DNA confinement in nanochannels: physics and biological applications

Walter Reisner, Jonas Nyvold Pedersen, Robert H Austin

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    DNA is the central storage molecule of genetic information in the cell, and reading that information is a central
    problem in biology. While sequencing technology has made enormous advances over the past decade, there is
    growing interest in platforms that can readout genetic information directly from long single DNA molecules,
    with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for
    ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning
    and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this
    review, we will discuss how the information contained in genomic-length single DNA molecules can be
    accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will
    stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for
    analysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effect
    of varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apart
    from the intense biological interest in extracting linear sequence information from elongated DNA molecules,
    from a physics view these systems are fascinating as they enable probing of single-molecule conformation in
    environments with dimensions that intersect key physical length-scales in the 1 nm to 100μm range.
    (Some figures may appear in colour only in the online journal)
    Original languageEnglish
    JournalReports on Progress in Physics
    Volume75
    Issue number10
    Number of pages34
    ISSN0034-4885
    DOIs
    Publication statusPublished - 2012

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