Single molecule sequencing of captured nucleic acids

A method for obtaining sequence information from a nucleic acid, the method comprising the steps of:

• contacting a sample comprising at least one target nucleic acid and other non-target molecules to at least one sequence-specific capture probe attached to a surface to produce target/probe duplexes;
• separating at least one of the duplexes from the non-target molecules;
• exposing the separated duplexes to at least one labeled nucleotide, wherein the label is attached to a nitrogenous base of the labeled nucleotide, in the presence of a polymerase having reduced exonuclease activity capable of catalyzing addition of the nucleotide to the duplex in a template-dependent manner, wherein the probe acts as a primer;
• and
• detecting incorporation of the nucleotide into the probe portion, thereby obtaining sequence information from the nucleic acid.

A method for obtaining sequence information from a nucleic acid, the method comprising the steps of:

• performing hybrid capture on a sample comprising at least one target nucleic acid and other non-target molecules to produce target/probe duplexes;
• separating at least one of the duplexes from the non-target molecules;
• and performing a sequencing by synthesis reaction on the separated target/probe
• duplexes in the presence of a polymerase having reduced exonuclease activity and at least one labeled nucleotide, wherein the label is attached to a nitrogenous base of the labeled nucleotide, and wherein the probe acts as a primer for the sequencing reaction.