Decoding DNA barcodes using a Cylindrical Nanopore*

A cylindrical nanopore device is the simplest experimental setup which can be used to determine the barcodes of a DNA by scanning it multiple times through the nanopore using an alternative voltage bias. We use Brownian dynamics simulation on a model coarse-grained dsDNA to estimate the marker (barcode) locations using the dwell time information. These simulation results provide insights, hard to decipher in an actual experiment. The barcodes introduce non-uniformity in the velocity profile of the monomers. We demonstrate that without accounting for the faster moving DNA segments, the barcode distances will be grossly underestimated if deciphered solely on the basis of the dwell time data for the barcodes. We explain the discrepancies using nonequilibrium tension propagation theory (Sakaue, Phys. E, 1996) and provide a recipe for accurate measurements of the barcodes. Our scheme can readily be generlaized to the multi-nanaopore setups, promising a better degree of reliability in barcodes obtained from the next generation nanopore sequencing devices.