Multi-scanning of single DNA Molecules in a Dual Nanopore Device

Single-molecule techniques can access to biomolecular information that is otherwise masked by ensemble averaging, and that can lead to new research discoveries or clinically applications. Solid-state nanopores offer a compact and electrical single-molecule sensing approach. However, single reads of molecules taken with solid-state nanopores generally do not possess sufficient quality for applications that otherwise require alignment of multiple reads of molecules from heterogeneous samples. Here we present a single-molecule manipulation and sensing approach based on a dual nanopore device that can linearize DNA and improve read quality by enabling repeated scanning at reduced speeds of the same molecule. A DNA molecule is first co-captured by the two pores with unbalanced voltage forces applied at the pores (tug-of-war state), and then repeatedly scanned back-and-forth by automated voltage control logic. The method enables detection of sequence-specific protein tags that are used for triggering the motion control during dual current sensing. We have achieved up to 100's of scans, and analysis of multiple scans from a single molecule demonstrates a reproducible binding pattern, or molecular barcode, with tag spacings corresponding to expected sequence positions of the tags.