Literature DB >> 15726245

Model for DNA hairpin denaturation.

S Cuesta-López1, M Peyrard, D J Graham.   

Abstract

We investigate the thermal denaturation of DNA hairpins using molecular dynamics simulations of a simple model describing the molecule at a scale of a nucleotide. The model allows us to analyze the different interacting features that determine how an hairpin opens, such as therole of the loop and the properties intrinsic to the stem.

Mesh：

Substances：

Year:  2005        PMID： 15726245     DOI： 10.1140/epje/e2005-00026-9

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN： 1292-8941            Impact factor:   1.890


  12 in total

1.  Sequence dependent rigidity of single stranded DNA.

Authors:  N L Goddard; G Bonnet; O Krichevsky; A Libchaber
Journal:  Phys Rev Lett       Date:  2000-09-11       Impact factor: 9.161

2.  Order of the phase transition in models of DNA thermal denaturation.

Authors:  N Theodorakopoulos; T Dauxois; M Peyrard
Journal:  Phys Rev Lett       Date:  2000-07-03       Impact factor: 9.161

3.  Thermodynamic basis of the enhanced specificity of structured DNA probes.

Authors:  G Bonnet; S Tyagi; A Libchaber; F R Kramer
Journal:  Proc Natl Acad Sci U S A       Date:  1999-05-25       Impact factor: 11.205

4.  Thermal denaturation of a helicoidal DNA model.

Authors:  Maria Barbi; Stefano Lepri; Michel Peyrard; Nikos Theodorakopoulos
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-12-23

5.  Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances.

Authors:  Christophe Pakleza; Jean A H Cognet
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

6.  Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.

Authors:  Eric J Sorin; Young Min Rhee; Bradley J Nakatani; Vijay S Pande
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

7.  DNA dynamically directs its own transcription initiation.

Authors:  Chu H Choi; George Kalosakas; Kim O Rasmussen; Makoto Hiromura; Alan R Bishop; Anny Usheva
Journal:  Nucleic Acids Res       Date:  2004-03-05       Impact factor: 16.971

8.  Statistical mechanics of a nonlinear model for DNA denaturation.

Authors: 
Journal:  Phys Rev Lett       Date:  1989-06-05       Impact factor: 9.161

9.  Dynamics and thermodynamics of a nonlinear model for DNA denaturation.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1993-01

10.  Entropy-driven DNA denaturation.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1993-01
View more
  2 in total

1.  Can we model DNA at the mesoscale?

Authors:  S Cuesta-López; J Errami; F Falo; M Peyrard
Journal:  J Biol Phys       Date:  2005-12       Impact factor: 1.365

2.  An AFM/rotaxane molecular reading head for sequence-dependent DNA structures.

Authors:  Brian A Ashcroft; Quinn Spadola; Shahid Qamar; Peiming Zhang; Gerald Kada; Rouvain Bension; Stuart Lindsay
Journal:  Small       Date:  2008-09       Impact factor: 13.281
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.