Oligonucleotides including pyrazolo[3,4-D]pyrimidine bases, bound in double stranded nucleic acids

Claim 3

A method in accordance with claim 1 wherein substantially all guanine base containing nucleotides of the substantially continuous sequence are replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one.

Claim 4

A triplex comprising: an oligonucleotide that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, said triplex forming oligonucleotide further comprising at least one cross-linking agent covalently attached to the oligonucleotide, and said duplex nucleic acid including the target sequence.

Claim 5

A triplex comprising: an oligonucleotide that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, said triplex forming oligonucleotide further comprising at least one cross-linking agent covalently attached to the oligonucleotide, and said duplex nucleic acid including the target sequence.

Claim 6

A triplex comprising: an oligonucleotide that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, and further wherein at least one adenine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide is replaced by the nucleotide of 4-amino-1H-pyrazolo[3,4-d]pyrimidine or by the nucleotide of 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-6(7H)-dione, and said duplex nucleic acid including the target sequence.

Claim 7

A triplex comprising: an oligonucleotide that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, and further wherein at least one adenine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide is replaced by the nucleotide of 4-amino-1H-pyrazolo[3,4-d]pyrimidine or by the nucleotide of 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-6(7H)-dione, and said duplex nucleic acid including the target sequence.

Claim 8

A triplex comprising a triplex forming oligonucleotide that is not a homopolymer and that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, the oligonucleotide having the formula ##STR11## wherein B is an independently selected heterocyclic base at least one of which is said 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one; R 1 independently is H, O-C 1-6 alkyl, OC 2-6 alkenyl, or F; R 2 independently is H or C 1-6 alkyl; r is an integer between approximately 5 to approximately 79; X 1 is independently O or S; X 2 is independently O or NH; r' is an integer between 0 and 5; r" is an integer between 0 and 1; Z and Z' each independently represent an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the Z group and/or the Z' group respectively, to a heterocyclic base of the oligonucleotide; W 1 is H, a phosphate or thiophosphate group, a tail moiety, or W 1 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 5'-end of the oligonucleotide; W 2 is H, a phosphate or thiophosphate group, a tail moiety, or W 2 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 3'-end of the oligonucleotide, where at least one of said B groups represents a 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one-1-yl radical, and said duplex nucleic acid including the target sequence.

Claim 9

A triplex comprising a triplex forming oligonucleotide that is not a homopolymer and that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, the oligonucleotide having the formula ##STR11## wherein B is an independently selected heterocyclic base at least one of which is said 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one; R 1 independently is H, O-C 1-6 alkyl, OC 2-6 alkenyl, or F; R 2 independently is H or C 1-6 alkyl; r is an integer between approximately 5 to approximately 79; X 1 is independently O or S; X 2 is independently O or NH; r' is an integer between 0 and 5; r" is an integer between 0 and 1; Z and Z' each independently represent an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the Z group and/or the Z' group respectively, to a heterocyclic base of the oligonucleotide; W 1 is H, a phosphate or thiophosphate group, a tail moiety, or W 1 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 5'-end of the oligonucleotide; W 2 is H, a phosphate or thiophosphate group, a tail moiety, or W 2 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 3'-end of the oligonucleotide, where at least one of said B groups represents a 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one-1-yl radical, and said duplex nucleic acid including the target sequence.

Claim 10

A triplex in accordance with claim 5, wherein substantially all guanine base containing nucleotides of the substantially continuous sequence of the oligonucleotide are replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one.

Claim 11

A triplex in accordance with claim 6, wherein all guanine base containing nucleotides of the substantially continuous sequence of the oligonucleotide are replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one.

Claim 12

A triplex in accordance with claim 5, wherein at least one adenine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide is replaced by the nucleotide of 4-amino-1H-pyrazolo[3,4-d]pyrimidine or by the nucleotide of 1H-pyrazolo[3,4-d]pyrimidin-4(5H)-6(7H)-dione.

Claim 13

A triplex in accordance with claim 6 where the glycosidic linkages between the heterocyclic bases B and the sugar moieties are of the β configuration.

Claim 14

A triplex in accordance with claim 9 where the R 1 group is H.

Claim 15

A triplex in accordance with claim 10 where R 2 is H or represents a cation.

Claim 16

A triplex in accordance with claim 6 where X 2 is O.

Claim 17

A triplex in accordance with claim 6 where at least one independently selected nucleotide of the oligonucleotide includes a Z that represents a cross-linking group.

Claim 18

A triplex in accordance with claim 6 where Z' represents a cross-linking group and r" is 1.

Claim 19

A triplex in accordance with claim 6 where W 1 represents a cross-linking group.

Claim 20

A triplex in accordance with claim 6 where W 2 represents a cross-linking group.

Claim 21

A triplex comprising a triplex forming oligonucleotide that is not a homopolymer and that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, the oligonucleotide having the formula ##STR12## wherein B is an independently selected heterocyclic base at least one of which is said 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one; X 2 independently is O or NH; r is an integer between approximately 5 to approximately 79; r' is an integer between 0 and 5; r" is an integer between 0 and 1; Z and Z' each independently represent an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the Z group and/or the Z' group respectively, to a heterocyclic base of the oligonucleotide; W 1 is H, a phosphate or thiophosphate group, a tail moiety, or W 1 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 5'-end of the oligonucleotide; W 2 is H, a phosphate or thiophosphate group, a tail moiety, or W 2 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 3'-end of the oligonucleotide, where at least one of said B groups represents a 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one-1-yl radical, and said duplex nucleic acid including the target sequence.

Claim 22

A triplex comprising a triplex forming oligonucleotide that is not a homopolymer and that includes a substantially continuous sequence of at least 6 nucleotides, which sequence is complementary in the triplex forming sense pursuant to the G/T or A/G recognition motif to a target sequence in duplex nucleic acid, at least one guanine base containing nucleotide in the substantially continuous sequence of the triplex forming oligonucleotide being replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, the oligonucleotide having the formula ##STR12## wherein B is an independently selected heterocyclic base at least one of which is said 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one; X 2 independently is O or NH; r is an integer between approximately 5 to approximately 79; r' is an integer between 0 and 5; r" is an integer between 0 and 1; Z and Z' each independently represent an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the Z group and/or the Z' group respectively, to a heterocyclic base of the oligonucleotide; W 1 is H, a phosphate or thiophosphate group, a tail moiety, or W 1 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 5'-end of the oligonucleotide; W 2 is H, a phosphate or thiophosphate group, a tail moiety, or W 2 is selected from an intercalator group, a lipophilic group, a minor groove binder group, a reporter group, a chelating group, or a cross-linking group, each of said groups including a linker arm that connects the W 1 group to the 3'-end of the oligonucleotide, where at least one of said B groups represents a 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one-1-yl radical, and said duplex nucleic acid including the target sequence.

Claim 23

A triplex in accordance with claim 17 wherein substantially all guanine base containing nucleotides of the substantially continuous sequence of the oligonucleotide are replaced by the nucleotide of 6-amino-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one.

Claim 24

A triplex in accordance with claim 18 where at least one independently selected nucleotide of the oligonucleotide includes a Z that represents a cross-linking group.

Claim 25

A triplex in accordance with claim 18 Z' represents a cross-linking group and r" is 1.

Claim 26

A triplex in accordance with claim 18 where W 2 represents a cross-linking group.

Claim 27

A triplex in accordance with claim 18 where W 1 represents a cross-linking group.

Claim 28

A triplex in accordance with claim 22 where W 1 includes the radical --CO--(CH 2 ) 3 --C 6 H 4 --N--[(CH 2 ) 2 Cl] 2 .

Claim 29

A triplex in accordance with claim 23 where W 1 represents --PO(OH)--(CH 2 ) 6 --NH--CO--(CH 2 ) 3 --C 6 H 4 --N--[(CH 2 ) 2 Cl] 2 .

Claim 30

A triplex in accordance with claim 22 where W 1 includes the N-methylcyclopropapyrroloindole radical.

Claim 31

A triplex in accordance with claim 25 where W 1 represents the radical ##STR13## where v is an integer approximately between 1 to 4, w is an integer approximately between 3-15, and y is an integer approximately between 3 and 10.

Claim 32

A triplex in accordance with claim 26 where v is 3, w is 8 and y is 6.

Claim 33

A triplex in accordance with claim 17 where X 2 is O.

Claim 34

A triplex in accordance with claim 17 where X 2 is NH.