Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics

Abstract

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the $\varphi$X174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.

5 pages, 4 figures, to appear in Phys. Rev. E

References in corpus (3)

• Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
• DNA denaturation bubbles at criticality
• Comment on "Bubble nucleation and cooperativity in DNA melting" [Phys. Rev. Letters 94, 035504 (2005), arXiv:cond-mat/0412591]

Cited by in corpus (13)

• Effect of salt concentration on the stability of heterogeneous DNA
• Thermodynamics of Twisted DNA with Solvent Interaction
• Driving denaturation: Nanoscale thermal transport as a probe of DNA melting
• The thermal denaturation of DNA studied with neutron scattering
• Base Pair Openings and Temperature Dependence of DNA Flexibility
• Stacking Interactions in Denaturation of DNA Fragments
• Helix untwisting and bubble formation in circular DNA
• Phase diagram of mechanically stretched DNA: The salt effect
• Pulling short DNA molecules having defects on different locations
• Anharmonic stacking in supercoiled DNA
• First-passage probability: a test for DNA Hamiltonian parameters
• Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
• Can we model DNA at the mesoscale ? Comment on: Fluctuations in the DNA double helix: A critical review