Sterol modified oligonucleotide duplexes having anticancer activity

Claim 2

A duplex of two strands of oligonucleotides each of which has the formula ##STR3## wherein each of B independently is a nucleotide base residue; the wavy line between the sugar and the base B represents a glycosidic bond of either α or of β configuration; X is S or O, with the proviso that there are no more than 3 X═S groups in each oligonucleotide; R 1 is H, OH, or F; R 2 is H, or F; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH 2 , hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 18; the linker is a group of 0 to 12 atom length covalently linking the A ring of the steroid skeleton to the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the two strands of the oligonucleotides are substantially complementary to one another for Watson Crick type base pairing and the two strands form a stable duplex in aqueous solution at physiological temperature.

Claim 3

The duplex of claim 1 wherein the two strands are identical with one another.

Claim 4

The duplex of claim 2 wherein the melting temperature of the duplex of the oligonucleotides is above approximately 25° C., as determined in an approximately 3.0 μmolar concentration of the duplex.

Claim 5

The duplex of claim 3 wherein R 1 and R 2 are both hydrogen and the wavy line represents glycosidic bonds of β configuration.

Claim 6

The duplex of claim 4 wherein W is hydrogen.

Claim 7

The duplex of claim 4 wherein the linker represents the group of the formula ##STR4##

Claim 8

The duplex of claim 4 wherein the linker is attached to the secondary hydroxyl group of cholesterol.

Claim 9

The duplex of claim 4 wherein the strand consists of 8 to 12 nucleotide units.

Claim 10

The duplex of claim 1 wherein the two strands are not identical with one another.

Claim 11

The duplex of claim 9 wherein the melting temperature of the duplex is above approximately 25° C., as determined in an approximately 3.0 μmolar concentration of the duplex.

Claim 12

The duplex of claim 10 wherein R 1 and R 2 are both hydrogen and the wavy line represents glycosidic bonds of β configuration.

Claim 13

The duplex of claim 11 wherein W is hydrogen.

Claim 14

The duplex of claim 11 wherein the linker represents the group of the formula ##STR5##

Claim 15

The duplex of claim 11 wherein the linker is attached to the secondary hydroxyl group of cholesterol.

Claim 16

The duplex of claim 11 wherein each strand consists of 8 to 14 nucleotide units.

Claim 17

A duplex of two strands of oligonucleotides each of which has the formula ##STR6## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in each oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 18; the linker is a group of 0 to 12 atom length covalently linking the A ring of the steroid skeleton to the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the two strands of the oligonucleotides are substantially complementary to one another for Watson Crick type base pairing and the two strands form a substantially stable duplex in aqueous solution at 25° C. or still higher temperatures.

Claim 18

A duplex of two strands of oligonucleotides each of which has the formula ##STR6## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in each oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 18; the linker is a group of 0 to 12 atom length covalently linking the A ring of the steroid skeleton to the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the two strands of the oligonucleotides are substantially complementary to one another for Watson Crick type base pairing and the two strands form a substantially stable duplex in aqueous solution at 25° C. or still higher temperatures.

Claim 19

The duplex of claim 16 wherein the linker is selected from the structures ##STR7##

Claim 20

The duplex of claim 16 where the linker is selected from the structures ##STR8##

Claim 21

The duplex of claim 18 wherein the linker is attached via the carbonyl to the secondary hydroxyl group of a cholesterol moiety.

Claim 22

The duplex of claim 19 wherein each strand consists of 8 to 14 nucleotide units.

Claim 23

The duplex of claim 20 wherein the two strands of the combination are identical and self-complementary, and have the sequence selected from the sequences CACACGGGTG (SEQUENCE ID NO: 5), GACACACGGGTGAT (SEQUENCE ID NO: 1), CACACGGGTGAT (SEQUENCE ID NO: 3), CACACGGGTGA (SEQUENCE ID NO: 4), CACACCGGTG fSEQUENCE ID NO: 18), CACCCGGGTG (SEQUENCE ID NO: 26), CACACGAGTG (SEQUENCE ID NO: 32), CACACGCGTG (SEOqENCE ID NO: 33), and CACACGTGTG (SEOUENCE ID NO: 34).

Claim 24

The duplex of claim 21 wherein the 3'-phosphate group of each strand is connected to the group of the formula ##STR9##

Claim 25

The duplex of claim 20 wherein the two strands of the combination are different but substantially complementary to one another, and wherein one of the strands has the sequence selected from the sequences CACACGGGTG fSEQUENCE ID NO: 5), GATAGCATATGCTA (SEQUENCE ID NO: 57), and GCTATTATCG (SEQUENCE ID NO: 46).

Claim 26

The duplex of claim 23 wherein the 3'-phosphate group of each strand is connected to the group of the formula ##STR10##

Claim 27

The duplex of claim 22 wherein X in each nucleotide unit is O.

Claim 28

The duplex of claim 25 wherein W is H.

Claim 29

The duplex of claim 24 wherein X in each nucleotide unit is O.

Claim 30

The duplex of claim 27 wherein W is H.

Claim 31

An oligonucleotide which has the formula ##STR11## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in the oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 14; the linker is a group of 0 to 12 atom length covalently linking the A ring of the steroid skeleton to the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the oligonucleotide is substantially self-complementary to itself to form a duplex by Watson Crick type base pairing, the sequence of the oligonucleotide being selected from the sequences CACACGGGTG (SEQUENCE ID NO: 5), GACACACGGGTGAT (SEQUENCE ID NO: 1)., CACACGGGTGAT (SEQUENCE ID NO: 3), CACACGGGTGA (SEQUENCE ID NO: 4), CACACCGGTG (SEQUENCE ID NO: 18), CACCCGGGTG (SEQUENCE ID NO: 26), CACACGAGTG (SEQUENCE ID NO: 32), CACACGCGTG (SEQUENCE ID NO: 33), and CACACGTGTG (SEQUENCE ID NO: 34).

Claim 32

An oligonucleotide which has the formula ##STR11## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in the oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 14; the linker is a group of 0 to 12 atom length covalently linking the A ring of the steroid skeleton to the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the oligonucleotide is substantially self-complementary to itself to form a duplex by Watson Crick type base pairing, the sequence of the oligonucleotide being selected from the sequences CACACGGGTG (SEQUENCE ID NO: 5), GACACACGGGTGAT (SEQUENCE ID NO: 1)., CACACGGGTGAT (SEQUENCE ID NO: 3), CACACGGGTGA (SEQUENCE ID NO: 4), CACACCGGTG (SEQUENCE ID NO: 18), CACCCGGGTG (SEQUENCE ID NO: 26), CACACGAGTG (SEQUENCE ID NO: 32), CACACGCGTG (SEQUENCE ID NO: 33), and CACACGTGTG (SEQUENCE ID NO: 34).

Claim 33

The oligonucleotide of claim 29 wherein W is H, X in each nucleotide unit is O, and where the linker is selected from the structures ##STR12##

Claim 34

A duplex of two strands of oligonucleotides each of which has the formula ##STR13## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in each oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 14; the linker is a group of 0 to 12 atom length covalently linking the steroid skeleton the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the two strands of the oligonucleitides are substantially complementary to one another for Watson Crick type base pairing and wherein one of the strands has the sequence selected from the sequences CACACGGGTG (SEQUENCE ID NO: 5), GATAGCATATGCTA (SEQUENCE ID NO: 57), and GCTATTATCG (SEQUENCE ID NO: 46).

Claim 35

A duplex of two strands of oligonucleotides each of which has the formula ##STR13## wherein each of B independently is a major naturally occurring nucleotide base residue selected from the group consisting of 1-N-uracil, 1-N-thymine, 1-N-cytosine, 9-N-adenine and 9-N-guanine residues; X is S or O, with the proviso that there are no more than 3 X═S groups in each oligonucleotide; W is H or YO(OH)XP-; Y is H, alkyl of 1-20 carbons, branched chain alkyl or cycloalkyl of 3 to 25 carbons, (CH 2 ) s OH, (CH 2 ) s NH2, hydroxy branched chain alkyl or hydroxy cycloalkyl of 3-25 carbons, amino branched chain alkyl of 3 to 25 carbons or amino cycloalkyl of 3 to 25 carbons, or a lipophilic group which may be connected to the phosphate residue with an appendant connecting group of 1 to 10 atom length, s is an integer between 2-25; n is an integer having a value between 8 and 14; the linker is a group of 0 to 12 atom length covalently linking the steroid skeleton the 3'-phosphate end of the oligonucleotide; R 3 is H, C 1 -C 6 alkyl, or C 2 -C 6 alkenyl and is attached to the A, B or C ring of the steroid skeleton, m is an integer having the values 0 to 4, i is an integer having the values 0 to 4, and R 4 is H or a C 1 to C 15 alkyl group, or a C 2 to C 15 alkenyl group having 1 to 3 double bonds and the R 4 group is attached to the D ring of the steroid skeleton; the nucleotide base residues B are selected such that the two strands of the oligonucleitides are substantially complementary to one another for Watson Crick type base pairing and wherein one of the strands has the sequence selected from the sequences CACACGGGTG (SEQUENCE ID NO: 5), GATAGCATATGCTA (SEQUENCE ID NO: 57), and GCTATTATCG (SEQUENCE ID NO: 46).

Claim 36

The duplex of claim 31 wherein W is H, X in each nucleotide unit is O, and where the linker is selected from the structures ##STR14##