Single DNA denaturation and bubble dynamics

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Single DNA denaturation and bubble dynamics. / Metzler, Ralf; Ambjörnsson, Tobias; Hanke, Andreas; Fogedby, Hans C.

In: Journal of Physics: Condensed Matter, Vol. 21, No. 3, 034111, 21.01.2009.

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Metzler, Ralf ; Ambjörnsson, Tobias ; Hanke, Andreas ; Fogedby, Hans C. / Single DNA denaturation and bubble dynamics. In: Journal of Physics: Condensed Matter. 2009 ; Vol. 21, No. 3.

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TY - JOUR

T1 - Single DNA denaturation and bubble dynamics

AU - Metzler, Ralf

AU - Ambjörnsson, Tobias

AU - Hanke, Andreas

AU - Fogedby, Hans C

PY - 2009/1/21

Y1 - 2009/1/21

N2 - 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.

AB - 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.

U2 - 10.1088/0953-8984/21/3/034111

DO - 10.1088/0953-8984/21/3/034111

M3 - Article

VL - 21

JO - Journal of Physics: Condensed Matter

JF - Journal of Physics: Condensed Matter

SN - 1361-648X

IS - 3

M1 - 034111

ER -