIV-1 in early and chronically
infected cells.
In addition, chimeric oligonucleotides having more than one type of
internucleoside linkage within the oligonucleotide have been
developed. Chimeric oligonucleotides contain deoxyribonucleosides
only, but have regions containing different internucleoside
linkages Pederson et al., U.S. Pat. No. 5,149,797, the teachings of
which are hereby incorporated by reference, discloses chimeric
oligonucleotides having an oligonucleotide phosphodiester or
oligonucleotide phosphorothioate core sequence flanked by
oligonucleotide, methylphosphonates or phosphoramidates. Furdon et
al., Nucleic Acids Res. 17: 9193 9204 (1989) discloses chimeric
oligonucleotides having regions of oligonucleotide phosphodiesters
in addition to either oligonucleotide phosphorothioate or
methylphosphonate regions. Quartin et al., Nucleic Acids Res.
17-7523 7562 (1989) discloses chimeric oligonucleotides having
regions of oligonucleotide phosphodiesters and oligonucleotide
methylphosphonates. Each of the above compounds contains
deoxyribonucleotide phosphorothioates, which have reduced duplex
stability. Atabekov et al., FEBS Letters 232: 96 98 (1988)
discloses chimeric oligonucleotides in which all internucleoside
linkages are phosphodiester linkages, but in which regions of
ribonucleotides and deoxyribonucleotides are mixed. Inoue et al.,
FEBS Letters, 215: 237 250 (1987) discloses chimeric
oligonucleotides having only phosphodiester linkages, and regions
of deoxyribonucleotides and 2'-OMe-ribonucleotides. None of these
compounds having solely phosphodiester linkages exhibit either
endonuclease or exonuclease resistance.
Many of these modified oligonucleotides have contributed to
improving the potential efficacy of the antisense oligonucleotide
therapeutic approach. However, certain deficiencies remain in the
known oligonucleotides, and these deficiencies can limit the
effectiveness of such oligonucleotides as therapeutic agents.
Wickstrom, J. Biochem. Biophys. Methods 13: 97 102 (1986) teaches
that oligonucleotide phosphodiesters are susceptible to
nuclease-mediated degradation. Such nuclease susceptibility can
limit the bioavailability of oligonucleotides in vivo. Agrawal et
al., Proc. Natl. Acad. Sci. USA 87: 1401 1405 (1990) teaches that
oligonucleotide phosphoramidates or methylphosphonates when
hybridized to RNA do not activate RNase H, the activation of which
can be important to the function of antisense oligonucleotides.
Agrawal et al., Nucleosides & Nucleotides 8: 5 6 (1989) teaches
that oligodeoxyribonucleotide phosphorothioates have reduced duplex
stability when hybridized to RNA.
There is, therefore, a need for improved oligonucleotides that
overcome the deficiencies of oligonucleotides that are known in the
art. Ideally, such oligonucleotides should be resistant to
nucleolytic degradation, should form stable duplexes with RNA, and
should activate RNase H when hybridized with RNA.
BRIEF SUMMARY OF THE INVENTION
The invention provides hybrid oligonucleotides (containing segments
of deoxy- and ribonucleotides) that resist nucleolytic degradation,
form stable duplexes with RNA or DNA, and activate RNase H when
hybridized with RNA. Oligonucleotides according to the invention
provide these features by having phosphorothioate and/or
phosphorodithioate internucleoside linkages and segments of
oligodeoxyribonucleotides as well as segments of either
oligoribonucleotides or 2'-substituted-oligoribonucleotides. For
purposes of the invention, the term "2'-substituted" means
substitution of the 2'--OH of the ribose molecule with, --O-lower
alkyl containing 1 6 carbon atoms, aryl or substituted aryl or
allyl having 2 6 carbon atoms e.g., 2'--OMe, 2'--O-allyl,
2'--O-aryl, 2'--O-alkyl, 2'-halo, or 2'-amino, but not with 2'--H,
wherein allyl, aryl, or alkyl groups may be unsubstituted or
substituted, e.g., with halo, hydroxy, trifluoromethyl, cyano,
nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl or amino
groups.
An object of the invention is to provide oligonucleotides that can
be used to analyze and explain the importance to the effectiveness
of antisense oligonucleotides of the parameters of nuclease
resistance, duplex stability and RNase H activation. Another object
of the invention is to provide oligonucleotides that are effective
for regulating cellular, pathogen, or viral gene expression at the
mRNA level. Yet another object of the invention is to provide
therapeutic oligonucleotides that have great efficacy in the
antisense oligonucleotide therapeutic approach. Oligonucleotides
according to the invention are useful in satisfying each of these
objects of the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows ion exchange HPLC analysis of nuclease treated
oligonucleotides. In
FIG. 1A shows ion exchange HPLC analyses of nuclease treated
oligonucleotides. Profiles A, B and C are of oligonucleotides F, C
and A (SEQ ID NOS:6,3 and 1, respectively), respectively after 420
minutes SVPD digestion.
FIG. 1B shows ion exchange HPLC analyses of nuclease treated
oligonucleotides. Profile A is of an undigested oligonucleotide
phosphodiester, and profile B is of the same after 1 minute SVPD
digestion (SVPD concentration one tenth that in FIG. 1A).
FIG. 2 shows results of RNase H activation studies for
oligonucleotides (SEQ ID NOS:1 3 and 5 8), as described in Example
4.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
In a first aspect, the invention provides oligonucleotides that are
useful for studying the parameters that are important for effective
antisense oligonucleotide action. For purposes of the invention,
the term oligonucleotide includes polymers of two or more
ribonucleotides, deoxyribonucleotides, or both, with ribonucleotide
and/or deoxyribonucleotide monomers being connected together via 5'
to 3' linkages which may include any of the linkages that are known
in the antisense oligonucleotide art. In addition, the term
oligonucleotides includes such molecules having modified nucleic
acid/bases and/or sugars, as well as such molecules having added
substituents, such as diamines, cholesteryl or other lipophilic
groups. Certain preferred combinations of monomers and
inter-monomer linkages are discussed in greater detail below.
It is generally believed that the activity of an antisense
oligonucleotide depends on the binding of the oligonucleotide to
the target nucleic acid, thus disrupting the function of the
target, either by hybridization arrest or by destruction of target
RNA by RNase H. These mechanisms of action suggest that two
parameters should be important to antisense oligonucleotide
activity: duplex stability and RNase H activation. Duplex stability
is important, since the oligonucleotide presumably must form a
duplex (or triplex in the Hoogsteen pairing mechanism) with the
target nucleic acid to act either by hybridization arrest or by
RNase H-mediated target destruction. RNase H activation (the
ability to activate RNase H when hybridized with target RNA) is
implicated when the target nucleic acid is RNA, since such
activation can lead to the effective destruction of the target RNA
molecule. In addition, for an antisense oligonucleotide to act in
vivo, it must survive long enough to interact with the target
nucleic acid. Given the fact that the in vivo environment contains
endonuclease and cxonuclease activities, a third parameter arises
from this requirement; namely that the antisense oligonucleotide
should resist nuclcolytic degradation.
To analyze and explain the importance of each of these parameters
to the effectiveness of antisense oligonucleotides, it is necessary
to have oligonucleotides that vary in each of these parameters. The
properties of several known oligonucleotides arc shown in Table I,
below.
TABLE-US-00001 TABLE I PROPERTIES OF OLIGONUCLEOTIDES Duplex
Nuclease RNase H Oligonucleotide Stability.sup.1 Resistance.sup.2
Activation.sup.3 Oligodeoxyribonucleotide - - Yes (phosphate)
Oligodeoxyribonucleotide Lower + Yes (phosphorothioate)
Oligodeoxyribonucleotide Lower ++ Yes (phosphorodithioate)
Oligodeoxyribonucleotide Lower + N.K. (selenoate)
Oligodeoxyribonucleotide Lower +++ No (phosphoramidate)
Oligoribonucleotide Higher - No (phosphate)
Oligodeoxyribonucleotide Higher + No (phosphorothioate)
2'-OMe-Oligonucleotide Higher + No (phosphate)
2'-OMe-Oligonucleotide Higher ++ No (phosphorothioate)
Oligodeoxyribonucleotide Lower +++ No (methylphosphonate)
.sup.1Duplex stability of oligonucleotide to complementary
oligoribonucleotide under physiological conditions, compared to
DNA-RNA stability. .sup.2Compared to DNA (phosphodiesterase
digestion). .sup.3Activation of RNase H by the duplex formed
between oligonucleotide and RNA. N.K.--Not known
Hybrid oligonucleotides according to the invention form more stable
duplexes with complementary RNA than oligodeoxyribonucleotide
phosphorothioates. In addition, they are more resistant to
endonucleolytic and exonucleolytic degradation than
oligodeoxyribonucleotide phosphorothioates and they normally
activate RNase H. Consequently, oligonucleotides according to the
invention complement the oligonucleotides shown in Table I in
studies of the parameters involved in the effectiveness of
antisense oligonucleotides.
With respect to this first aspect of the invention,
oligonucleotides according to the invention can have any
oligonucleotide sequence, since complementary oligonucleotides used
in such study can be prepared having any oligonucleotide sequence.
Oligonucleotides according to this aspect of the invention are
characterized only by the following features. First, at least some
of the internucleoside linkages present in oligonucleotides
according to the invention are phosphorothioate and/or
phosphorodithioate linkages. In various embodiments, the number of
phosphorothioate and/or phosphorodithioate internucleotide linkages
can range from 1 to as many internucleotide linkages as are present
in the oligonucleotide. Thus, for purposes of the invention, the
term oligonucleotide phosphorothioate and/or phosphorodithioate is
intended to encompass every such embodiment. In a preferred
embodiment, oligonucleotides according to the invention will range
from about 2 to about 50 nucleotides in length, and most preferably
from about 6 to about 50 nucleotides in length. Thus, in this
preferred embodiment, oligonucleotides according to the invention
will have from 1 to about 49 phosphorothioate and/or
phosphorodithioate internucleotide linkages.
A second feature of oligonucleotides according to this aspect of
the invention is the presence of deoxyribonucleotides.
Oligonucleotides according to the invention contain at least one
deoxyribonucleotide. Preferably oligonucleotides according to the
invention contain four or more deoxyribonucleotides in a contiguous
block, so as to provide an activating segment for RNase H. In
certain preferred embodiments, more than one such activating
segment will be present. Such segments may be present at any
location within the oligonucleotide. There may be a majority of
deoxyribonucleotides in oligonucleotides according to the
invention. In fact, such oligonucleotides may have as many as all
but one nucleotide being deoxyribonucleotides. Thus, in a preferred
embodiment, having from about 2 to about 50 nucleotides or most
preferably from about 6 to about 50 nucleotides, the number of
deoxyribonucleotides present will range from 1 to about 49
deoxyribonucleotides.
A third feature of oligonucleotides according to this aspect of the
invention is the presence of ribonucleotides, 2'-substituted
ribonucleotides or combinations thereof. For purposes of the
invention, the term "2'-substituted" means substitution of the
2'--OH of the ribose molecule with, e.g. 2'--OMe, 2'--O-allyl,
2'--O-aryl, 2'--O-alkyl, 2'-halo, or 2'-amino, but not with 2'-II,
wherein allyl, aryl, or alkyl groups may be unsubstituted or
substituted, e.g. with halo, hydroxy, trifluoromethyl, cyano,
nitro, acyl, acyloxy, alkoxy, carboxyl, carbalkoxyl or amino
groups. Oligonucleotides according to the invention contain at
least one ribonueleotide and/or 2'-substituted ribonucleotide. In a
preferred embodiment, such oligonucleotides have 6 or more
ribonucleotides and/or 2'-substituted ribonucleotides to enhance
duplex stability, Such ribonucleotides and/or 2'-substituted
ribonucleotides can be present singly, in pairs, or in larger
contiguous segments, and may be present at any position within the
oligonucleotide or at multiple positions within the
oligonucleotide. Such ribonucleotides and/or 2'-substituted
ribonucleotides may comprise as many as all but one nucleoside
within the oligonucleotides. Thus, in a preferred embodiment,
having from about 2 to about 50 nucleotides or most preferably from
about 6 to about 50 nucleotides, the number of ribonucleosides or
2'-substituted ribonucleotides will range from about 1 to about 49
deoxyribonucleotides.
The ability to vary the numbers and positions of phosphorothioate
and/or phosphorodithioate internucleotide linkages,
deoxyribonucleotides, and ribonucleotides or 2'-substituted
ribonucleotides allows the investigator to examine in detail how
each of these variables affects the parameters of nuclease
resistance, duplex stability and RNase H activation. The ability to
vary the size of the oligonucleotide allows examination of yet
another parameter. In addition, smaller oligos (e.g., dimers) can
be used as building blocks for larger oligos. Thus, the embodiments
described above are useful in such studies.
In a second aspect, the invention provides hybrid oligonucleotides
that are effective in inhibiting viruses, pathogenic organisms, or
the expression of cellular genes. The ability to inhibit such
agents is clearly important to the treatment of a variety of
disease states. Oligonucleotides according to this aspect of the
invention share the characteristics of the above-described
oligonucleotides, except that the oligonucleotide sequence of
oligonucleotides according to this aspect of the invention is
complementary to a nucleic acid sequence that is from a virus, a
pathogenic organism or a cellular gene. Preferably such
oligonucleotides are from about 6 to about 50 nucleotides in
length. For purposes of the invention, the term "oligonucleotide
sequence that is complementary to a nucleic acid sequence" is
intended to mean an oligonucleotide sequence (2 to about 50
nucleotides) that binds to the nucleic acid sequence under
physiological conditions, e.g. by Watson-Crick base pairing
(interaction between oligonucleotide and single-stranded nucleic
acid) or by Hoogsteen base pairing (interaction between
oligonucleotide and double-stranded nucleic acid) or by any other
means including in the case of a oligonucleotide binding to RNA,
pseudoknot formation. Such binding (by Watson Crick base pairing)
under physiological conditions is measured as a practical matter by
observing interference with the function of the nucleic acid
sequence.
The nucleic acid sequence to which an oligonucleotide according to
the invention is complementary will vary, depending upon the agent
to be inhibited. In many cases the nucleic acid sequence will be a
virus nucleic acid sequence. The use of antisense oligonucleotides
to inhibit various viruses is well known, and has recently been
reviewed in Agrawal, Trends in Biotech 10:152 158 (1992). Viral
nucleic acid sequences that are complementary to effective
antisense oligonucleotides have been described for many viruses,
including human immunodeficiency virus type 1 (U.S. Pat. No.
4,806,463, the teachings of which are hereby incorporated by
reference), herpes simplex virus (U.S. Pat. No. 4,689,320, the
teachings of which are hereby incorporated by reference), influenza
virus (U.S. Pat. No. 5,194,428, the teachings of which are hereby
incorporated by reference), and human papilloma virus (Storey et
al., Nucleic Acids Res. 19:4109 4114 (1991)). Sequences
complementary to any of these nucleic acid sequences can be used
for oligonucleotides according to the invention, as can be
oligonucleotide sequences complementary to nucleic acid sequences
from any other virus. Additional viruses that have known nucleic
acid sequences against which antisense oligonucleotides can be
prepared include foot and mouth disease virus (See Robertson et
al., J. Virology 54: 651 (1985); Harris et al., J. Virology 36: 659
(1980)), yellow fever virus (See Rice et al., Science 229: 726
(1985)), varicella-zoster virus (See Davison and Scott, J. Gen.
Virology 67: 2279 (1986), and cucumber mosaic virus (See Richards
et al., Virology 89: 395 (1978)).
Alternatively, oligonucleotides according to the invention can have
an oligonucleotide sequence complementary to a nucleic acid
sequence of a pathogenic organism. The nucleic acid sequences of
many pathogenic organisms have been described, including the
malaria organism, Plasmodium falciparum, and many pathogenic
bacteria. Oligonucleotide sequences complementary to nucleic acid
sequences from any such pathogenic organism can be used in
oligonucleotides according to the invention. Examples of pathogenic
eukaryotes having known nucleic acid sequences against which
antisense oligonucleotides can be prepared include Trvpanosom
abrucei gambiense and Leishmania (See Campbell et al., Nature 311:
350 (1984)), Fasciola hepatica (See Zurita et al., Proc. Natl.
Acad. Sci. USA 84: 2340 (1987). Antifungal oligonucleotides can be
prepared using a target hybridizing region having an
oligonucleotide sequence that is complementary to a nucleic acid
sequence from, e.g., the chitin synthetase gene, and antibacterial
oligonucleotides can be prepared using, e.g., the alanine racemase
gene.
In yet another embodiment, the oligonucleotides according to the
invention can have an oligonucleotide sequence complementary to a
cellular gene or gene transcript, the abnormal expression or
product of which results in a disease state. The nucleic acid
sequences of several such cellular genes have been described,
including prion protein (Stahl and Prusiner, FASEB J. 5: 2799 2807
(1991)), the amyloid-like protein associated with Alzheimer's
disease (U.S. Pat. No. 5,015,570, the teachings of which are hereby
incorporated by reference), and various well-known oncogenes and
proto-oncogenes, such as c-myb c-myc, c-abl and n-ras. In addition,
oligonucleotides that inhibit the synthesis of structural proteins
or enzymes involved largely or exclusively in spermatogenesis,
sperm motility, the binding of the sperm to the egg or any other
step affecting sperm viability may be used as contraceptives.
Similarly, contraceptives for women may be oligonucleotides that
inhibit proteins or enzymes involved in ovulation, fertilization,
implantation or in the biosynthesis of hormones involved in those
processes.
Hypertension may be controlled by oligodeoxynucleotides that
suppress the synthesis of angiotensin converting enzyme or related
enzymes in the renin/angiotensin system; platelet aggregation may
be controlled by suppression of the synthesis of enzymes necessary
for the synthesis of thromboxane A2 for use in myocardial and
cerebral circulatory disorders, infarcts, arteriosclerosis,
embolism and thrombosis; deposition of cholesterol in arterial wall
may be inhibited by suppression of the synthesis of fatty acid
co-enzyme A; cholesterol acyl transferase in arteriosclerosis;
inhibition of the synthesis of cholinephosphotransferase may be
useful in hypolipidemia.
There are numerous neural disorders in which hybridization arrest
may be used to reduce or eliminate adverse effects of the disorder.
For example, suppression of the synthesis of monoamine oxidase may
be used in Parkinson's disease; suppression of catechol o-methyl
transferase may be used to treat depression; and suppression of
indole N-methyl transferase may be used in treating
schizophrenia.
Suppression of selected enzymes in the arachidonic acid cascade
which leads to prostaglandins and leukotrienes may be useful in the
control of platelet aggregation, allergy, inflammation, pain and
asthma.
Suppression of the protein expressed by the multidrug resistance
(mdr) gene, which can be responsible for development of resistance
of tumors to a variety of anti-cancer drugs and is a major
impediment in chemotherapy may prove to be beneficial in the
treatment of cancer. Oligonucleotide sequences complementary to
nucleic acid sequences from any of these genes can be used for
oligonucleotides according to the invention, as can be
oligonucleotide sequences complementary to any other cellular gene
or gene transcript, the abnormal expression or product of which
results in a disease state.
Antisense regulation of gene expression in plant cells has been
described in U.S. Pat. No. 5,107,065, the teachings of which are
hereby incorporated by reference.
In a third aspect, the invention provides therapeutic
pharmaceutical formulations of oligonucleotides that are effective
for treating virus infection, infections by pathogenic organisms,
or disease resulting from abnormal gene expression or from the
expression of an abnormal gene product. Such therapeutic
pharmaceutical formulations comprise the oligonucleotides according
to the second aspect of the invention in a pharmaceutically
acceptable carrier.
In a fourth aspect, the invention provides a method for inhibiting
the gene expression of a virus, a pathogenic organism or a cellular
gene, the method comprising the step of providing oligonucleotides
according to the invention to cells infected with the virus or
pathogenic organism in the former two cases or to cells generally
in the latter case. Such methods are useful in studying gene
expression and the function of specific genes.
In a fifth aspect, the invention provides a method of treating a
diseased human or animal in which the disease results from
infection with a virus or pathogenic organism, or from the abnormal
expression or product of a cellular gene. The method comprises
administering therapeutic pharmaceutical formulations of
oligonuclcotides according to the invention to the diseased human
or animal. Preferably, the routes of such administration will
include oral, intranasal, rectal and topical administration. In
such methods of treatment according to the invention the
oligonucleotides may be administered in conjunction with other
therapeutic agents, e.g., AZT in the case of AIDS.
A variety of viral diseases may be treated by the method of
treatment according to the invention, including AIDS, ARC, oral or
genital herpes, papilloma warts, flu, foot and mouth disease,
yellow fever, chicken pox, shingles, adult T cell-leukemia, and
hepatitis. Among fungal diseases that may be treatable by the
method of treatment according to the invention are candidiasis,
histoplasmosis, cryptococcocis, blastomycosis, aspergillosis,
sporotrichosis, chromomycosis, dermatophytosis and
coccidioidomycosis. The method might also be used to treat
rickettsial diseases (e.g., typhus, Rocky Mountain spotted fever),
as well as sexually transmitted diseases caused by Chiamydia
trachomatis or Lymnhogranuloma venereum. A variety of parasitic
diseases may be treated by the method according to the invention,
including amebiasis, Chegas' disease, toxoplasmosis,
pneumocystosis, giardiasis, cryptosporidiosis, trichomoniasis, and
Pneumocystis carini pneumonia; also worm (helminthic) diseases such
as ascariasis, filariasis, trichinosis, schistosomiasis and
nematode or cestode infections. Malaria may be treated by the
method of treatment of the invention regardless of whether it is
caused by P. falciparum, P. vivax, P. orale, or P. malariae.
The infectious diseases identified above may all be treated by the
method of treatment according to the invention because the
infectious agents for these diseases are known and thus
oligonucleotides according to the invention can be prepared, having
oligonucleotide sequence that is complementary to a nucleic acid
sequence that is an essential nucleic acid sequence for the
propagation of the infectious agent, such as an essential gene.
Other disease states or conditions that may be treatable by the
method according to the invention are those which result from an
abnormal expression or product of a cellular gene. These conditions
may be treated by administration of oligonucleotides according to
the invention, and have been discussed earlier in this
disclosure.
Oligonucleotides according to the invention can be synthesized by
procedures that are well known in the art. Alternatively, and
preferably such oligonucleotides can be synthesized by the
H-phosphonate approach described in U.S. Pat. No. 5,149,798, the
teachings of which are hereby incorporated by reference, and in
Agrawal and Tang, Tetrhadron Lett. 31: 7541 7544 (1990).
Oligonucleotides according to the invention can be made even more
resistant to nucleolytic degradation through the addition of cap
structures at the 5' and/or 3' end.
The following examples are intended to further illustrate certain
preferred embodiments of the invention and are not intended to be
limiting in nature.
EXAMPLE 1
Synthesis of Hybrid Oligonucleotide Phosphorothioates
Hybrid oligonucleotide phosphorothioates were synthesized on CPG on
a 5 6 .mu.mole scale on an automated synthesizer (model 8700,
Millipore, Milford, Mass.) using the H-phosphonate approach
described in U.S. Pat. No. 5,149,798. Deoxynucleoside
H-phosphonates were obtained from Millipore. 2'--OMe ribonucleotide
H-phosphonates were synthesized by standard procedures. Segments of
oligonucleotides containing 2'--OMe nucleoside were assembled by
using 2'--OMe ribonucleoside H-phosphonates for the desired cycles.
Similarly, segments of oligonucleotides containing
deoxyribonucleosides were assembled by using deoxynucleoside
H-phosphonates for the desired cycles. After assembly, CPG bound
oligonucleotide H-phosphonate was oxidized with sulfur to generate
the phosphorothioate linkage. Oligonucleotides were then
deprotected in concentrated NH,OH at 40.degree. C. for 48
hours.
Crude oligonucleotide (about 500 A.sub.280 units) was analyzed on
reverse low pressure chromatography on a C.sub.18 reversed phase
medium. The DMT group was removed by treatment with 80% aqueous
acetic acid, then the oligonucleotides were dialyzed against
distilled water and lyophilized.
The oligonucleotides synthesized are. shown in Table 11, below.
Oligonucleotides A-correspond to SEQ ID NOS:1 6, respectively.
TABLE-US-00002 TABLE II HYBRID OLIGONUCLEOTIDE PHOSPHOROTHIOATES'
SYNTHESIZED Oligo Structure A .sup.5' A C A C C C A A T T C T G A A
A A T G G .sup.3' B A C A C C C A A T T C U G A A A A U G G C A C A
C C C A A T T C T G A A A A U G G D A C A C C C A A T T C U G A A A
A U G G E A C A C C C A A U T C T G A A A A T G G F A C A C C C A A
U U C U G A A A A U G G Underlined sequences contain 2'-OMe
ribonucleoside. *All internucleoside linkages are phosphorothioate
linkages for oligos A-F.
EXAMPLE 2
Relative Nuclease Resistance of Hybrid Oligonucleotide
Phosphorothioates
To test the relative nuclease resistance of various hybrid
oligonucleotide phosphorothioates, the oligonucleotides were
treated with snake venom phosphodiesterase (SVPD). About 0.2
A.sub.280 units of oligos A, C and F were dissolved in 500 .mu.l
buffer (40 mM NH.sub.4CO.sub.3, pH 0.4+20 mM MgCl.sub.2) and mixed
with 0.1 units SVPD. The mixture was incubated at 37.degree. C. for
420 minutes. After 0, 200 and 420 minutes, 165 .mu.l aliquots were
removed and analyzed using ion exchange HPLC. The results are shown
in FIG. 1. Oligonucleotide F (SEQ ID NO:6) was very resistant to
phosphodiesterase, whereas oligonucleotide A (SEQ ID NO:1) was
digested almost to completion and oligonucleotide C (SEQ ID NO:3)
was digested to 50% (panel A). An oligonucleotide phosphodiester
was digested to about 80% in one minute using one tenth of the
concentration of SVPD. (panel B)
These results indicate that the presence of 2'--OMe ribonucleotides
in an oligonucleotide phosphorothioate enhances resistance to
exonucleolytic digestion and that this enhanced resistance
increases when a larger proportion of 2'--OMe ribonucleotides are
used. Due to the similar character and behavior of ribonucleotides,
other 2'-substituted ribonucleotides and 2'--OMe ribonucleotides,
these results also suggest that similar enhancement of nuclease
resistance would be obtained for hybrid oligonucleotide
phosphorothioates and/or phosphorodithioates having
ribonucleotides, 2'-substituted ribonucleotides, or a mixture of
ribonucleotides and 2'-substituted ribonucleotides.
EXAMPLE 3
Relative Duplex Stability of Hybrid Oligonucleotide
Phospohorothioates
Oligonucleotides A F (SEQ ID NOS:1 6) were tested for the relative
stability of duplexes formed between them and complementary
oligodeoxyribonucleotides, and with complementary
oligoribonucleotides. In separate reactions, each oligonucleotide
A-F (SEQ ID NOS:1 6) was mixed with an equivalent quantity (0.2
A.sub.280 units) of its complementary oligonucleotide in 150 mM
NaCl, 10 mM Na.sub.2PO.sub.4, 1 mM EDTA, pH 7. The mixture was
heated to 85.degree. C. for 5 minutes, then cooled to 30.degree. C.
The temperature was then increased from 30.degree. C. to 80.degree.
C. at a rate of 1.degree. C. p minute and A.sub.280 was recorded as
a function of temperature. The results are shown in Table III,
below, where oligonucleotides A F correspond to SEQ ID NOS:1 6,
respectively.
TABLE-US-00003 TABLE III MELTING TEMPERATURE OF DUPLEXES DNA-RNA
Duplex DNA-DNA Duplex DNA-RNA Duplex w/Magnesium Differences in
Differences in Difference in Tm compared Tm compared Tm compared to
oligo- to oligo- Tm DNA-RNA to oligo- Tm DNA nucleotide A Tm RNA
nucleotide A Duplex-Tm DNA Tm RNA nucleotide A Oligonucleotide
(.degree. C.) (.degree. C.) (.degree. C.) (.degree. C.) Duplex
(.degree. C.) (.degree. C.) (.degree. C.) A 51.1 0 43.4 0 -7.7 48.1
0 B 48.3 -2.8 50.9 7.5 2.6 58.4 10.3 C 49.9 -1.2 48.9 5.5 -1.0 54.2
6.1 D 45.1 -6.0 50.9 7.5 5.8 56.1 8.0 E 47.2 -3.9 51.1 7.7 3.9 56.5
8.4 F 47.6 -3.5 61.1 17.7 13.5 69.1 21.0
These results reveal that when the complementary oligonucleotide is
an oligoribonucleotide, the presence of 2'--OMe ribonucleotides
enhances duplex stability, and that this enhancement increases with
increased proportions of 2'--OMe ribonucleotides. These results
should be similarly applicable to hybrid oligonucleotide
phosphorothioates and/or phosphorodithioates containing
ribonucleotides, 2'-substituted ribonucleotides, or mixtures of
ribonucleotides and 2'-substituted ribonucleotides. Thus, the
hybrid oligonucleotide phosphorothioates and/or phosphorodithioates
according to the invention should bind viral RNA or virus,
pathogenic organism or cellular mRNA with greater affinity than
ordinary oligodeoxynucleotide phosphorothioates.
EXAMPLE 4
Activation of RNase H by Hybrid Oligonucleotlde
Phosphorothioates
Oligonucleotide phosphorothioates and various hybrid
oligonucleotide phosphorothioates were studied for their RNase H
activation properties. Oligonucleotide A (SEQ ID NO:1) (Table II),
an oligonucleotide phosphorothioate which is known to activate
RNase H, was used as a control. oligonucleotide F (SEQ ID NO:6) (a
2'--OMe analog of oligonucleotide phosphorothioate) and
oligonucleotides C, B, and E (SEQ ID NOS:3,2 and 5, respectively),
hybrid oligonucleotides, were studied for their ability to activate
RNase H.
To carry out the experiment, a complementary .sup.32-mer
oligoribonucleotide was synthesized (FIG. 2) and kinased at the
5'-end, .sup.32P-labeled 32-mer RNA (0.003 A.sub.280 units; 0.01
.mu.g) and oligonucleotides (0.0635 A.sub.280 units; 1.9 .mu.g)
were mixed in the 20 .mu.l of buffer (0.15 M NaCl, 0.01 MgCl.sub.2
0.01 M Tris-HCI, pH 7.9, containing 0.001 M DTT. The mixture was
incubated with 6 units of RNase H (E. coli) at 37.degree. C.
Aliquots of 4.5 .mu.l were removed at 0, 15, 30, and 60 minutes and
analyzed on polyacrylamide gel electrophoresis.
Oligonucleotide A (SEQ ID NO:1) (Duplex A in FIG. 2) showed site
specific cleavage of RNA by RNase H. Oligonucleotide F (SEQ ID
NO:6) (2'--OMe analog; Duplex B) showed no cleavage of RNA in
presence of RNase H. Hybrid oligonucleotide B, C, and E (SEQ ID
NOS:2, 3 and 5, respectively) (Duplexes C, D, and E, respectively)
showed site specific cleavage of RNA by RNase H. Duplex F, in which
a mismatched oligonucleotide phosphorothioate (SEQ ID NO:7) was
studied showed no cleavage of RNA. Lane G shows that in presence of
RNase H, RNA was not cleaved.
EXAMPLE 5
Inhibition of HIV by Hybrid Oligonucleotide Phosphorothioates
Hybrid oligonucleotide phosphorothioates were tested for their
ability to inhibit HIV-1 in tissue culture. H9 lymphocytes were
infected with HIV-1 virions (=0.01 0.1 TCID.sub.90/cell) for one
hour at 37.degree. C. After one hour, unadsorbed virions were
washed and the infected cells were divided among wells of 24 well
plates. To the infected cells, an appropriate concentration (from
stock solution) of oligonucleotide was added to obtain the required
concentration in 2 ml medium. The cells were then cultured for four
days. At the end of four days, level of HIV-1 expression was
measured by synthetic formation, p24 expression and reverse
transcriptase activity. The level of expression of p24 was compared
between oligonucleotide treated and untreated (no drug) infected
cells. (Table IV)
All of the hybrid oligonucleotide phosphorothioates tested showed
significant inhibition of synthetic formation, p24 expression and
reverse transcriptase, without significant cytotoxicity. These
results indicate that hybrid oligonucleotide phosphorothioates
containing 2'--OMe ribonucleotides are more effective as inhibitors
of gene expression compared to oligodioxynucleotide phosphoration.
Similar effectiveness would be expected for hybrid oligonucleotide
phosphorothioates and/or phosphorodithioates containing
ribonucleosides, 2'-substituted ribonucleosides, or a mixture of
ribonucleosides and 2'-substituted ribonucleosides. The activity of
compounds listed in Table III are listed in Table IV below, where
oligonucleotides A F correspond to SEQ ID NOS:1 6,
respectively.
TABLE-US-00004 TABLE IV Anti-HIV activity of oligonucleotides
(listed in Table III) Inhibition of Inhibition of Reverse
Oligonucleotides Syncytia formed p24 (%) Transcriptase (%) Oligo A
++ 93 88 Oligo B ++ 95 97 Oligo C + 98 97 Oligo D + 98 83 Oligo E
+++ 90 94 Oligo F +++ 88 91 +Control ++++ -Control - +Control =
HIV-1 Infected cells without oligonucleotides -Control = Uninfected
cells without oligonucleotides 1. Number of Syncytia formed in
oligonucleotides treated cells were compared with the number of
syncytia 2. Inhibition is compared to untreated infected cells.
SEQUENCE LISTINGS
1
8 1 20 DNA Artificial Sequence Oligonucleotide phosphorothioate. 1
acacccaatt ctgaaaatgg 20 2 20 DNA Artificial Sequence Hybrid
Oligonucleotide. 2 acacccaatt cugaaaaugg 20 3 20 DNA Artificial
Sequence Hybrid oligonucleotide. 3 acacccaatt ctgaaaaugg 20 4 20
DNA Artificial Sequence Hybrid oligonucleotide. 4 acacccaatt
cugaaaaugg 20 5 20 DNA Artificial Sequence Hybrid oligonucleotide.
5 acacccaaut ctgaaaatgg 20 6 20 DNA Artificial Sequence 2'-OMe
analog of oligonucleotide phosphorothioate. 6 acacccaauu cugaaaaugg
20 7 20 DNA Artificial Sequence Oligonucleotide. 7 acagacttac
ctcagataat 20 8 32 DNA Artificial Sequence Oligonucleotide. 8
uacagcugug gguuaagacu uuuaccuauu ug 32
* * * * *