Decoding DNA Barcodes using a Double-Nanopore System

DNA barcode detection has imporatnt applications in conservation biology, taxonomy research, identifying disease vectors, authenticating herbal products, and unambiguously labeling food specimens. Recent experiments (Dekker et al., Nano Lett. 2016; X. Liu et al., Small 2019) explored the possibilities of determining sequences with greater accuracy by ``flossing” the DNA multiple times through multi-nanopore systems. We use Brownian dynamics simulation to study a model coarse-grained dsDNA threading through a double-nanopore setup. Several markers/tags are annexed along the dsDNA replicating the barcodes studied experimantally. The DNA segment containing the barcodes is scanned several hundred times using an alternating bias present in each pore. The separation among the markers (barcodes) is calculated using the velocity and time of arrival of the markers in respective pores during the chain’s motion from left to right pore and vice versa. However, our studies clearly show that a straight forward method underestimates barcode separation due to chain’s non-monotonic velocity profile. We propose alternative method to rectify this which we believe is relevant for experiments.