Model for DNA hairpin denaturation.
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.
Cuesta-López
S
S
Dept. Física de la Materia Condensada, Universidad de Zaragoza, c/Pedro Cerbuna s/n, 50009 Zaragoza, Spain.
Peyrard
M
M
Graham
D J
DJ
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
D004247:DNA
Phys Rev Lett. 2000 Jul 3;85(1):6-9
10991145
Phys Rev Lett. 1989 Jun 5;62(23):2755-2758
10040080
Nucleic Acids Res. 2003 Feb 1;31(3):1075-85
12560506
Proc Natl Acad Sci U S A. 1999 May 25;96(11):6171-6
10339560
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Jan;47(1):684-695
9960044
Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Dec;68(6 Pt 1):061909
14754236
Biophys J. 2003 Aug;85(2):790-803
12885628
Phys Rev Lett. 2000 Sep 11;85(11):2400-3
10978020
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Jan;47(1):R44-R47
9960075
Nucleic Acids Res. 2004 Mar 05;32(4):1584-90
15004245
Nucleic Acids Res. 1993 Jul 11;21(14):3287-93
7688117
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8602-6
9671724