Patent ID: 8790873

Claim:
A method for detecting a plurality of target nucleic acids from a nucleic acid sample, comprising: a) contacting a DNA array-bound probe with: (i) a DNA interrogation probe, and (ii) an RNA nucleic acid sample comprising at least one target nucleic acid, wherein the array-bound probe and the interrogation probe hybridize to the target nucleic acid such that the 3′ end of the array-bound probe and the 5′ end of the interrogation probe are directly adjacent to one another and ligatable by DNA ligase, and wherein the interrogation probe contains a detectable label; b) adding an effective amount of ATP to a solution of at least two different DNA ligase enzymes, thereby charging the at least one of the at least two different DNA ligase enzymes to form a DNA ligase-AMP intermediate complex, wherein the at least two different DNA ligase enzymes comprise at least a first ligase which when charged to form a DNA ligase-AMP intermediate complex possesses activity to form a 5′ to 5′ pyrophosphate bond on the interrogation probe 5′ terminus, and at least a second ligase which is a mutant ligase unable to form a DNA ligase-AMP intermediate complex, but which possesses an activity of forming a covalent phosphodiester bond from the 5 ′ to 5 ′ pyrophosphate bond of the interrogation probe and the 3′ hydroxyl terminus of the array-bound probe; c) depleting ATP from the solution of at least two different DNA ligase enzymes; d) adding the solution of at least two different DNA ligase enzymes to step a), thereby ligating the 3′ end of the array-bound probe to the 5′ end of the interrogation probe; and e) detecting the ligated product.