Genome Mapping using a Dual Nanopore Device*

We have developed a dual nanopore device that features feedback-driven dynamic control over single translocating dsDNA.  In this device, active control logic “catches molecules in the act” of translocating between two closely separated pores.  The molecules are halted in a “tug-of-war” configuration whereby a molecule experiences competing electrophoretic forces generated by the two pores.   The control logic is then used to dynamically adjust the opposing forces to scan the DNA molecule back and forth (“DNA flossing”).  We will discuss recent new results from our dual-pore system and accompanying simulations, including improvements such as zoom scanning and recapture protocols that enable acquisition of a tremendous degree of statistics from a captured single labeled DNA.  We will next discuss bioinformatic approaches that enable alignment of single-molecule dual-pore scans and construction of consensus alignments with application to intermediate size genomes, such as E. Coli.