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Portrait of Jonas Tegenfeldt. Photo: Kennet Ruona

Jonas Tegenfeldt

Professor, Coordinator Nanobiology & Neuronanoscience

Portrait of Jonas Tegenfeldt. Photo: Kennet Ruona

Single-molecule denaturation mapping of DNA in nanofluidic channels

Author

  • Walter Reisner
  • Niels B. Larsen
  • Asli Silahtaroglu
  • Anders Kristensen
  • Niels Tommerup
  • Jonas Tegenfeldt
  • Henrik Flyvbjerg

Summary, in English

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.

Department/s

  • Solid State Physics
  • NanoLund

Publishing year

2010

Language

English

Pages

13294-13299

Publication/Series

Proceedings of the National Academy of Sciences

Volume

107

Issue

30

Document type

Journal article

Publisher

National Acad Sciences

Topic

  • Condensed Matter Physics

Keywords

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

Status

Published

ISBN/ISSN/Other

  • ISSN: 1091-6490