Mass spectrometric methods for sequencing nucleic acids

A method for determining the sequence of a target nucleic acid molecule, comprising:

• a) immobilizing a nucleic acid promoter-containing probe on a solid support, wherein:
• the nucleic acid promoter-containing probe comprises at least 5 nucleotides at the 3′-end of the coding strand that is complementary to a single stranded region at the 3′-end of the target nucleic acid, and a double-stranded portion that comprises the promoter, which is oriented to permit transcription of a hybridized target nucleic acid molecule;
• b) hybridizing the target nucleic acid to the single-stranded portion of the immobilized nucleic acid probe;
• c) transcribing the target nucleic acid with an RNA polymerase to produce a plurality of base-specifically terminated RNA transcripts, wherein the RNA polymerase recognizes the promoter;
• d) determining the molecular weight value of each base-specifically terminated RNA transcript by mass spectrometry;
• and
• e) determining the sequence of the nucleic acid by aligning the base-specifically terminated RNA transcripts according to molecular weight.