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DNA Barcodes Using a Dual Nanopore Device

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DNA Barcoding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2744))

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Abstract

We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781–20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a \( \frac{48500}{2400}\cong 24 \) base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258–5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.

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Acknowledgments

The research has been supported by a subcontract by The Royal Institution for the Advancement of Learning, McGill University, CA, from the parent grant number 1R21HG011236-01 from the National Human Genome Research Institute at the National Institute of Health. The authors thank Arthur Rand and William B. Dunbar from Nooma Bio for sharing the experimental data used in Fig. 2a. All computations were carried out using STOKES High-Performance Computing Cluster at UCF.

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Authors and Affiliations

  1. University of Central Florida, Orlando, FL, USA

    Swarnadeep Seth & Aniket Bhattacharya

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  1. Swarnadeep Seth
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  2. Aniket Bhattacharya
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Correspondence to Aniket Bhattacharya .

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Editors and Affiliations

  1. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA

    Robert DeSalle

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Seth, S., Bhattacharya, A. (2024). DNA Barcodes Using a Dual Nanopore Device. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3581-0_12

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  • DOI: https://doi.org/10.1007/978-1-0716-3581-0_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3580-3

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