Advanced

Single DNA denaturation and bubble dynamics

Metzler, Ralf ; Ambjörnsson, Tobias LU ; Hanke, Andreas and Fogedby, Hans C (2009) In Journal of Physics: Condensed Matter 21(3).
Abstract
While the Watson–Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland–Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two... (More)
While the Watson–Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland–Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins. (Less)
Please use this url to cite or link to this publication:
author
; ; and
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Physics: Condensed Matter
volume
21
issue
3
article number
034111
publisher
IOP Publishing
external identifiers
  • scopus:63649111557
ISSN
0953-8984
DOI
10.1088/0953-8984/21/3/034111
language
English
LU publication?
no
id
93cbb960-6ba6-44c0-884e-cb4268e3801b
alternative location
http://stacks.iop.org/0953-8984/21/i=3/a=034111?key=crossref.d4b176b2663b82f6eb64c6e1c3b116ae
date added to LUP
2019-05-03 11:30:23
date last changed
2020-10-07 06:26:14
@article{93cbb960-6ba6-44c0-884e-cb4268e3801b,
  abstract     = {While the Watson–Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland–Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.},
  author       = {Metzler, Ralf and Ambjörnsson, Tobias and Hanke, Andreas and Fogedby, Hans C},
  issn         = {0953-8984},
  language     = {eng},
  month        = {01},
  number       = {3},
  publisher    = {IOP Publishing},
  series       = {Journal of Physics: Condensed Matter},
  title        = {Single DNA denaturation and bubble dynamics},
  url          = {http://dx.doi.org/10.1088/0953-8984/21/3/034111},
  doi          = {10.1088/0953-8984/21/3/034111},
  volume       = {21},
  year         = {2009},
}