Nucleotide analogs
The invention provides nucleotide analogs for use in sequencing nucleic acid molecules.
1 . A nucleotide analog having the structure:
wherein X 1 is O or S;
X 2 is OH or PO 4 ;
X 3 is H or OH;
R 1 is D or Q, wherein
D is a detectable moiety, and
Q is a quenching moiety capable of modulating signal produced by a detectable moiety;
where R 1 is D, R 2 is Q capable of modulating signal produced by D,
where R 1 comprises Q, R 2 is D;
X 4 is selected from the group consisting of O, N, and S;
B is selected from the group consisting of a purine, a pyrimidine and derivatives thereof, and
R 2 is linked to B by a cleavable linkage X 5 .
2 . The nucleotide analog of claim 1 , wherein B is selected from the group consisting of cytosine, uracil, thymine, adenine, guanine, and analogs thereof.
3 . The nucleotide analog of claim 1 , wherein the detectable moiety D is selected from the group consisting of fluorescein, BODIPY, EDANS, rhodamine, Cy3, Cy5, and derivatives thereof.
4 . The nucleotide analog of claim 1 , wherein the quenching moiety Q is selected from the group consisting of fluorescein, BODIPY, EDANS, rhodamine, Cy3, Cy5, DABCYL, and derivatives thereof.
5 . The nucleotide analog of claim 1 , wherein the cleavable linkage X 5 is a chemically cleavable linkage.
6 . The nucleotide analog of claim 1 , wherein the chemically cleavable linkage is a disulfide bond.
7 . The nucleotide analog of claim 1 , wherein the cleavable linkage X 5 is a photochemically cleavable linkage.
8 . The nucleotide analog of claim 7 , wherein the photochemically cleavable linkage is selected from the group consisting of o-nitrobenzyl and derivatives thereof.
9 . The nucleotide analog of claim 1 , wherein the cleavable linkage is selected from the group consisting of
and derivatives thereof.
10 . The nucleotide analog of claim 1 , wherein X 1 is S.
11 . The nucleotide analog of claim 1 , wherein X 2 is PO 4 .
12 . The nucleotide analog of claim 10 , wherein X 2 is PO 4 .
13 . A method for nucleic acid sequence determination, comprising the steps of:
a) exposing a target nucleic acid to a primer that is complementary to at least a portion of the target nucleic acid under conditions suitable for hybridizing the primer to the target nucleic acid, a nucleotide analog of claim 1 , and a polymerizing agent, under conditions suitable for extending the primer in a template-dependent manner;
b) detecting incorporation of a nucleotide in each extended primer;
c) treating each hybridized extended primer of b) such that R 2 is removed; and
d) repeating steps a), b) and c), thereby determining the sequence of the target nucleic acid.
14 . The method of claim 13 , R 2 being removed photochemically.
15 . The method of claim 13 , R 2 being removed by treating the hybridized extended primer with a reducing agent.
16 . The method of claim 15 , the reducing agent being selected from the group consisting of dithiothreitol and tris(2-carboxyethyl) phosphine hydrochloride.
17 . The method of claim 15 , further comprising treating the hybridized extended primer with a capping agent.
18 . The method of claim 17 , the capping agent being iodoacetamide.
19 . The method of claim 13 , wherein X 2 is PO 4 , the method further comprising treating the hybridized extended primer of b) with an enzyme to remove said PO 4 , such that the extended primer can be further extended in subsequent steps.
20 . The method of claim 13 , wherein said target nucleic acid is attached to a substrate.
21 . The method of claim 13 , wherein said target nucleic acid is individually optically resolvable.