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

    Cite this

    Sørensen, Kristian Tølbøl ; Lopacinska, Joanna M. ; Tommerup, Niels ; Silahtaroglu, Asli ; Kristensen, Anders ; Marie, Rodolphe . / Automation of a single-DNA molecule stretching device. In: Review of Scientific Instruments. 2015 ; Vol. 86. pp. 063702.
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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-timeimage 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-basedmicrofluidics.",
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    year = "2015",
    doi = "10.1063/1.4922068",
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    Automation of a single-DNA molecule stretching device. / Sørensen, Kristian Tølbøl; Lopacinska, Joanna M.; Tommerup, Niels; Silahtaroglu, Asli; Kristensen, Anders; Marie, Rodolphe .

    In: Review of Scientific Instruments, Vol. 86, 2015, p. 063702.

    Research output: Contribution to journalJournal articleResearchpeer-review

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    AU - Sørensen, Kristian Tølbøl

    AU - Lopacinska, Joanna M.

    AU - Tommerup, Niels

    AU - Silahtaroglu, Asli

    AU - Kristensen, Anders

    AU - Marie, Rodolphe

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    PY - 2015

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    N2 - 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-timeimage 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-basedmicrofluidics.

    AB - 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-timeimage 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-basedmicrofluidics.

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