Sequencing by incorporation

A method for sequencing a nucleic acid, the method comprising:

• (i) providing a nucleic acid template and a primer;
• (ii) incubating the nucleic acid template and the primer with a polymerase and one or more nucleotide analogs having formula (III),
• thereby adding at least one of the one or more nucleotide analogs to the primer, resulting In an extended primer, wherein R1 comprises a nucleoside, a nucleotide, a nucleatide analog, or a nucleoside analog, R2 comprises a chain terminating blocking group, which blocking group comprises a detectable label, and R3 comprises a hydrogen or a negative charge, and wherein R2 comprises a compound having formula (V) or formula (VI);
• wherein R4 comprises one or more of a linker moiety and the detectable label:
• (iii) detecting the detectable label, thereby detecting the at least one of the one or more nucleotide analogs and removing the blocking group from the extended primer;
• or, removing the blocking group from the extended primer and detecting the detectable label, thereby detecting the at least one of the one or more nucleotide analogs;
• (iv) removing a 3′-phosphate from the extended primer, thereby producing an extendable primer;
• and,
• (v) repeating steps (ii) through (v), thereby sequencing the nucleic acid template.