Patent ID: 7705222

Claim:
A system for nucleic acid sequencing comprising: a) a scanning probe microscope; b) a surface comprising microfluidic channels; c) at least two coded probes attached to the surface, the at least two coded probes comprising two or more identifiably different nano-barcodes that can generate different detectable signals and each of the coded probes comprising a probe molecule attached to at least one of the nano-barcodes, wherein the nano-barcodes are selected from the group consisting of carbon nanotubes, fullerenes, submicrometer metallic barcodes, nanoparticles, quantum dots, combinations thereof, and the nano-barcodes made from nano-tag elements; d) one or more target molecules ligated to the at least two coded probes, wherein the coded probes bind to different locations on the target molecules and are adjacent each other on the target molecules, ligated coded probes are formed by ligating the coded probes, and the microfludic channels are configured to align the ligated coded probes such that the ligated coded probes are aligned in the direction of microfluidic flow in the microfluidic channels and organized on the surface by molecular combing; and e) a free-flow electrophoresis device that is configured to align a plurality of coded probes on the surface of a substrate.