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Photo of Tobias Ambjörnsson

Tobias Ambjörnsson

Senior lecturer

Photo of Tobias Ambjörnsson

How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model.

Author

  • Michaela Reiter-Schad
  • Erik Werner
  • Jonas Tegenfeldt
  • Bernhard Mehlig
  • Tobias Ambjörnsson

Summary, in English

When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands are separated. The statistical physics of this process has a long history and is commonly described in terms of the Poland-Scheraga (PS) model. Crucial to this model is the configurational entropy for a melted region (compared to the entropy of an intact region of the same size), quantified by the loop factor. In this study, we investigate how confinement affects the DNA melting transition, by using the loop factor for an ideal Gaussian chain. By subsequent numerical solutions of the PS model, we demonstrate that the melting temperature depends on the persistence lengths of single-stranded and double-stranded DNA. For realistic values of the persistence lengths, the melting temperature is predicted to decrease with decreasing channel diameter. We also demonstrate that confinement broadens the melting transition. These general findings hold for the three scenarios investigated: 1. homo-DNA, i.e., identical basepairs along the DNA molecule, 2. random sequence DNA, and 3. "real" DNA, here T4 phage DNA. We show that cases 2 and 3 in general give rise to broader transitions than case 1. Case 3 exhibits a similar phase transition as case 2 provided the random sequence DNA has the same ratio of AT to GC basepairs (A - adenine, T - thymine, G - guanine, C - cytosine). A simple analytical estimate for the shift in melting temperature is provided as a function of nanochannel diameter. For homo-DNA, we also present an analytical prediction of the melting probability as a function of temperature.

Department/s

  • Computational Biology and Biological Physics - Has been reorganised
  • Solid State Physics
  • NanoLund: Centre for Nanoscience

Publishing year

2015

Language

English

Publication/Series

Journal of Chemical Physics

Volume

143

Issue

11

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Topic

  • Physical Chemistry (including Surface- and Colloid Chemistry)
  • Biophysics
  • Other Physics Topics

Status

Published

ISBN/ISSN/Other

  • ISSN: 0021-9606