Automation of a single-DNA molecule stretching device

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

doi:10.1063/1.4922068

Automation of a single-DNA molecule stretching device

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

University of Copenhagen

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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 language	English
Journal	Review of Scientific Instruments
Volume	86
Pages (from-to)	063702
Number of pages	6
ISSN	0034-6748
DOIs	https://doi.org/10.1063/1.4922068
Publication status	Published - 2015

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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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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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AU - Sørensen, Kristian Tølbøl

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AU - Tommerup, Niels

AU - Silahtaroglu, Asli

AU - Kristensen, Anders

AU - Marie, Rodolphe

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PY - 2015

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Automation of a single-DNA molecule stretching device

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