Pyrimidine derivatives and oligonucleotides containing same
First Claim
Patent Images
1. A compound having the structure (1):
-
and tautomers, solvates and salts thereof, whereinR1 is an oligonucleotide, a protecting group, a linker or —
H;
R2 is A(Z)X1, wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R2 is not amine NH2, protected amine NH2, nitro or cyano;
R27 is independently —
CH═
, —
N═
, —
C(C1-C8 alkyl)═
or —
C(halogen)═
, but no adjacent R27 are both —
N═
, or two adjacent R27 are taken together to form a ring having the structure, wherein Ra is independently —
CH═
, —
N═
, —
C(C1-8alkyl)═
or —
C(halogen)═
, but no adjacent Ra are both —
N═
;
R34 is —
O—
, —
S—
or —
N(CH3)—
; and
X1 is 1, 2 or 3.
1 Assignment
0 Petitions
Accused Products
Abstract
Compounds having structure (1)
wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.
-
Citations
30 Claims
-
1. A compound having the structure (1):
-
and tautomers, solvates and salts thereof, wherein R1 is an oligonucleotide, a protecting group, a linker or —
H;
R2 is A(Z)X1, wherein A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R2 is not amine NH2, protected amine NH2, nitro or cyano;
R27 is independently —
CH═
, —
N═
, —
C(C1-C8 alkyl)═
or —
C(halogen)═
, but no adjacent R27 are both —
N═
, or two adjacent R27 are taken together to form a ring having the structure,wherein Ra is independently —
CH═
, —
N═
, —
C(C1-8alkyl)═
or —
C(halogen)═
, but no adjacent Ra are both —
N═
;R34 is —
O—
, —
S—
or —
N(CH3)—
; and
X1 is 1, 2 or 3. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30)
wherein R1 is an optionally protected monosaccharide;
R2A is —
OH;
R5 is independently —
H or a protecting group;
R6 is —
O—
, —
S—
, —
NH—
or —
CH2—
,R21 is H, —
OH, halogen or a moiety that enhances the nuclease stability of an oligonucleotide;
R24 is a halogen;
R27 is independently —
CH═
, —
N═
, —
C(C1-C8alkyl)═
or —
C(halogen ═
—
C(halogen)═
, but no adjacent R27 are both —
N═
, or two adjacent R27 are taken together to form a ring having the structure,where Ra is independently —
CH═
, —
N═
, —
C(C1-8alkyl)═
or —
C(halogen)═
, but no adjacent Ra are both —
N═
;R34 is —
O—
, —
S—
or —
N(CH3)—
;
R37 is —
O—
, —
CH2—
or —
CF2—
;
R47 is —
O—
or —
S—
;
R50 is —
CH2—
, —
C(O)—
, —
(CH2)—
O—
(CH2)2—
—
(CH2)2—
O—
(CH2)2—
, —
(CH2)2—
NR5—
(CH2)2—
, —
(CH2)2—
S—
(CH2)2—
, —
CH(N(R5)2)—
, —
CH(COOR5)—
or —
C(CH3)—
, —
C(C2C5)—
but adjacent moieties are not C(O);
R52 is —
(CHR52A)—
(R52B)—
CHR52A—
, —
CHR52A—
O—
CHR52A—
, —
CHR52A—
S—
CHR52A—
, —
CHR52A—
NR5—
CHR52A—
, C1-C10 alkylene optionally substituted with 1 or 2 moieties selected from the group consisting of C1-C6 alkyl, —
OR5, ═
O, —
NO2, —
N3, —
CN, —
COOR5, or —
N(R5)2, wherein any heteroatom is separated from the nitrogen atoms that R52 is linked to by one methylene and one or more —
CHR52A—
;
R52A is —
H or C1-C6 alkyl;
R52B is a bond;
R59 is —
R6—
R60—
;
R60 is —
(CH2)Z3—
(R61)Z1—
(CH2)Z2—
;
R61 is —
O—
, —
S—
, —
NR5—
, —
C(O)—
, —
CH2—
O—
CH2—
, —
CH2—
NR5—
CH2—
or CH2—
S—
CH2—
;
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.
-
-
12. The compound of claim 1 wherein R1 is an oligonucleotide having the structure (2):
-
wherein D is —
OH, protected —
OH, an oligonucleotide coupling group or a solid support;
D1 is an oligonucleotide coupling group, —
OH, protected —
OH or a solid support, wherein D1 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 R21, provided that D and D1 are not both an oligonucleotide coupling group or they are not both a solid support;
R4 is independently a phosphodiester linkage or a phosphodiester substitute linkage, wherein R4 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 R21;
R21 is independently —
H, —
OH, halogen or a moiety that enhances the oligonucleotide against nuclease cleavage;
R37 is independently —
O—
, —
CH2—
, —
CF2—
;
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)
-
-
13. The compound of claim 12 wherein R4 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—
CH2—
O-5′
, 2′
-S—
CH2—
O-5′
, 3′
-O—
CH2—
O-5′
, 2′
-O—
CH2—
O-5′
, 3′
O—
P(Me)(S)—
O-5′
, 3′
-CH2—
N(CH3)—
O-5′
, 2′
-CH2—
N(CH3)—
O-5′
, or 3′
-R38—
P(N2)(O)—
O-5′
, whereinR38 independently is —
O—
, —
CH2—
or —
NH—
;
R39 is a protecting group;
.R40 independently is hydrogen, a protecting group, C1-C12 alkyl optically substituted with one, or two —
O—
, —
C(O)—
, —
OC(O)—
, —
C(O)O—
, —
OR42, —
SR43, —
C(O)NR39, —
C(O)N(R41)2, —
NR41—
, —
N(R41)2, halo, —
CN, or —
NO2 moieties, or both R40 together with the nitrogen atom to which they are attached formor both R40 together are a protecting group; R41 independently is hydrogen, a protecting group, alkyl (C1-C4 or both R41 together are a protecting group;
R42 is hydrogen or a protecting group;
R43 is C1-6 alkyl or a protecting group; and
R45 is —
H, a counter ion orR46 is alkyl containing 1-8 carbon atoms.
- -O—
-
14. The compound of claim 12 wherein R2 is —
- R6—
(CH2)tNR5C(NR5)(NR3)2, —
R6—
(CH2)tNR5C(NR5)N(R3)2, —
R6—
CH2—
CHR31—
N(R3)2, —
R6—
(R7)v—
N(R3)2, —
R6—
(CH2)t—
N(R3)2, —
(CH2)1-2—
O—
(CH2)t—
N(R3)2,R3 is independently —
H, —
CH3, —
CH2CH3, —
(CH2)w—
N(R33)2 or a protecting group, or both R3 together are a protecting group, or when R2 is —
R6—
(CH2)t—
N(R3)2 —
R6—
(CH2)t—
N(R33)2, one R3 is —
H, —
CH2CH3, a protecting group or —
(CH2)w—
N(R33)2 and the other R3 is —
H, —
CH3, —
CH2CH3, —
(CH2)w—
N(R33)2, —
CH(N[R33]2)—
N(R33)2,R5 is independently H or a protecting group;
R6 is independently —
S—
, —
NR5—
, —
O—
or —
CH2—
;
R7 is independently linear alkyl having 1, 2, 3 or 4 carbon atoms optionally substituted with one —
CH═
CH—
, —
C≡
C—
or —
CH2—
O—
CH2—
moiety, or R7 is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single —
CH3, —
CN, ═
O, —
OH or protected hydroxyl, provided that the carbon atoms in any —
CH═
CH—
or —
CH2—
O—
CH2—
moiety are not substituted with ═
O, —
OH or protected hydroxy;
R8 is linear alkylene having 1 or 2 carbon atoms wherein one alkylene carbon atom is optionally substituted with a single —
CH3, —
CN, ═
O, —
OH or protected hydroxyl, or R8 is absent;
R28 is independently —
CH2—
, —
CH(CH3)—
, —
CH(OCH3)—
, —
CH(OR5)—
or —
O—
, but both are not —
O—
;
R29 is independently —
N—
, —
N(CH3)—
, —
CH—
, —
C(CH3)—
, but both are not —
N(CH3)—
;
R30 is —
H or —
N(R3)2;
R31 is the side chain of an amino acid;
R33 is independently —
H, —
CH3, —
CH2CH3 or a protecting group;
R35 is H, C1-C4 alkyl or a protecting group;
R36 is —
H, —
CH3, —
CH2CH3, a protecting group or an optionally protected monosaccharide;
t is 1, 2, 3 or 4, but when R6 is —
O—
, —
S—
or —
NR5—
, t is 2, 3 or 4;
v is independently 0, 1 or 2; and
w is independently 1 or 2.
- R6—
-
15. The compound of claim 14 wherein R2 is —
- CH2—
(CH2)tN(R3)2, —
NR5—
(CH2)tN(R3)2, —
S—
(CH2)tN(R3)2, —
O—
(CH2)tN(R3)2, —
O—
(CH2)tNR5C(NR5)(NR3)2, —
O—
(CH2)tNR5C(NR5)N(R3)2, —
(CH2)1-2—
O—
(CH2)tN(R3)2, —
R6—
CH2—
CHR31—
N(R3)2, —
R6—
(R7)v—
N(R3)2, —
R6—
(CH2)t—
NR5C(NR5)(NR3)2, —
R6—
(CH2)tNR5C(NR5)N(R3)2, or —
CH2—
(CH2)tNR5C(NR5)(NR3)2. —
CH2—
(CH2)tNR5C(NR5)N(R3)2.
- CH2—
-
16. The compound of claim 15 wherein t is 2 or 3.
-
17. The compound of claim 16 wherein R3 independently is —
- H, —
CH3, —
C2H5 or a protecting group.
- H, —
-
18. The compound of claim 17 wherein R2 is —
- O—
(CH2)2—
NH2, —
O—
(CH2)3—
NH2, —
O—
(CH2)2—
N(CH3)2, —
O—
(CH2)3—
N(CH3)2, —
O—
(CH2)2—
NHCH3, —
O—
(CH2)3—
NHCH3, —
O—
CH2—
CH(CH3)—
NH2, —
CH2—
O—
(CH2)2—
NH2, —
CH2—
O—
(CH2)3—
NH2 or —
(CH2)2—
O—
(CH2)2—
NH2.
- O—
-
19. The compound of claim 12 wherein R21 is independently —
- H, —
OH, halogen, protected hydroxyl, —
O-methyl, —
O-ethyl, —
O-n-propyl, —
O-allyl, —
O—
(CH2)2OH, —
O—
(CH2)3OH, —
O—
(CH2)2F, —
O—
(CH2)sR65, —
O—
(CH2)2—
[O—
(CH2)2]r—
R65, —
O—
(CH2)r—
O—
(CH2)r—
O—
(CH2)r—
R65) —
O—
(CH2)t—
O—
(CH2)r—
O—
(CH2)r—
R65, —
NH-methyl, —
NH-ethyl, —
NH-n-propyl, —
NH—
(CH2)2OH, —
NH—
(CH2)3OH, —
NH—
(CH2)sR65, —
S-methyl, —
S-ethyl, —
S-n-propyl, —
S-allyl, —
S—
(CH2)2OH, —
S—
(CH2)3OH —
S—
(CH2)2—
F, —
S—
(CH2)s—
R65, or —
S—
(CH2)2—
[O—
(CH2)2]rR65, whereinR65 is —
H, —
F, —
OH, —
OCH3, —
NH2, —
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.
- H, —
-
20. The compound of claim 19 wherein R21 is independently —
- H, —
OH, —
F, protected hydroxyl, —
OCH3, —
O—
CH2CH3, —
O—
CH2CH2OH, —
O—
CH2CH2F, —
O—
CH2CH2CH3, —
O—
CH2CH2CH2OH, —
O—
CH2CH2CH2F, —
O—
CH2CF2H, —
O—
CH2CF3 or —
O—
CH2CH2—
O—
CH3.
- H, —
-
21. 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 therefore 5-(1-butynyl)cytosine.
-
22. The compound of claim 12 wherein D1 is H-phosphonate, a methylphosphonamidite, a β
- -cyanoethylphosphoramidite or a phosphoramidite.
-
23. A compound having the structure (4)
and tautomers, solvates and salts thereof wherein, R1, R2 and R27 have the meanings given in claim 1; -
R24 is a halogen;
R25 is —
SH, —
OH, ═
S or ═
O.
-
-
24. The compound of claim 23 wherein R1 is —
- H or an optionally protected monosaccharide.
-
25. The compound of claim 24 wherein the optionally protected monosaccharide is 2′
- -deoxy-R21-substituted ribose, wherein R21 is H, —
OH, halogen or a moiety that enhances the nuclease stability of an oligonucleotide containing the optionally protected 2′
-deoxy-R21-substituted ribose, 2′
-deoxyribose or ribose.
- -deoxy-R21-substituted ribose, wherein R21 is H, —
-
26. The compound of claim 25 wherein R21 is —
- H, —
OH, —
F, protected hydroxyl, —
OCH3, —
O—
CH2CH3, —
O—
CH2CH2OH, —
O—
CH2CH2F, —
O—
CH2CH2CH3, —
O—
CH2CH2CH2OH, —
O—
CH2CH2CH2F, —
O—
CH2CF2H, —
O—
CH2CF3 or —
O—
CH2CH2—
O—
CH3.
- H, —
-
27. The compound of claim 1 having the structure (1):
-
and tautomers, solvates and salts thereof, wherein R1 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;
R2 is A(Z)X1, but R2 is not amine, protected amine, nitro or cyano;
R5 is H or a protecting group;
R27 is indepedently —
CH═
, —
N═
, —
C(C1-C8alkyl)═
or —
C(halogen)═
, but no adjacent R27 are both —
N═
, or two adjacent R27 are taken together to form a ring having the structure,R34 is —
O—
, —
S—
or —
N(CH3)—
;
Ra is independently —
CH═
, —
N═
, —
C(C1-8 alkyl)═
or —
C(halogen)═
, but no adjacent Ra 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;
C1-C8 alkyl, —
OR5, ═
O, —
NO2, —
N3, —
COOR5, —
N(R5)2, or —
CN groups, C1-C8 alkyl substituted with —
OH, ═
O, —
NO2, —
N3, —
COOR5, —
N(R5)2, or —
CN groups, or any of the foregoing in which —
CH2—
is replaced with —
O—
, —
NH—
or —
N(C1-C8 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 —
NH2, —
CHO, —
SH, —
CO2Y, OY.
-
-
28. The compound of claim 27 wherein Z is bonded to a detectable label.
-
29. The compound of claim 27 wherein R1 is an oligonucleotide.
-
30. The compound of claim 27 wherein R1 is an optionally protected monosaccharide.
Specification