Single-molecule denaturation mapping of DNA in nanofluidic channels

Research output: Contribution to journalArticle


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.


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

Subject classification (UKÄ) – MANDATORY

  • Condensed Matter Physics


  • DNA optical mapping, DNA barcoding, DNA denaturation, nanochannel
Original languageEnglish
Pages (from-to)13294-13299
JournalProceedings of the National Academy of Sciences
Issue number30
Publication statusPublished - 2010
Publication categoryResearch