Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control

We present the first electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA (dsDNA). Previously developed dual-pore "DNA flossing" control generates multiple scans of tagged regions of each captured DNA. The control logic was extended here in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during DNA flossing; and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. New analysis methods were developed to produce consensus alignments from each multi-scan event. The combined multi-scanning and multi-capture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1x across 2,355 resolvable sites (68% of reference sites) of the E. coli genome was achieved after 5.6 hours of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed inter-tag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 inter-site intervals shorter than 200 bp in the E. coli reference map. Proof of concept results on estimating distances in repetitive regions of the E. coli genome are also provided. With an appropriately designed array and future refinements to the control logic, higher throughput implementations can enable human-sized genome and epigenome mapping applications.