Bubbles and denaturation in DNA

Abstract

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular dynamics studies, were premature. This could either imply that the present PBD should be improved or that biological activity can only be predicted in a more complex frame work that involves interactions with proteins and super helical stresses. In this article, we give detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as function of position and bubble size and the so-called $l$-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.

15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG 2006

References in corpus (9)

• Order of the phase transition in models of DNA thermal denaturation
• Theory of Bubble Nucleation and Cooperativity in DNA Melting
• Structurally specific thermal fluctuations identify functional sites for DNA transcription
• Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
• Can one predict DNA Transcription Start Sites by studying bubbles?
• Healing Length and Bubble Formation in DNA
• Lengthscales and Cooperativity in DNA Bubble Formation
• An intermediate phase in DNA melting
• Towards more realistic dynamical models for DNA secondary structure

Cited by in corpus (20)

• Effect of salt concentration on the stability of heterogeneous DNA
• Thermodynamics of Twisted DNA with Solvent Interaction
• Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
• Modelling DNA Response to THz Radiation
• Thermal and mechanical properties of a DNA model with solvation barrier
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Helix untwisting and bubble formation in circular DNA
• J-factors of short DNA molecules
• Twisting and Bending Stress in DNA Minicircles
• Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
• Theoretical investigation of finite size effects at DNA melting
• Phase diagram of mechanically stretched DNA: The salt effect
• Theoretical and Experimental Investigations of DNA Open States
• Pulling short DNA molecules having defects on different locations
• Modeling the interaction of DNA with alternating fields
• Adding a New Dimension to DNA Melting Curves
• Comment on "Bubble nucleation and cooperativity in DNA melting" [Phys. Rev. Letters 94, 035504 (2005), arXiv:cond-mat/0412591]
• On the thermodynamics of DNA in the Peyrard-Bishop-Dauxois model
• Structural Analysis of DNA molecule in a confined shell