Literature DB >> 12005666

Roles of stiffness and excluded volume in DNA denaturation.

Enrico Carlon1, Enzo Orlandini, Attilio L Stella.   

Abstract

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, P approximately l(-c). If excluded volume effects are fully taken into account, c = 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.

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Year:  2002        PMID: 12005666     DOI: 10.1103/PhysRevLett.88.198101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  12 in total

1.  A three-state model with loop entropy for the overstretching transition of DNA.

Authors:  Thomas R Einert; Douglas B Staple; Hans-Jürgen Kreuzer; Roland R Netz
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

2.  Analysis of a DNA simulation model through hairpin melting experiments.

Authors:  Margaret C Linak; Kevin D Dorfman
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

3.  Entropy-driven genome organization.

Authors:  Davide Marenduzzo; Cristian Micheletti; Peter R Cook
Journal:  Biophys J       Date:  2006-02-24       Impact factor: 4.033

4.  Mismatches and bubbles in DNA.

Authors:  Yan Zeng; Giovanni Zocchi
Journal:  Biophys J       Date:  2006-03-24       Impact factor: 4.033

5.  Computer simulation study of molecular recognition in model DNA microarrays.

Authors:  Arthi Jayaraman; Carol K Hall; Jan Genzer
Journal:  Biophys J       Date:  2006-09-15       Impact factor: 4.033

6.  Dynamics of intramolecular recognition: base-pairing in DNA/RNA near and far from equilibrium.

Authors:  R Bundschuh; U Gerland
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-07       Impact factor: 1.890

7.  A mesoscale model of DNA and its renaturation.

Authors:  E J Sambriski; D C Schwartz; J J de Pablo
Journal:  Biophys J       Date:  2009-03-04       Impact factor: 4.033

8.  Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways.

Authors:  E J Sambriski; V Ortiz; J J de Pablo
Journal:  J Phys Condens Matter       Date:  2008-12-17       Impact factor: 2.333

9.  Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis.

Authors:  E J Sambriski; D C Schwartz; J J de Pablo
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-08       Impact factor: 11.205

10.  Stacking interactions in denaturation of DNA fragments.

Authors:  M Zoli
Journal:  Eur Phys J E Soft Matter       Date:  2011-07-14       Impact factor: 1.890

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