Pyrimidine derivatives and oligonucleotides containing same

Claim 2

A compound having the structure (1): ##STR38## and tautomers, solvates and salts thereof, wherein R 1 is an oligonucleotide, a protecting group, a linker or --H; R 2 is A(Z) X1 , wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R 2 is not amine, protected amine, nitro or cyano; R 27 is independently --CH═, --N═, --C(C 1 -C 8 alkyl)═ or --C(halogen)═, but no adjacent R 27 are both --N═, or two adjacent R 27 are taken together to form a ring having the structure, ##STR39## where R a is independently --CH═, --N═, --C(C 1-8 alkyl)═ or --C(halogen)═, but no adjacent R a are both --N═; R 34 is --O--, --S-- or --N(CH 3 )--; and X1 is 1, 2 or 3.

Claim 3

The compound of claim 1 wherein R 2 is --R 2C --R 2D , wherein R 2C is a short spacer chain and R 2D is a hydrogen bond donor moiety or a moiety having a net positive charge of at least about +0.5 at pH 6-8 in aqueous solutions.

Claim 4

The compound of claim 1 wherein R 2 is --R 6 --(CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 , --R 6 --CH 2 --CHR 31 --N(R 3 ) 2 , --R 6 --(R 7 ) v --N(R 3 ) 2 , --R 6 --(CH 2 ) t --N(R 3 ) 2 , --(CH 2 ) 1-2 --O--(CH 2 ) t --N(R 3 ) 2 , ##STR40## R 3 is independently --H, --CH 3 , --CH 2 CH 3 , --(CH 2 ) w --N(R 33 ) 2 or a protecting group, or both R 3 together are a protecting group, or when R 2 is --R 6 --(CH 2 ) t --N(R 3 ) 2 , one R 3 is --H, --CH 3 , --CH 2 CH 3 , a protecting group or --(CH 2 ) w --N(R 33 ) 2 and the other R 3 is --H, --CH 3 , --CH 2 CH 3 , --(CH 2 ) w --N(R 33 ) 2 , --CH(N[R 33 ] 2 )--N(R 33 ) 2 , ##STR41## R 5 is independently H or a protecting group; R 6 is independently --S--, --NR 5 --, --O-- or --CH 2 --; R 7 is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one --CH═CH--, --C.tbd.C-- or --CH 2 --O--CH 2 -- moiety, or R 7 is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single --CH 3 , --CN, ═O, --OH or protected hydroxyl, provided that the carbon atoms in any --CH═CH-- or --CH 2 --O--CH 2 -- moiety are not substituted with ═O, --OH or protected hydroxyl; R 8 is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single --CH 3 , --CN, ═O, --OH or protected hydroxyl, or R 8 is absent; R 28 is independently --CH 2 --, --CH(CH 3 )--, --CH(OCH 3 )--, --CH(OR 5 )-- or --O--, but both are not --O--; R 29 is independently --N--, --N(CH 3 )--, --CH--, --C(CH 3 )--, but both are not --N(CH 3 )--; R 30 is --H or --N(R 3 ) 2 ; R 31 is the side chain of an amino acid; R 33 is independently --H, --CH 3 , --CH 2 CH 3 or a protecting group; R 35 is H, C 1 -C 4 alkyl or a protecting group; R 36 is --H, --CH 3 , --CH 2 CH 3 , a protecting group or an optionally protected monosaccharide; t is 1, 2, 3 or 4, but when R 6 is --O--, --S-- or --NR 5 --, t is 2, 3 or 4; v is independently 0, 1 or 2; and w is independently 1 or 2.

Claim 5

The compound of claim 3 wherein R 2 is --CH 2 --(CH 2 ) t N(R 3 ) 2 , --NR 5 --(CH 2 ) t N(R 3 ) 2 , --S--(CH 2 ) t N(R 3 ) 2 , --O--(CH 2 ) t N(R 3 ) 2 , --O--(CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 , --(CH 2 ) 1-2 --O--(CH 2 ) t N(R 3 ) 2 , --R 6 --CH 2 --CHR 31 --N(R 3 ) 2 , --R 6 --(R 7 ) v --N(R 3 ) 2 , --R 6 --(CH 2 ) t --NR 5 C(NR 5 )(NR 3 ) 2 , or --CH 2 (CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 .

Claim 6

The compound of claim 4 wherein t is 2.

Claim 7

The compound of claim 5 wherein R 3 independently is --H, --CH 3 --C 2 H 5 or a protecting group.

Claim 8

The compound of claim 6 wherein R 2 is --O--(CH 2 ) 2 --NH 2 , --O--(CH 2 ) 3 --NH 2 , --O--(CH 2 ) 2 --N(CH 3 ) 2 , --O--(CH 2 ) 3 --N(CH 3 ) 2 , --O--(CH 2 ) 2 --NHCH 3 , --O--(CH 2 ) 3 --NHCH 3 , --O--CH 2 --CH(CH 3 )--NH 2 , --CH 2 --O--(CH 2 ) 2 --NH 2 , --CH 2 --O--(CH 2 ) 3 --NH 2 or --(CH 2 ) 2 --O--(CH 2 ) 2 --NH 2 .

Claim 9

The compound of claim 3 wherein t is 2 or 3.

Claim 10

The compound of claim 1 wherein R 1 comprises --H, an optionally protected monosaccharide, hydroxyl, phosphate or hydrogen phosphonate.

Claim 11

The compound of claim 1 wherein R 1 is optionally protected 2'-deoxy-R 21 -substituted ribose, 2'-deoxyribose or ribose, wherein R 21 is H, --OH, halogen or a moiety that enhances the nuclease stability of an oligonucleotide containing the optionally protected 2'-deoxy-R 21 -substituted ribose, 2'-deoxyribose or ribose.

Claim 12

The compound of claim 1 having the structure designated by the numbers selected from the group consisting of (104), (105), (133), (134), (111), (112), (113), (115), (135), (136), (137), (138), (139), (120), (121), (121A), (143), (122), (123), (125), or (126): ##STR42## wherein R 1 is an optionally protected monosaccharide; R 2A is --OH; R 5 is independently --H or a protecting group; R 6 is --O--, --S--, --NH-- or --CH 2 --, R 21 is H, --OH, halogen or a moiety that enhances the nuclease stability of an oligonucleotide; R 24 is a halogen; R 27 is independently --CH═, --N═, --C(C 1 -C 8 alkyl)═ or --C(halogen ═, but no adjacent R 27 are both --N═, or two adjacent R 27 are taken together to form a ring having the structure, ##STR43## where R a is independently --CH═, --N═, --C(C 1-8 alkyl)═ or --C(halogen)═, but no adjacent R a are both --N═; R 34 is --O--, --S-- or --N(CH 3 )--; R 37 is --O--, --CH 2 -- or --CF 2 --; R 47 is --O-- or --S--; R 50 is --CH 2 --, --C(O)--, --(CH 2 ) 2 --O--(CH 2 ) 2 --, --(CH 2 ) 2 --NR 5 --(CH 2 ) 2 --, --(CH 2 ) 2 --S--(CH 2 ) 2 --, --CH(N(R 5 ) 2 )--, --CH(COOR 5 )-- or --C(CH 3 )--, --C(C 2 C 5 )-- but adjacent moieties are not C(O); R 52 is --(CHR 52A )--(R 52B )--CHR 52A --, --CHR 52A --O--CHR 52A --, --CHR 52A --S--CHR 52A --, --CHR 52A --NR 5 --CHR 52 A--, C 1 -C 10 alkylene optionally substituted with 1 or 2 moieties selected from the group consisting of C 1 -C 6 alkyl, --OR 5 , ═O, --NO 2 , --N 3 , --CN, --COOR 5 , or --N(R 5 ) 2 , wherein any heteroatom is separated from the nitrogen atoms that R 52 is linked to by one methylene and one or more --CHR 52A --; R 52A is --H or C 1 -C 6 alkyl; R 52B is a bond; R 59 is --R 6 --R 60 --; R 60 is --(CH 2 ) Z3 --(R 61 ) Z1 --(CH 2 ) Z2 --; R 61 is --O--, --S--, --NR 5 --, --C(O)--, --CH 2 --O--CH 2 --, --CH 2 --NR 5 --CH 2 -- or CH 2 --S--CH 2 --; Z1 is 0 or 1; Z2 is 1, 2 or 3; Z3 is 1, 2 or 3; Y is 1, 2, 3 or 4; CBZ is carboxybenzoyl; Fmoc is 9-fluorenylmethoxycarbonyl; iPr is isopropyl; and Ac is acetyl.

Claim 13

The compound of claim 1 wherein R 1 is an oligonucleotide having the structure (2): ##STR44## wherein D is --OH, protected --OH, an oligonucleotide coupling group or a solid support; D 1 is an oligonucleotide coupling group, --OH, protected --OH or a solid support, wherein D 1 is bonded to one 2' or 3' position in the oligonucleotide of structure (2) and the adjacent 2' or 3' position in structure (2) is substituted with R 21 , provided that D and D 1 are not both an oligonucleoide coupling group or they are not both a solid support; R 4 is independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R 4 is bonded to one 2' or 3' position in the structure (2) oligonucleotide and the adjacent 2' or 3' position in structure (2) is substituted with R 21 ; R 21 is independently --H, --OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage; R 37 is independently --O--, --CH 2 --, --CF 2 --; n is an integer from 0 to 98; and B independently is a purine or pyrimidine base or a protected derivative thereof, provided that at least one B is a base of structure (3) ##STR45##

Claim 14

The compound of claim 12 wherein R 4 is independently 3'-O--P(S)(S)--O-5', 3'-O--P(S)(O)--O-5', 3'-O--P(O)(O)--O-5', 3'-O--P(Me)(O)--O-5', 3'-NH--P(O)(O)--O-5', 3'-S--CH 2 --O-5', 2'-S--CH 2 --O-5', 3'-O--CH 2 --O-5', 2'-O--CH 2 --O-5', 3'O--P(Me)(S)--O-5', 3'-CH 2 --N(CH 3 )--O-5', 2'-CH 2 --N(CH 3 )--O-5', or 3'-R 38 --P(N 2 )(O)--O-5', wherein R 38 independently is --O--, --CH 2 -- or --NH--; R 39 is a protecting group; R 40 independently is hydrogen, a protecting group, C 1 -C 12 alkyl optionally substituted with one, or two --O--, --C(O)--, --OC(O)--, --C(O)O--, --OR 42 , --SR 43 , --C(O)NR 39 --, --C(O)N(R 41 ) 2 , --NR 41 --, --N(R 41 ) 2 , halo, --CN, or --NO 2 moieties, or both R 40 together with the nitrogen atom to which they are attached form ##STR46## or both R 40 together are a protecting group; R 41 independently is hydrogen, a protecting group, alkyl (C 1 -C 4 or both R 41 together are a protecting group; R 42 is hydrogen or a protecting group; R 43 is C 1-6 alkyl or a protecting group; and R 45 is --H, a counter ion or ##STR47## R 46 is alkyl containing 1-8 carbon atoms.

Claim 15

The compound of claim 12 wherein R 2 is --R 6 --(CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 , --R 6 --CH 2 --CHR 31 --N(R 3 ) 2 , --R 6 --(R 7 ) v --N(R 3 ) 2 , --R 6 --(CH 2 ) t --N(R 3 ) 2 , --(CH 2 ) 1-2 --O--(CH 2 ) t --N(R 3 ) 2 , ##STR48## R 3 is independently --H, --CH 3 , --CH 2 CH 3 , --(CH 2 ) w --N(R 33 ) 2 or a protecting group, or both R 3 together are a protecting group, or when R 2 is --R 6 --(CH 2 ) t --N(R 3 ) 2 , one R 3 is --H, --CH 2 CH 3 , a protecting group or --(CH 2 ) w --N(R 33 ) 2 and the other R 3 is --H, --CH 3 , --CH 2 CH 3 , --(CH 2 ) w --N(R 33 ) 2 , --CH(N[R 33 ] 2 )--N(R 33 ) 2 , ##STR49## R 5 is independently H or a protecting group; R 6 is independently --S--, --NR 5 --, --O-- or --CH 2 --; R 7 is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one --CH═CH--, --C.tbd.C-- or --CH 2 --O--CH 2 -- moiety, or R 7 is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single --CH 3 , --CN, ═O, --OH or protected hydroxyl, provided that the carbon atoms in any --CH═CH-- or --CH 2 --O--CH 2 -- moiety are not substituted with ═O, --OH or protected hydroxyl; R 8 is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single --CH 3 , --CN, ═O, --OH or protected hydroxyl, or R 8 is absent; R 28 is independently --CH 2 --, --CH(CH 3 )--, --CH(OCH 3 )--, --CH(OR 5 )-- or --O--, but both are not --O--; R 29 is independently --N--, --N(CH 3 )--, --CH--, --C(CH 3 )--, but both are not --N(CH 3 )--; R 30 is --H or --N(R 3 ) 2 ; R 31 is the side chain of an amino acid; R 33 is independently --H, --CH 3 , --CH 2 CH 3 or a protecting group; R 35 is H, C 1 -C 4 alkyl or a protecting group; R 36 is --H, --CH 3 , --CH 2 CH 3 , a protecting group or an optionally protected monosaccharide; t is 1, 2, 3 or 4, but when R 6 is --O--, --S-- or --NR 5 --, t is 2, 3 or 4; v is independently 0, 1 or 2; and w is independently 1 or 2.

Claim 16

The compound of claim 14 wherein R 2 is --CH 2 --(CH 2 ) t N(R 3 ) 2 , --NR 5 --(CH 2 ) t N(R 3 ) 2 , --S--(CH 2 ) t N(R 3 ) 2 , --O--(CH 2 ) t N(R 3 ) 2 , --O--(CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 , --(CH 2 ) 1-2 --O--(CH 2 ) t N(R 3 ) 2 , --R 6 --CH 2 --CHR 31 --N(R 3 ) 2 , --R 6 --(R 7 ) v --N(R 3 ) 2 , --R 6 --(CH 2 ) t --NR 5 C(NR 5 )(NR 3 ) 2 , or --CH 2 (CH 2 ) t NR 5 C(NR 5 )(NR 3 ) 2 .

Claim 17

The compound of claim 15 wherein t is 2 or 3.

Claim 18

The compound of claim 16 wherein R 3 independently is --H, --CH 3 , --C 2 H 5 or a protecting group.

Claim 19

The compound of claim 17 wherein R 2 is --O--(CH 2 ) 2 --NH 2 , --O--(CH 2 ) 3 --NH 2 , --O--(CH 2 ) 2 --N(CH 3 ) 2 , --O--(CH 2 ) 3 --N(CH 3 ) 2 , --O--(CH 2 ) 2 --NHCH 3 , --O--(CH 2 ) 3 --NHCH 3 , --O--CH 2 --CH(CH 3 )--NH 2 , --CH 2 --O--(CH 2 ) 2 --NH 2 , --CH 2 --O--(CH 2 ) 3 --NH 2 or --(CH 2 ) 2 --O--(CH 2 ) 2 --NH 2 .

Claim 20

The compound of claim 12 wherein R 21 is independently --H, --OH, halogen, protected hydroxyl, --O-methyl, --O-ethyl, --O-n-propyl, --O-allyl, --O--(CH 2 ) 2 OH, --O--(CH 2 ) 3 OH, --O--(CH 2 ) 2 F, --O--(CH 2 ) s R 65 , --O--(CH 2 ) 2 --[O--(CH 2 ) 2 ] r R 65 , --O--(CH 2 ) r --O--(CH 2 ) r --O--(CH 2 ) r --R 65 ), --NH-methyl, --NH-ethyl, --NH-n-propyl, --NH--(CH 2 ) 2 OH, --NH--(CH 2 ) 3 OH, --NH--(CH 2 ) s R 65 , --S-methyl, --S-ethyl, --S-n-propyl, --S-allyl, --S--(CH 2 ) 2 OH, --S--(CH 2 ) 3 OH --S--(CH 2 ) 2 F, --S--(CH 2 ) s R 65 , or --S--(CH 2 ) 2 --[O--(CH 2 ) 2 ] r R 65 , wherein R 65 is --H, --F, --OH, --OCH 3 , --NH 2 , --SH, protected hydroxyl, protected amino or protected thiol; r is 1, 2, 3 or 4; and s is 2, 3, 4, 5, 6, 7 or 8.

Claim 21

The compound of claim 19 wherein R 21 is independently --H, --OH, --F, protected hydroxyl, --OCH 3 , --O--CH 2 CH 3 , --O--CH 2 CH 2 OH, --O--CH 2 CH 2 F, --O--CH 2 CH 2 CH 3 , --O--CH 2 CH 2 CH 2 OH, --O--CH 2 CH 2 CH 2 F, --O--CH 2 CF 2 H, --O--CH 2 CF 3 or --O--CH 2 CH 2 --O--CH 3 .

Claim 22

The compound of claim 12 wherein B independently are selected from the group consisting of a base of structure (3), guanosine, adenine, thymine, uracil, cytosine, 5-methylcytosine, 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine, 5-(1-butynyl)uracil therefor 5-(1-butynyl)cytosine.

Claim 23

The compound of claim 12 wherein D 1 is H-phosphonate, a methylphosphonamidite, a β-cyanoethylphosphoramidite or a phosphoramidite.

Claim 24

A compound having the structure (4) ##STR50## and tautomers, solvates and salts thereof wherein, R 1 , R 2 and R 27 have the meanings given in claim 1; R 24 is a halogen; R 25 is --SH, --OH, ═S or ═O.

Claim 25

The compound of claim 23 wherein R 1 is --H or an optionally protected monosaccharide.

Claim 26

The compound of claim 24 wherein the optionally protected monosaccharide is 2'-deoxy-R 21 -substituted ribose, wherein R 21 is H, --OH, halogen or a moiety that enhances the nuclease stability of an oligonucleotide containing the optionally protected 2'-deoxy-R 21 -substituted ribose, 2'-deoxyribose or ribose.

Claim 27

The compound of claim 25 wherein R 21 is --H, --OH, --F, protected hydroxyl, --OCH 3 , --O--CH 2 CH 3 , --O--CH 2 CH 2 OH, --O--CH 2 CH 2 F, --O--CH 2 CH 2 CH 3 , --O--CH 2 CH 2 CH 2 OH, --O--CH 2 CH 2 CH 2 F, --O--CH 2 CF 2 H, --O--CH 2 CF 3 or --O--CH 2 CH 2 --O--CH 3 .

Claim 28

The compound of claim 1 having the structure (1): ##STR51## and tautomers, solvates and salts thereof, wherein R 1 is a protecting group, an oligonucleotide, a nucleic acid, a polysaccharide, an optionally protected monosaccharide, hydroxyl, phosphate, hydrogen phosphonate, halo, azido, protected hydroxyl, or --H; R 2 is A(Z) X1 , but R 2 is not amine, protected amine, nitro or cyano; R 5 is H or a protecting group; R 27 is independently --CH═, --N═, --C(C 1 -C 8 alkyl)═ or --C(halogen)═, but no adjacent R 27 are both --N═, or two adjacent R 27 are taken together to form a ring having the structure, ##STR52## R 34 is --O--, --S-- or --N(CH 3 )--; R a is independently --CH═, --N═, --C(C 1-8 alkyl)═ or --C(halogen)═, but no adjacent R a are both --N═; A is a backbone chain of 2-16 carbon atoms, any 1, 2 or 3 of which are optionally replaced with N, O or S atoms, wherein the backbone chain is optionally substituted independently with 1, 2 or 3 of the following: C 1 -C 8 alkyl, --OR 5 , ═O, --NO 2 , --N 3 , --COOR 5 , --N(R 5 ) 2 , or --CN groups, C 1 -C 8 alkyl substituted with --OH, ═O, --NO 2 , --N 3 , --COOR 5 , --N(R 5 ) 2 , or --CN groups, or any of the foregoing in which --CH 2 -- is replaced with --O--, --NH-- or --N(C 1 -C 8 alkyl); X1 is 1, 2 or 3; Y is H, 2-hydroxypyridine, N-hydroxysuccinimide, p-nitrophenyl, acylimidazole, maleimide, trifluoroacetate, an imido, a sulfonate, an imine 1,2-cyclohexanedione, glyoxal or an alpha-halo ketone; and Z independently is --NH 2 , --CHO, --SH, --CO 2 Y, OY.

Claim 29

The compound of claim 27 wherein Z is bonded to a detectable label.

Claim 30

The compound of claim 27 wherein R 1 is an oligonucleotide.

Claim 31

The compound of claim 27 wherein R 1 is an optionally protected monosaccharide.