Chain terminators, the use thereof for nucleic acid sequencing and synthesis and a method of their preparation
First Claim
1. A compound of the structure I:
- Or a salt thereof, whereinB is a nucleobase, X and Z independently are oxygen or sulphur, Y is hydrogen or a protected or unprotected hydroxy, R1 is hydrocarbyl, which optionally is substituted with a functional group selected from the group consisting of tertiary amino, nitro, cyano and halogen, R2 is hydrogen hydrocarbyl, which optionally is substituted with a functional group selected from the group consisting of tertiary amino, nitro, cyano and halogen, A is an electron withdrawing or electron donating group capable of moderating the acetyl stability of the compound I, L1 and L2 are hydrocarbon linkers, which may be the same or different, L2, when present, being either (I) connected to L1 via the group A, or (ii) directly connected to L1, the group A then being connected to one of linkers L1 and L2, F is a dye label, Q is a coupling group for F, and l, m and n independently are 0 or 1, with the proviso that l is 1 when m is 1, and l is 1 and m is 1 when n is 1.
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Accused Products
Abstract
The invention relates to compounds of general structure (I) or salts thereof, wherein B is a nucleobase, X and Z independently are oxygen or sulphur, Y is hydrogen or hydroxy, which optionally may be protected, R1 is hydrocarbyl, which optionally is substituted with a functional group, R2 is hydrogen or hydrocarbyl, which optionally is substituted with a functional group, A is an electron withdrawing or electron donating group capable of moderating the acetal stability of compound (I), L1 and L2 are hydrocarbon linkers, which may be the same or different, L2, when present, being either (i) connected to L1 via the group A, or (ii) directly connected to L1, the group A then being connected to one of linkers L1 and L2, F is a dye label, Q is a coupling group for F, and l, m and n independently are 0 or 1, with the proviso that l is 1 when m is 1, and l is 1 and m is 1 when n is 1. The compounds of formula (I) are useful as deactivatable chain extension terminators. The invention also relates to the use of the compounds (I) in nucleic acid synthesis and nucleic acid sequencing as well as to a method of preparing compounds of Formula (I).
164 Citations
15 Claims
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1. A compound of the structure I:
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Or a salt thereof, wherein B is a nucleobase, X and Z independently are oxygen or sulphur, Y is hydrogen or a protected or unprotected hydroxy, R1 is hydrocarbyl, which optionally is substituted with a functional group selected from the group consisting of tertiary amino, nitro, cyano and halogen, R2 is hydrogen hydrocarbyl, which optionally is substituted with a functional group selected from the group consisting of tertiary amino, nitro, cyano and halogen, A is an electron withdrawing or electron donating group capable of moderating the acetyl stability of the compound I, L1 and L2 are hydrocarbon linkers, which may be the same or different, L2, when present, being either (I) connected to L1 via the group A, or (ii) directly connected to L1, the group A then being connected to one of linkers L1 and L2, F is a dye label, Q is a coupling group for F, and l, m and n independently are 0 or 1, with the proviso that l is 1 when m is 1, and l is 1 and m is 1 when n is 1. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
ar a salt thereof, wherein B, X, Z, R1, R2, Q, F, m and n are as defined in claim 1, and p and q independently are integers from 1 to 10, by reacting a compound of Formula II;
or a salt thereof, wherein B and X are as defined above, with a compound of Formula III;
wherein R1, R2, Z and p are as defined above, and R3 is hydrocarbyl, to produce a compound of Formula IV;
or a salt thereof, wherein B, X, Z, R1, R2, R3 and p are as defined above, optionally reacting the latter with a diamine H2N—
(CH2)q—
NH2, wherein q is as defined above, to produce a compound of Formula V;
wherein B, X, Z, R1, R2, p and q are as defined above, and optionally coupling a dye label F to the terminal amino group.
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14. A method of synthesizing nucleic acid oligo or polynucleotides comprising adding a compound of claim 1 to a nucleic acid synthesis reaction under conditions effective to incorporate said compound into said oligo-or polynucleotide.
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15. The compound according to claims 1 or 2, wherein said halogen is selected from the group consisting of fluoride, chloride, bromide, and iodide.
Specification