Single-molecule denaturation mapping of DNA in nanofluidic channels

Walter Reisner, Niels Bent Larsen, Asli Silahtaroglu, Anders Kristensen, Niels Tommerup, Jonas O. Tegenfeldt, Henrik Flyvbjerg

    Research output: Contribution to journalJournal articleResearchpeer-review


    Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.
    Original languageEnglish
    JournalProceedings of the National Academy of Sciences of the United States of America
    Issue number30
    Pages (from-to)13294-13299
    Publication statusPublished - 2010


    • DNA denaturation
    • DNA optical mapping
    • nanochannel
    • DNA barcoding

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