Local cooperativity mechanism in the DNA melting transition
نویسندگان
چکیده
منابع مشابه
Local cooperativity mechanism in the DNA melting transition.
We propose a statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsically accounts for the cooperativity related to the free energy penalt...
متن کاملBubble nucleation and cooperativity in DNA melting.
Bubbles in DNA are related to fundamental processes such as duplication and transcription. Using a new ensemble technique to trap intermediate states, we present direct measurements of the average length of the denaturation bubble and the statistical weights of the bubble states in the temperature-driven melting of DNA oligomers. For a bubble flanked by double-stranded regions, we find a nuclea...
متن کاملComment on "bubble nucleation and cooperativity in DNA melting".
The conclusions presented by Ares et al. [1] rely on not converged calculations and should be considered with caution. Zeng et al. investigated the temperature evolution of the length of bubbles close to the melting of short DNA sequences and concluded that the average size of ‘‘bubbles in the middle’’ reaches a plateau equal to the number of AT pairs before the two strands separate [2]. Ares e...
متن کاملTheory of Bubble Nucleation and Cooperativity in DNA Melting
Saúl Ares, 2 N. K. Voulgarakis, K. Ø. Rasmussen, and A. R. Bishop Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganés, Madrid, Spain Department of Physics, Universit...
متن کاملKinetic Pathways of the DNA Melting Transition
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a φ-field theory to calculate the critical droplet profile, the initial growth modes, and the exponent γ characterizing the divergence of the susceptibility near the spinodal. In the PDB model, we us...
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ژورنال
عنوان ژورنال: Physical Review E
سال: 2005
ISSN: 1539-3755,1550-2376
DOI: 10.1103/physreve.71.041909