Lengthscales and Cooperativity in DNA Bubble Formation

Abstract

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. The analysis is based on the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach.

References in corpus (4)

• Why is the DNA Denaturation Transition First Order?
• Roles of stiffness and excluded volume in DNA denaturation
• Theory of Bubble Nucleation and Cooperativity in DNA Melting
• Structurally specific thermal fluctuations identify functional sites for DNA transcription

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• Does the dynamics of sine-Gordon solitons predict active regions of DNA?
• Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"
• Theoretical and Experimental Investigations of DNA Open States
• Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
• Simple Combined Model for Nonlinear Excitations in DNA
• Solitons in a double pendulums chain model, and DNA roto-torsional dynamics
• Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
• LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA
• On the thermodynamics of DNA in the Peyrard-Bishop-Dauxois model
• Thermomechanical Stability and Mechanochemical Response of DNA: a Minimal Mesoscale Model