Patent ID: 7344841

Claim:
A method of sequence-specific amplification of assay signals produced in the analysis of a target nucleic acid sequence, the method permitting real-time monitoring of amplified signal and comprising the following steps: (a) providing a temperature-controlled sample containment device that permits real-time recording of optical assay signals produced within said device, and a temperature control means for controlling the temperature of said device; (b) providing within said sample containment device a set of interrogation probes, said interrogation probes being capable of forming a hybridization complex with a target nucleic acid and being attached to beads, wherein said beads are associated with a chemically or physically distinguishable characteristic that identifies the interrogation probes attached thereto; (c) contacting said interrogation probes with the target sequence to form a hybridization complex between the interrogation probes and the target sequence; (d) contacting said hybridization complex with a second oligonucleotide probe, said second probe comprising a label and capable of being ligated to the interrogation probes contained within the hybridization complex; (e) providing conditions suitable for ligating said second labeled oligonucleotide probe to the interrogation probe; (f) detecting the optical signals from the second labeled probes; and (g) performing one or more annealing-ligating-detecting-denaturing cycles, each cycle increasing the number of ligated probes in arithmetic progression and involving the following steps: (i) providing a first temperature for the formation of the hybridization complex; (ii) providing a second temperature for ligase-catalyzed ligation of the interrogation probe and the second labeled probe to occur to thereby generate a ligation product, wherein ligation is associated with a change in optical signature of beads associated with the ligation product; (iii) imaging and/or recording optical signals from the ligation product thereby permitting real-time monitoring of amplified signal emanating from the ligation product; and (iv) providing a third temperature for denaturing all hybridization complexes.