Automation of a single-DNA molecule stretching device

Kristian Tølbøl Sørensen, Joanna M. Lopacinska, Niels Tommerup, Asli Silahtaroglu, Anders Kristensen, Rodolphe Marie

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    Abstract

    We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free flowing in micro- and nanofluidics emit low fluorescence and change shape, thus challenging the image analysis for machine vision. We demonstrate a set of image processing steps that increase the intrinsically low signal-to-noise ratio associated with single-molecule fluorescence microscopy. Furthermore, we demonstrate how to estimate the length of molecules by continuous real-time
    image stitching and how to increase the effective resolution of a pressure controller by pulse width modulation. The sequence of image-processing steps addresses the challenges of genomic-length DNA visualization; however, they should also be general to other applications of fluorescence-based
    microfluidics.
    Original languageEnglish
    JournalReview of Scientific Instruments
    Volume86
    Pages (from-to)063702
    Number of pages6
    ISSN0034-6748
    DOIs
    Publication statusPublished - 2015

    Bibliographical note

    C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License

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