US5824796A
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Cross-linking oligonucleotides
Assignee: Nanogen Inc
•
Filing: 1994-11-04
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Granted: 1998-10-20
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Expires: 2014-11-04
Abstract
Abstract This invention is directed to novel substituted nucleotide bases with a crosslinking arm which accomplish crosslinking between specific sites on adjoining strands of oligonucleotides or oligodeoxynucleotides. The invention is also directed to oligonucleotides comprising at least one of these crosslinking agents and to the use of the resulting novel oligonucleotides for diagnostic and therapeutic purposes. The crosslinking agents of the invention are of the following formula (I'): R.sub.1 --B--(CH.sub.2).sub.q --(Y).sub.r --(CH.sub.2).sub.m --A'(I') wherein, R 1 is hydrogen, or a sugar moiety or analog thereof optionally substituted at its 3' or its 5' position with a phosphorus derivative attached to the sugar moiety by an oxygen and including groups Q 1 Q 2 and Q 3 or with a reactive precursor thereof suitable for nucleotide bond formation; Q 1 is hydroxy, phosphate or diphosphate; Q 2 is ═O or ═S; Q 3 is CH 2 --R', S--R', O--R', or N--R'R"; each of R' and R" is independently hydrogen or C 1-6 alkyl; B is a nucleic acid base or analog thereof that is a component of an oligonucleotide; Y is a functional linking group; each of m and q is independently 0 to 8, inclusive; r is 0 or 1; and A' is a leaving group. This invention is also directed to novel 3,4-disubstituted and 3,4,-trisubstituted pyrazolo 3,4-d!-pyrimidines and to the use of these nucleic acid bases in the preparation of oligonucleotides. The invention includes nucleosides and mono- and oligonucleotides comprising at least one of these pyrazolopyrimidines, and to the use of the resulting novel oligonucleotides for diagnostic purposes.
Inventors
- 👤 Charles R. Petrie
- 👤 Rich B. Meyer
- 👤 John C. Tabone
- 👤 Gerald D. Hurst
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-10-29 13:16
CPC Classifications
C; C07; C07D; C07D487/00; C07D487/02; C07D487/04; C07H; C07H19/00; C07H19/02; C07H19/04; C07H19/06; C07H19/10; C07H21/00; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6816; C12Q1/70; C12Q1/701; C12Q1/708
Claims Analysis
Total Claims: 19
Claim 1
Independent Claim
268 words
An oligonucleotide having at least one nucleotide of the formula R.sub.1 --B--(CH.sub.2).sub.q --(Y).sub.r --(CH.sub.2).sub.m --A' wherein R 1 is a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group, wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group; B is a heterocyclic base selected from purine and pyrazolo 3,4-d!pyrimidine groups wherein the (CH 2 ) q group is attached to the 7-position or 8 position of the purine and 3-position of the pyrazolo 3,4-d!pyrimidine groups and the R 1 group is attached to the 9-position of the purine and to the 1-position of the pyrazolo 3,4-d!pyrimidine groups; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to the --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; m is 1 to 8, inclusive; q is 0 to 8, inclusive; r is 0 or 1; and A' is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, where each of R'" and R"" is independently C 1-6 alkyl or aryl or R'" and R"" together form a C 1-6 alkylene bridge.
Claim 2
Dependent Claim
268 words
An oligonucleotide having at least one nucleotide of the formula R.sub.1 --B--(CH.sub.2).sub.q --(Y).sub.r --(CH.sub.2).sub.m --A' wherein R 1 is a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group, wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group; B is a heterocyclic base selected from purine and pyrazolo 3,4-d!pyrimidine groups wherein the (CH 2 ) q group is attached to the 7-position or 8 position of the purine and 3-position of the pyrazolo 3,4-d!pyrimidine groups and the R 1 group is attached to the 9-position of the purine and to the 1-position of the pyrazolo 3,4-d!pyrimidine groups; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to the --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; m is 1 to 8, inclusive; q is 0 to 8, inclusive; r is 0 or 1; and A' is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, where each of R'" and R"" is independently C 1-6 alkyl or aryl or R'" and R"" together form a C 1-6 alkylene bridge.
Claim 3
Dependent Claim
19 words
An oligonucleotide according to claim 1 wherein B is selected from adenine-8-yl, guanine-8-yl, 4-aminopyrazolo 3,4-d!pyrimidin-3-yl, and 4-amino-6-oxopyrazolo 3,4-d!pyrimidin-3-yl groups.
Claim 4
Dependent Claim
23 words
An oligonucleotide according to claim 1 wherein m is 1, 2 or 3; q is 2, 3, or 4; and r is 1.
Claim 5
Dependent Claim
13 words
An oligonucleotide according to claim 1 wherein the R 1 group is 1-(β-D-ribofuranosyl).
Claim 6
Dependent Claim
13 words
An oligonucleotide according to claim 1 wherein the R 1 group is 1-(β-D-2-deoxyribofuranosyl).
Claim 7
Dependent Claim
13 words
An oligonucleotide according to claim 1 wherein the R 1 group is 1-(β-D-2-O-methyl-ribofuranosyl).
Claim 8
Dependent Claim
26 words
An oligonucleotide according to claim 1 wherein the group --(CH 2 ) q --(Y) r --(CH 2 ) m --A' is 3-iodoacetamidopropyl, 3-(4-bromobutyramido)propyl, 4-iodoacetamidobutyl, or 4-(4-bromobutyramido)butyl.
Claim 9
Dependent Claim
327 words
A compound of the formula ##STR10## where R 1 is H, or a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate alkylphosphate or alkanephosphonate group, or a reactive precursor of said phosphate, thiophosphate, alkylphosphate or alkanephosphonate group which precursor is suitable for internucleotide bond formation; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A" where A" is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, where each of R'" and R"" is independently C 1-6 alkyl or aryl or R'" and R"" together form a C 1-6 alkylene bridge, or A" is an intercalator group, a metal ion chelator or a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1 provided that when A" is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, then m is not 0; each of R 4 and R 6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 10
Dependent Claim
327 words
A compound of the formula ##STR10## where R 1 is H, or a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate alkylphosphate or alkanephosphonate group, or a reactive precursor of said phosphate, thiophosphate, alkylphosphate or alkanephosphonate group which precursor is suitable for internucleotide bond formation; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A" where A" is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, where each of R'" and R"" is independently C 1-6 alkyl or aryl or R'" and R"" together form a C 1-6 alkylene bridge, or A" is an intercalator group, a metal ion chelator or a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1 provided that when A" is a group selected from chloro, bromo, iodo, SO 2 R'", S + R'"R"" and a radical which activates the carbon to which it is attached for nucleophilic substitution, then m is not 0; each of R 4 and R 6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 11
Dependent Claim
29 words
A compound in accordance with claim 8 where each of R 4 and R 6 is independently selected from a group consisting of H, OH and NH 2 .
Claim 12
Dependent Claim
226 words
A compound of the formula ##STR11## where R 1 is H, or a 1-(β-D-ribofuranosyl) or 1-(β-D-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group, or a reactive precursor of said phosphate, thiophosphate, alkylphosphate or alkanephosphonate group which precursor is suitable for internucleotide bond formation; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A" and A" is a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1, and each of R 4 and R6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 13
Dependent Claim
226 words
A compound of the formula ##STR11## where R 1 is H, or a 1-(β-D-ribofuranosyl) or 1-(β-D-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group, or a reactive precursor of said phosphate, thiophosphate, alkylphosphate or alkanephosphonate group which precursor is suitable for internucleotide bond formation; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A" and A" is a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--, trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1, and each of R 4 and R6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 14
Dependent Claim
29 words
A compound in accordance with claim 10 where each of R 4 and R 6 is independently selected from a group consisting of H, OH and NH 2 .
Claim 15
Dependent Claim
15 words
A compound in accordance with claim 11 where the reporter group is biotin or 2,4-dinitrobenzene.
Claim 16
Dependent Claim
208 words
An oligonucleotide having at least one nucleotide of the formula ##STR12## wherein R 1 is a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A and A is a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--,trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1, and each of R 4 and R6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 17
Dependent Claim
208 words
An oligonucleotide having at least one nucleotide of the formula ##STR12## wherein R 1 is a 1-(β-D-ribofuranosyl) or 1-(β-D-2-deoxyribofuranosyl) group which is optionally substitituted on one or more of its hydroxyl functions with a Z group wherein Z independently is methyl or a phosphate, thiophosphate, alkylphosphate or alkanephosphonate group; R 3 is (CH 2 ) q --(Y) r --(CH 2 ) m --A and A is a reporter group; Y is a functional linking group selected from a group consisting of --O--, --S--, --NR'--, --NH--CO--, trifluoroacetamido and phtalimido groups where R' is H or C 1-6 alkyl, and at least one of the (CH 2 ) m and (CH 2 ) q groups is directly linked to said --O--, --S--, --NR'--, NH--CO--,trifluoroacetamido and phtalimido groups and the other of said (CH 2 ) m and (CH 2 ) q groups is linked to the heterocyclic base with a carbon to carbon bond; each of m and q is independently 0 to 8, inclusive; r is 0 or 1, and each of R 4 and R6 is independently H, OR, SR, NHOR, NH 2 , or NH(CH 2 ) t NH 2 where R is H or C 1-6 alkyl and t is an integer from 0 to 12.
Claim 18
Dependent Claim
29 words
An oligonucleotide in accordance with claim 13 where each of R 4 and R 6 is independently selected from a group consisting of H, OH and NH 2 .
Claim 19
Dependent Claim
15 words
An oligonucleotide in accordance with claim 14 where the reporter group is biotin or 2,4-dinitrobenzene.
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