Flossing DNA in a Dual Nanopore Device

Abstract

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single molecule data. Here we present an active control technique termed \"flossing\" that uses a dual nanopore device to trap a protein-tagged DNA molecule and perform up to 100s of back-and-forth electrical scans of the molecule in a few seconds. The protein motifs bound to 48 kb{lambda} DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multi-scan data to produce averaged inter-tag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.