Single-molecule denaturation mapping of DNA in nanofluidic channels

Publication: Research - peer-reviewJournal article – Annual report year: 2010

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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
JournalNational Academy of Sciences. Proceedings
Publication date2010
Volume107
Journal number30
Pages13294-13299
ISSN0027-8424
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 50

Keywords

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