Literature DB >> 19669567

Nonlinearity in DNA and its relation to specific functions.

Boian Alexandrov1, Kim Ø Rasmussen, Alan R Bishop.   

Abstract

In memory of Alwyn Scott, we discuss the connection between the nonlinear dynamics of double-stranded DNA, experimental findings, and specific DNA functions. We begin by discussing how thermally induced localized openings (bubbles) of the DNA double-strand are important for interpreting dynamic force spectroscopy data. Then, we demonstrate a correlation between the sequence-dependent propensity for bubble formation and transcription initiation and other regulatory effects in viral DNA. Finally, we discuss the possibility of a connection between DNA dynamics and the ability of repair proteins to recognize ultraviolet-radiation damage.

Year:  2009        PMID： 19669567      PMCID： PMC2660394          DOI： 10.1007/s10867-009-9125-4

Source DB:  PubMed          Journal:  J Biol Phys        ISSN： 0092-0606            Impact factor:   1.365


  23 in total

1.  Strain-induced metal-insulator phase coexistence in perovskite manganites.

Authors:  K H Ahn; T Lookman; A R Bishop
Journal:  Nature       Date:  2004-03-25       Impact factor: 49.962

2.  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

3.  Length and statistical weight of bubbles in DNA melting.

Authors:  Yan Zeng; Awrasa Montrichok; Giovanni Zocchi
Journal:  Phys Rev Lett       Date:  2003-09-30       Impact factor: 9.161

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

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

5.  Allostery in a coarse-grained model of protein dynamics.

Authors:  Dengming Ming; Michael E Wall
Journal:  Phys Rev Lett       Date:  2005-11-02       Impact factor: 9.161

6.  Classical statistical mechanics of constraints: a theorem and application to polymers.

Authors:  M Fixman
Journal:  Proc Natl Acad Sci U S A       Date:  1974-08       Impact factor: 11.205

7.  Sequencing DNA by dynamic force spectroscopy: limitations and prospects.

Authors:  N K Voulgarakis; A Redondo; A R Bishop; K O Rasmussen
Journal:  Nano Lett       Date:  2006-07       Impact factor: 11.189

8.  Discrete breathers in nonlinear network models of proteins.

Authors:  B Juanico; Y-H Sanejouand; F Piazza; P De Los Rios
Journal:  Phys Rev Lett       Date:  2007-12-07       Impact factor: 9.161

9.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

10.  1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG).d(CGCAACGC) containing a thymine photodimer.

Authors:  J Kemmink; R Boelens; T Koning; G A van der Marel; J H van Boom; R Kaptein
Journal:  Nucleic Acids Res       Date:  1987-06-11       Impact factor: 16.971
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  2 in total

1.  The Physics of Life and Quantum Complex Matter: A Case of Cross-Fertilization.

Authors:  Nicola Poccia; Antonio Bianconi
Journal:  Life (Basel)       Date:  2011-09-29

2.  Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.

Authors:  Kristy Nowak-Lovato; Ludmil B Alexandrov; Afsheen Banisadr; Amy L Bauer; Alan R Bishop; Anny Usheva; Fangping Mu; Elizabeth Hong-Geller; Kim Ø Rasmussen; William S Hlavacek; Boian S Alexandrov
Journal:  PLoS Comput Biol       Date:  2013-01-17       Impact factor: 4.475
  2 in total

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