Massive parallel method for decoding DNA and RNA

A method for sequencing a nucleic acid which comprises detecting the identity of a nucleotide analogue incorporated into the end of a growing strand of DNA in a polymerase reaction, wherein the nucleotide analogue is any of the following:

• wherein R (a) represents a small, chemically cleavable, chemical group capping the oxygen at the 3′ position of the deoxyribose of tl deoxyribonucleotide analogue, (b) does not interfere with recognition of the analogue as a substrate by a DNA polymerase, (c) is stable during a DNA polymerase reaction, and (d) does not contain a ketone group;
• wherein OR is not a methoxy group or an ester group;
• wherein the covalent bond between the 3′-oxygen and R is stable during a DNA polymerase reaction;
• wherein tag represents a detectable fluorescent moiety;
• wherein Y represents a chemically cleavable, chemical linker which (a) does not interfere with recognition of the analogue as a substrate by a DNA polymerase and (b) is stable during a DNA polymerase reaction;
• wherein the nucleotide analogue:
• i) is recognized as a substrate by a DNA polymerase,
• ii) is incorporated at the end of a growing strand of DNA during a DNA polymerase reaction,
• iii) produces a 3′-OH group on the deoxyribose upon cleavage of R, and
• iv) no longer includes a tag on the base upon cleavage of Y;
• and wherein if the nucleotide analogue is:
• (A), it is capable of forming hydrogen bonds with cytosine or a cytosine nucleotide analogue;
• (B), it is capable of forming hydrogen bonds with thymine or a thymine nucleotide analogue;
• (C), it is capable of forming hydrogen bonds with guanine or a guanine nucleotide analogue;
• or (D), it is capable of forming hydrogen bonds with adenine or an adenine nucleotide analogue.