Synthesis of four-color 3′-O-allyl modified photocleavable fluorescent nucleotides and related methods

1. A method for determining the sequence of a DNA comprising performing the following steps for each residue of the DNA to be sequenced:

(a) contacting the DNA with a DNA polymerase in the presence of (i) a primer and (ii) four fluorescent nucleotide analogues under conditions permitting the DNA polymerase to catalyze DNA synthesis, wherein (1) the nucleotide analogues consist of an analogue of dGTP, an analogue of dCTP, an analogue of dTTP or dUTP, and an analogue of dATP, (2) each nucleotide analogue comprises (i) a base selected from the group consisting of adenine, guanine, cytosine, thymine, or uracil and analogues thereof, (ii) a deoxyribose, (iii) a fluorophore photocleavably attached to the base, and (iv) an allyl moiety bound to the 3′-oxygen of the deoxyribose, so that a nucleotide analogue complementary to the residue being sequenced is bound to the DNA by the DNA polymerase, and (3) each of the four analogues has a predetermined fluorescence wavelength which is different than the fluorescence wavelengths of the other three analogues;

(b) removing unbound nucleotide analogues;

(c) determining the identity of the bound nucleotide analogues; and

(d) following step (c), except with respect to the final DNA residue to be sequenced, (i) chemically cleaving from the bound nucleotide analogue the allyl moiety bound to the 3′-oxygen atom of the deoxyribose and (ii) photocleaving the fluorophore from the bound nucleotide analogue, wherein steps (d)(i) and (d)(ii) can be performed concurrently or in any order, and step (d)(i) is performed using a Pd catalyst at a pH of about 8.8,

thereby determining the sequence of the DNA.

2. The method of claim 1 , wherein chemically cleaving the allyl moiety bound to the 3′-oxygen atom is performed using Na 2 PdCl 4 .

3. The method of claim 1 , wherein the primer is a self-priming moiety.

4. The method of claim 1 , wherein the DNA is bound to a solid substrate.

5. The method of claim 4 , wherein the DNA is bound to the solid substrate via 1,3-dipolar azide-alkyne cycloaddition chemistry.

6. The method of claim 4 , wherein about 1000 or fewer copies of the DNA are bound to the solid substrate.

7. The method of claim 1 , wherein the four fluorescent nucleotide analogues are 3′-O-allyl-dGTP-PC-Bodipy-FL-510, 3′-O-allyl-dATP-PC-ROX, 3′-O-allyl-dCTP-PC-Bodipy-650 and 3′-O-allyl-dUTP-PC-R6G.

8. The method of claim 1 , wherein the DNA polymerase is a 9° N polymerase.

9. The method of claim 1 , wherein in step d) (ii) the fluorophore is photocleaved under near UV radiation (λ˜355 nm).