Enhanced triple-helix and double-helix formation with oligomers containing modified purines

Claim 2

An oligomer comprising from 2 to 30 nucleomonomers wherein at least one of said nucleomonomers comprises a base having the formula (1) or (2): ##STR11## wherein Pr is hydrogen or a monovalent or divalent protecting group; W is N or CH; R 2 is aryl, heteroaryl or 1-alkynylheteroaryl; R 8 is OH, SH, NPr, NHPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; R 10 is independently H, OH, CN, F, Cl, Br, I, alkyl (C1-12), alkenyl (C2-12), alkynyl (C2-12), aryl (C6-9), heteroaryl (C4-9), or both R 10 , taken together with the carbon atoms to which they are linked at positions 11 and 12, form (a) a 5 or 6 membered carbocyclic ring or, (b) a 5 or 6 membered heterocyclic ring comprising 1-3 N, O or S ring atoms, provided that no 2 adjacent ring atoms are O--O, S--S, O--S or S--O, and wherein any unsaturated C atom of the carbocyclic or heterocyclic ring is substituted by R 11 and any saturated carbons contain 2 R 11 substituents, wherein; R 11 is independently H, alkyl (C1-4), alkenyl (C2-4), alkynyl (C2-4), OR 12 , SR 12 , or N(R 12 ) 2 or halogen provided that there are no more than four halogens per 5 or 6 member ring; R 12 is independently H, or alkyl (C1-4); and salts thereof.

Claim 3

The oligomer of claim 1 wherein at least one base has the formula (2) and R 10 at position 11 is H and R 10 at position 12 is methyl, R 10 at position 12 is H or R 10 at position 11 is methyl, or R 10 at position 11 is H and R 10 at position 12 is 1-propynyl.

Claim 4

The oligomer of claim 1 wherein adjacent nucleomonomers are linked by linkages or substitute linkages and the oligomer contains at least one substitute linkage.

Claim 5

The oligomer of claim 3 wherein the substitute linkage is selected from the group consisting of phosphoramidate, phosphorothioate, methylphosphonate, riboacetal, 3'-N-methylhydroxylamine, thionomethylphosphonate, phosphorodithioate, 2'-thioformacetal, formacetal, and 3'-thioformacetal.

Claim 6

The oligomer of claim 4 wherein the substitute linkage is a phosphorothioate, formacetal or 3'-thioformacetal linkage.

Claim 7

The oligomer of claim 1 wherein at least one base has the formula (1) and R 2 is phenyl, 2-s-triazinyl, 2-, 3- or 4-pyridyl, 2-, 4- or 5-pyrimidinyl, 2- or 3-thienyl, 2-, 4- or 5-thiazolyl, 2- or 4-imidazolyl, 2-, 4- or 5-oxazoyl, 2- or 3-furanyl, 2- or 3-pyrrolyl, phenyl-ethynyl, 2-, 3- or 4-pyridine-ethyl, 2-, 4- or 5-pyrimidine-ethynyl, 2-, or 3-thiophene-ethynyl, 2-, 4- or 5-thiazole-ethynyl, 2- or 4-imidazole-ethynyl, s-triazine-ethynyl, 2- or 3-furan-ethynyl, 2-, 4- or 5-oxazole-ethynyl or 2- or 3-pyrrol-ethynyl.

Claim 8

The oligomer of claim 1 having from 8 to 30 nucleomonomers and uniform polarity.

Claim 9

The oligomer of claim 7 having 2 to 12 substitute linkages or nucleomonomers at the 5'-end and at the 3'-end which comprise nuclease stable domains, and 3 to 26 substitute linkages or nucleomonomers which comprise at least one RNase H competent domain consisting of 3 or more contiguous substitute linkages selected from the group consisting of phosphorothioate and phosphorodithioate linkages disposed between the nuclease stable domains.

Claim 10

The oligomer of claim 1 comprising 2, 3, 4, 5 or 6 nucleomonomers.

Claim 11

A method of synthesizing the oligomer of claim 1, comprising the steps of: synthesizing a protected nucleomonomer synthon having a protecting group and a base and further having a coupling group capable of coupling to a nucleomonomer or oligomer; coupling the nucleomonomer synthon to an acceptor nucleomonomer or oligomer; removing the protecting group; and repeating the cycle until said oligomer is synthesized.

Claim 12

The method of claim 10 wherein the coupling group is a phosphoramidite or a hydrogen phosphonate coupling group.

Claim 13

The oligomer of claim 1 wherein at least one base has the formula (2) and both R 10 are taken together with the carbon atoms to which they are linked at positions 11 and 12 to form a 6-membered ring, said base having the formula (23) or (25) ##STR12## wherein each Q is independently N or CR 11 .

Claim 14

The oligomer of claim 12 wherein adjacent nucleomonomers are linked by linkages or substitute linkages and at least one nucleomonomer linkage is a substitute linkage.

Claim 15

The oligomer of claim 12 wherein adjacent nucleomonomers are linked by linkages or substitute linkages and at least one nucleomonomer linkage is a phosphorothioate linkage.

Claim 16

The oligomer of claim 12 wherein adjacent nucleomonomers are linked by substitute linkages and all nucleomonomer substitute linkages are phosphorothioate linkages.

Claim 17

The oligomer of claim 13 wherein the substitute linkage is selected from the group consisting of phosphoramidite, phosphorothioate, methylphosphonate, riboacetal, 3'-N-methylhydroxylamine, thionomethylphosphonate, phosphorodithioate, 2'-thioformacetal, formacetal, and 3'-thioformacetal.

Claim 18

The oligomer of claim 12 complexed with a cationic lipid.

Claim 19

The oligomer of claim 12 having from 8 to 30 nucleomonomers and uniform polarity.

Claim 20

The oligomer of claim 18 having 2 to 12 substitute linkages or nucleomonomers at the 5'-end and at the 3'-end which comprise nuclease stable domains, and 3 to 26 substitute linkages or nucleomonomers which comprise at least one RNase H competent domain consisting of 3 or more contiguous substitute linkages selected from the group consisting of phosphorothioate and phosphorodithioate linkages disposed between the nuclease stable domains.

Claim 21

An oligomer of the formula (5); ##STR13## wherein each R 1 is independently H, PO 3 -2 , or a blocking group; each R 3 is independently selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; each X 1 is independently selected from the group consisting of --P(S)(O)--, --P(S)(S)--, --P(O)(O)--, --P(CH 3 )(O)-- and --P(CH 3 )(S)--; n is an integer from 0 to 98; and B is a base, provided that at least one B is of formula (1) or (2): ##STR14## wherein Pr is H or a monovalent or divalent protecting group; W is N or CH; R 2 is aryl, heteroaryl or 1-alkynylheteroaryl; R 8 is OH, SH, a NPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; R 10 is independently H, OH, CN, halogen (F, Cl, Br, I), alkyl (C1-12), alkenyl (C2-12), alkynyl (C2-12), aryl (C6-9), heteroaryl (C4-9), or both R 10 , taken together with the carbon atoms to which they are linked at positions 11 and 12, form (a) a 5 or 6 membered carbocyclic ring or, (b) a 5 or 6 membered heterocyclic ring comprising 1-3 N, O or S ring atoms, provided that no 2 adjacent ring atoms are O--O, S--S, O--S or S--O, and wherein any unsaturated C atom of the carbocyclic or heterocyclic ring is substituted by R 11 and any saturated carbons contain 2 R 11 substituents, wherein; R 11 is independently H, alkyl (C1-4), alkenyl (C2-4), alkynyl (C2-4), OR 12 , SR 12 , or N(R 12 ) 2 or halogen provided that there are no more than four halogens per 5 or 6 member ring; and R 12 is independently H, or alkyl (C1-4).

Claim 22

An oligomer of the formula (5); ##STR13## wherein each R 1 is independently H, PO 3 -2 , or a blocking group; each R 3 is independently selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; each X 1 is independently selected from the group consisting of --P(S)(O)--, --P(S)(S)--, --P(O)(O)--, --P(CH 3 )(O)-- and --P(CH 3 )(S)--; n is an integer from 0 to 98; and B is a base, provided that at least one B is of formula (1) or (2): ##STR14## wherein Pr is H or a monovalent or divalent protecting group; W is N or CH; R 2 is aryl, heteroaryl or 1-alkynylheteroaryl; R 8 is OH, SH, a NPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; R 10 is independently H, OH, CN, halogen (F, Cl, Br, I), alkyl (C1-12), alkenyl (C2-12), alkynyl (C2-12), aryl (C6-9), heteroaryl (C4-9), or both R 10 , taken together with the carbon atoms to which they are linked at positions 11 and 12, form (a) a 5 or 6 membered carbocyclic ring or, (b) a 5 or 6 membered heterocyclic ring comprising 1-3 N, O or S ring atoms, provided that no 2 adjacent ring atoms are O--O, S--S, O--S or S--O, and wherein any unsaturated C atom of the carbocyclic or heterocyclic ring is substituted by R 11 and any saturated carbons contain 2 R 11 substituents, wherein; R 11 is independently H, alkyl (C1-4), alkenyl (C2-4), alkynyl (C2-4), OR 12 , SR 12 , or N(R 12 ) 2 or halogen provided that there are no more than four halogens per 5 or 6 member ring; and R 12 is independently H, or alkyl (C1-4).

Claim 23

The oligomer of claim 20 wherein at least one R 1 is H, PO 3 -2 , DMT, MMT, H-phosphonate, methyl phosphoramidite, methylphosphoramidite, β-cyanoethylphosphoramidite or alkylphosphoramidite.

Claim 24

The oligomer of claim 20 wherein each R 3 is independently H, OH, F or O-allyl.

Claim 25

The oligomer of claim 20 wherein at least one R 3 is O-methyl, O-ethyl or O-propyl.

Claim 26

The oligomer of claim 20 wherein at least one base has the formula (2) and R 10 at position 11 is H and R 10 at position 12 is methyl, R 10 at position 12 is H or R 10 at position 11 is methyl, or R 10 at position 11 is H and R 10 at position 12 is 1-propynyl.

Claim 27

The oligomer of claim 20 wherein at least one base has the formula (2) and both R 10 are taken together with the carbon atoms to which they are linked at positions 11 and 12 to form a 6-membered ring, said base having the formula (23) or (25) ##STR15## wherein each Q is independently N or CR 11 .

Claim 28

The oligomer of claim 20 having a covalent link between the 5'-nucleomonomer and the 3' nucleomonomer whereby a circular oligomer is formed.

Claim 29

The oligomer of claim 20 conjugated to a solid support or label.

Claim 30

The oligomer of claim 20 which is a dimer, trimer, tetramer, pentamer or hexamer.

Claim 31

The oligomer of claim 20 complexed with a cationic lipid.

Claim 32

A method of synthesizing the oligomer of claim 20, comprising the steps of: synthesizing a protected nucleomonomer synthon having a protecting group and a base and further having a coupling group capable of coupling to a nucleomonomer or oligomer; coupling the nucleomonomer synthon to an acceptor nucleomonomer or oligomer; removing the protecting group; and repeating the cycle until said oligomer is synthesized.

Claim 33

The method of claim 30 wherein the coupling group is a phosphoramidite or a hydrogen phosphonate coupling group.

Claim 34

A nucleomonomer having the structural formula (3) or (4): ##STR16## wherein each R 1 is independently H or a blocking group; R 2 is aryl, heteroaryl or 1-alkynylheteroaryl; R 3 is selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; R 8 is OH, SH, NPr, NHPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; R 10 is independently H, OH, CN, halogen (F, Cl, Br, I), alkyl (C1-2), alkenyl (C2-12), alkynyl (C2-12), aryl (C6-9), heteroaryl (C4-9), or both R 10 , taken together with the carbon atoms to which they are linked at positions 11 and 12, form (a) a 5 or 6 membered carbocyclic ring or, (b) a 5 or 6 membered heterocyclic ring comprising 1-3 N, O or S ring atoms, provided that no 2 adjacent ring atoms are O--O, S--S, O--S or S--O, and wherein any unsaturated C atom of the carbocyclic or heterocyclic ring is substituted by R 11 and any saturated carbons contain 2 R 11 substituents, wherein; R 11 is independently H, alkyl (C1-4), alkenyl (C2-4), alkynyl (C2-4), OR 12 , SR 12 , or N(R 12 ) 2 or halogen provided that there are no more than four halogens per 5 or 6 member ring; R 12 is independently H, or alkyl (C1-4); W is CH or N; and Pr is H or a monovalent or divalent protecting group.

Claim 35

A nucleomonomer having the structural formula (3) or (4): ##STR16## wherein each R 1 is independently H or a blocking group; R 2 is aryl, heteroaryl or 1-alkynylheteroaryl; R 3 is selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; R 8 is OH, SH, NPr, NHPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; R 10 is independently H, OH, CN, halogen (F, Cl, Br, I), alkyl (C1-2), alkenyl (C2-12), alkynyl (C2-12), aryl (C6-9), heteroaryl (C4-9), or both R 10 , taken together with the carbon atoms to which they are linked at positions 11 and 12, form (a) a 5 or 6 membered carbocyclic ring or, (b) a 5 or 6 membered heterocyclic ring comprising 1-3 N, O or S ring atoms, provided that no 2 adjacent ring atoms are O--O, S--S, O--S or S--O, and wherein any unsaturated C atom of the carbocyclic or heterocyclic ring is substituted by R 11 and any saturated carbons contain 2 R 11 substituents, wherein; R 11 is independently H, alkyl (C1-4), alkenyl (C2-4), alkynyl (C2-4), OR 12 , SR 12 , or N(R 12 ) 2 or halogen provided that there are no more than four halogens per 5 or 6 member ring; R 12 is independently H, or alkyl (C1-4); W is CH or N; and Pr is H or a monovalent or divalent protecting group.

Claim 36

The nucleomonomer of claim 32 wherein R 3 is hydrogen, hydroxy fluorine, O-methyl or O-allyl.

Claim 37

The nucleomonomer of claim 32 wherein R 1 is a blocking group selected from the group consisting of DMT, MMT, FMOC, phenoxyacetyl, a silyl ether, hydrogen phosphonate, methylphosphonamidite, methylphosphoramidite and β-cyanoethylphosphoramidite.

Claim 38

The nucleomonomer of claim 32 wherein R 1 at the 3' position is selected from the group consisting of hydrogen phosphonate, N,N-diisopropylamino-β-cyanoethoxyphosphine, N,N-diisopropyl-aminomethoxyphosphine, N,N-diethylamino-β-cyanoethoxyphosphine, N,N-morpholino-β-cyanoethoxyphosphine, N,N-morpholino-methoxyphosphine, N,N-diisopropylaminomethyl-phosphonamidite, N,N-diethylaminomethylphosphonamidite, bis-morpholino-phosphine, N,N-dimethylamino-β-cyanoethyl-mercaptophosphine, 2-chlorophenyl phosphate, 4-chlorophenyl phosphate, 2,4-dichlorophenyl phosphate, 2,4-dibromophenyl phosphate, 2-chlorophenyl thiophosphate, 4-chlorophenyl thiophosphate, 2,4-dichlorophenyl thiophosphate, and 2,4-dibromophenyl thiophosphate.

Claim 39

The nucleomonomer of claim 32 having a structure of formula (4) wherein each R 10 is independently H, OH, CN, halogen, alkyl (C1-9), 1-alkenyl (C2-8), 1-alkynyl (C2-8), aryl (C6-7), or heteroaryl (C4-6).

Claim 40

The nucleomonomer of claim 32 of the formula: ##STR17## wherein Q is independently N or CR 11 .

Claim 41

The nucleomonomer of claim 37 wherein R 3 is hydrogen, hydroxy fluorine, or O-allyl.

Claim 42

The nucleomonomer of claim 37 wherein both R 1 are hydrogen and R 3 is hydroxy.

Claim 43

The nucleomonomer of claim 38 wherein both R 1 are hydrogen and R 3 is hydroxy.

Claim 44

The nucleomonomer of claim 37 wherein R 1 is a blocking group selected from the group consisting of DMT, MMT, FMOC, phenoxyacetyl, a silyl ether, hydrogen phosphonate, methylphosphonamidite, methylphosphoramidite and β-cyanoethylphosphoramidite.

Claim 45

The nucleomonomer of claim 37 wherein R 1 at the 3' position is selected from the group consisting of hydrogen phosphonate, N,N-diisopropylamino-β-cyanoethoxyphosphine, N,N-diisopropyl-aminomethoxyphosphine, N,N-diethylamino-β-cyanoethoxyphosphine, N,N-morpholino-β-cyanoethoxyphosphine, N,N-morpholino-methoxyphosphine, N,N-diisopropylaminomethyl-phosphonamidite, N,N-diethylamino-methylphosphonamidite, bis-morpholino-phosphine, N,N-dimethylamino-β-cyanoethyl-mercaptophosphine, 2-chlorophenyl phosphate, 4-chlorophenyl phosphate, 2,4-dichlorophenyl phosphate, 2,4-dibromophenyl phosphate, 2-chlorophenyl thiophosphate, 4-chlorophenyl thiophosphate, 2,4-dichlorophenyl thiophosphate, and 2,4-dibromophenyl thiophosphate.

Claim 46

The nucleomonomer of claim 37 wherein both R 1 are hydrogen and R 3 is hydrogen.

Claim 47

The nucleomonomer of claim 32 wherein both R 1 are hydrogen and R 3 is hydrogen.

Claim 48

An oligomer comprising from 2 to 30 nucleomonomers wherein at least one of said nucleomonomers comprises a base having the formula: ##STR18## wherein Pr is H or a monovalent or divalent protecting group; R 2 is 1-propynyl; R 8 is OH, SH, NPr, NHPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; and W is N or CH and salts thereof.

Claim 49

An oligomer comprising from 2 to 30 nucleomonomers wherein at least one of said nucleomonomers comprises a base having the formula: ##STR18## wherein Pr is H or a monovalent or divalent protecting group; R 2 is 1-propynyl; R 8 is OH, SH, NPr, NHPr or NH 2 ; R 9 is H, OH, SH, NPr, NHPr or NH 2 ; and W is N or CH and salts thereof.

Claim 50

The oligomer of claim 45 wherein adjacent nucleomonomers are linked by linkages or substitute linkages and the oligomer contains at least one substitute linkage.

Claim 51

The oligomer of claim 45 having from 8 to 30 nucleomonomers and uniform polarity.

Claim 52

The oligomer of claim 45 wherein the substitute linkage is selected from the group consisting of phosphoramidate, phosphorothioate, methylphosphonate, riboacetal, 3'-N-methylhydroxylamine, thionomethylphosphonate, phosphorodithioate, 2'-thioformacetal, formacetal, and 3'-thioformacetal.

Claim 53

The oligomer of claim 48 wherein the substitute linkage is selected from the group consisting of phosphorothioate and formacetal.

Claim 54

The oligomer of claim 45 wherein R 8 is OH and R 9 is NH 2 or NHPr.

Claim 55

The oligomer of claim 45 complexed with a cationic lipid.

Claim 56

An oligomer of the formula (5): ##STR19## wherein each R 1 is independently H, PO 3 -2 , or a blocking group; each R 3 is independently selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; each X 1 is independently selected from the group consisting of --P(S)(O)--, --P(S)(S)--, --P(O)(O)--, --P(CH 3 )(O)-- and --P(CH 3 )(S)--; n is an integer from 0 to 98; and B is a base, provided that at least one B is of formula: ##STR20## wherein R 2 is 1-propynyl; R 8 is OH or SH; R 9 is NPr, NHPr or NH 2 ; Pr is H or a monovalent or divalent protecting group; and W is N or CH.

Claim 57

An oligomer of the formula (5): ##STR19## wherein each R 1 is independently H, PO 3 -2 , or a blocking group; each R 3 is independently selected from the group consisting of H, OH, F, NH 2 , OCH 3 , OC 2 H 5 , OC 3 H 7 , SCH 3 , SC 2 H 5 , SC 3 H 7 , OC 3 H 5 , and SC 3 H 5 ; each X 1 is independently selected from the group consisting of --P(S)(O)--, --P(S)(S)--, --P(O)(O)--, --P(CH 3 )(O)-- and --P(CH 3 )(S)--; n is an integer from 0 to 98; and B is a base, provided that at least one B is of formula: ##STR20## wherein R 2 is 1-propynyl; R 8 is OH or SH; R 9 is NPr, NHPr or NH 2 ; Pr is H or a monovalent or divalent protecting group; and W is N or CH.

Claim 58

The oligomer of claim 52 wherein at least one R 1 is H, PO 3 -2 , DMT, MMT, H-phosphonate, methyl phosphonamidite, methylphosphoramidite, β-cyanoethylphosphoramidite or alkylphosphoramidite.

Claim 59

The oligomer of claim 53 wherein each X 1 is --P(S)(O)--.

Claim 60

The oligomer of claim 54 complexed with a cationic lipid.

Claim 61

The oligomer of claim 52 wherein each R 3 is independently H, OH, F or O-allyl.

Claim 62

The oligomer of claim 52 wherein at least one R 3 is O-methyl, O-ethyl or O-propyl.

Claim 63

The oligomer of claim 52 complexed with a cationic lipid.