Patent ID: 7964352

Claim:
A method of sequencing a target nucleic acid comprising the following steps: (i) attaching the 5′-end of a primer to a solid surface; (ii) hybridizing a target nucleic acid to the primer attached to the solid surface to form a hybridized primer/target nucleic acid complex; (iii) obtaining a polymerase and one or more compounds according to formula I, II, III, IV, V, VI or VII: wherein R 1 =triphosphate; R 2 ═H or OH; R 3 and R 4 are each independently selected from the group consisting of H, a C 1 -C 12 straight chain or branched alkyl, a C 2 -C 12 straight chain or branched alkenyl or polyenyl, a C 2 -C 12 straight chain or branched alkynyl or polyalkynyl, and an aromatic group, with the proviso that at least one of R 3 and R 4 is H; R 5 , R 7 and R 8 are each independently selected from the group consisting of H, OCH 3 , NO 2 , CN, a halide, a C 1 -C 12 straight chain or branched alkyl, a C 2 -C 12 straight chain or branched alkenyl or polyenyl, a C 2 -C 12 straight chain or branched alkynyl or polyalkynyl, and an aromatic group; R 6 is a group of the structure: wherein X═CH 2 , CH═CH, C ≡C, O, S, or NH; Y═CH 2 , O, or NH; n=an integer from 0-12; m=an integer from 0-12; and Dye=a fluorophore, with the proviso that compounds of different formulas I-VII have different fluorophores; (iv) reacting the hybridized primer/target nucleic acid complex with a polymerase and one or more of the compounds of step (iii) to form a growing primer strand via a polymerase reaction; (v) imaging the growing primer strand to identify the incorporated compound of step (iv) via its fluorophore; (vi) exposing the solid surface with the growing primer strand to a light source to remove a photocleavable terminating moiety of the formula: resulting in an extended primer with naturally-occurring components; and (vii) repeating steps (iv) through (vi) one or more times to identify a plurality of bases in the target nucleic acid, where the extended primer of step (vi) of the previous cycle reacts in place of the hybridized primer/target nucleic acid complex in step (iv) of the subsequent cycle.