Modified nucleotides
First Claim
1. A modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3′
- -OH blocking group covalently attached thereto, such that the 3′
carbon atom has attached a group of the structure
—
O-Z wherein Z is any of —
C(RIV)2—
O—
R″
, —
C(R′
)2—
N(R″
)2, —
C(R′
)2—
N(H)R″
, —
C(RIV)2—
S—
R″ and
—
C(R″
)2—
F, wherein —
C(RIV)2—
O—
R″
is of the formula —
CR4(R5)—
O—
CR4(R5)—
OR6 or of the formula —
CR4(R5)—
O—
CR4(R5)—
SR6; and
wherein —
C(RIV)2—
S—
R″
is of the formula —
CR4(R5)—
S—
CR4(R5)—
OR6 or of the formula —
CR4(R5)—
S—
CR4(R5)—
SR6;
wherein each R″
is or is part of a removable protecting group;
each R′
is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group;
or (R′
)2 represents an alkylidene group of formula ═
C(R′
″
)2 wherein each R′
″
may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups;
each R4 and R5 is independently a hydrogen atom or an alkyl group;
R6 is alkyl, cycloalkyl, alkenyl, cycloalkenyl or benzyl; and
wherein said molecule may be reacted to yield an intermediate in which each R″
is exchanged for H or, where Z is —
C(R′
)2—
F, the F is exchanged for OH, SH or NH2, preferably OH, which intermediate dissociates under aqueous conditions to afford a molecule with a free 3′
OH;
with the proviso that where Z is —
C(RIV)2—
S—
R″
, both RIV groups are not H.
2 Assignments
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Accused Products
Abstract
The invention provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3′-OH blocking group covalently attached thereto, such that the 3′ carbon atom has attached a group of the structure —O-Z wherein Z is any of —C(R′)2-O—R″, —C(R′)2-N(R″)2, —C(R′)2-N(H)R″, —C(R′)2-S—R″ and —C(R′)2-F, wherein each R″ is or is part of a removable protecting group; each R′ is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; or (R′)2 represents an alkylidene group of formula ═C(R′″)2 wherein each R′″ may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and wherein said molecule may be reacted to yield an intermediate in which each R″ is exchanged for H or, where Z is —C(R′)2-F, the F is exchanged for OH, SH or NH2, preferably OH, which intermediate dissociates under aqueous conditions to afford a molecule with a free 3′OH; with the proviso that where Z is —C(R′)2-S—R″, both R′ groups are not H.
381 Citations
55 Claims
-
1. A modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3′
- -OH blocking group covalently attached thereto, such that the 3′
carbon atom has attached a group of the structure
—
O-Zwherein Z is any of —
C(RIV)2—
O—
R″
, —
C(R′
)2—
N(R″
)2, —
C(R′
)2—
N(H)R″
, —
C(RIV)2—
S—
R″ and
—
C(R″
)2—
F,wherein —
C(RIV)2—
O—
R″
is of the formula —
CR4(R5)—
O—
CR4(R5)—
OR6 or of the formula —
CR4(R5)—
O—
CR4(R5)—
SR6; and
wherein —
C(RIV)2—
S—
R″
is of the formula —
CR4(R5)—
S—
CR4(R5)—
OR6 or of the formula —
CR4(R5)—
S—
CR4(R5)—
SR6;
wherein each R″
is or is part of a removable protecting group;
each R′
is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group;
or (R′
)2 represents an alkylidene group of formula ═
C(R′
″
)2 wherein each R′
″
may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups;
each R4 and R5 is independently a hydrogen atom or an alkyl group;
R6 is alkyl, cycloalkyl, alkenyl, cycloalkenyl or benzyl; and
wherein said molecule may be reacted to yield an intermediate in which each R″
is exchanged for H or, where Z is —
C(R′
)2—
F, the F is exchanged for OH, SH or NH2, preferably OH, which intermediate dissociates under aqueous conditions to afford a molecule with a free 3′
OH;
with the proviso that where Z is —
C(RIV)2—
S—
R″
, both RIV groups are not H.- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50)
- -OH blocking group covalently attached thereto, such that the 3′
-
12. A nucleoside, nucleotide or polynucleotide molecule of formula PN—
- O-allyl, wherein PN is said nucleoside or nucleotide or is a 3′
terminal nucleotide of said polynucleotide;
and said nucleoside or nucleotide further comprises in addition to the allyl blocking group a detectable label linked to the base thereof by a cleavable or non-cleavable linker. - View Dependent Claims (13, 14, 15, 51, 52, 53, 54)
- O-allyl, wherein PN is said nucleoside or nucleotide or is a 3′
-
16. A method of converting a compound of formula R—
- O-allyl, R2N(allyl), RNH(allyl), RN(allyl)2 or R—
S-allyl to a corresponding compound in which the allyl group is removed and replaced by hydrogen, said method comprising the steps of reacting a compound of formula R—
O-allyl, R2N(allyl), RNH(allyl), RN(allyl)2 or R—
S-allyl in aqueous solution with a transition metal comprising a transition metal and one or more ligands selected from the group comprising water-soluble phosphine and water-soluble nitrogen-containing phosphine ligands, wherein the or each R is a water-soluble biological molecule. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
- O-allyl, R2N(allyl), RNH(allyl), RN(allyl)2 or R—
-
49. (canceled)
-
55. (canceled)
Specification