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Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13294-9. doi: 10.1073/pnas.1007081107. Epub 2010 Jul 7.

Single-molecule denaturation mapping of DNA in nanofluidic channels.

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1
Department of Physics, McGill University, Montreal, QC, Canada. reisner@physics.mcgill.ca

Abstract

Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-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.

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PMID:
20616076
PMCID:
PMC2922186
DOI:
10.1073/pnas.1007081107
[Indexed for MEDLINE]
Free PMC Article
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