Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface.
In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA (ssDNA) as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness.
Park
Jae Hyun
JH
Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
Aluru
N R
NR
J Comput Chem. 2005 Dec;26(16):1701-18
16211538
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
8744570
Electrophoresis. 2001 Aug;22(12):2424-32
11519946
Nat Nanotechnol. 2007 Feb;2(2):121-8
18654231
Electrophoresis. 2009 Mar;30(5):792-818
19260004
Annu Rev Phys Chem. 2000;51:129-52
11031278
Biophys J. 2005 Apr;88(4):2472-93
15665128
Biophys J. 1995 Oct;69(4):1528-35
8534823
Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179-83
6941276
Appl Phys Lett. 2008 Dec 22;93(25):253104
19529784
Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1355-63
15272157
Phys Rev A Gen Phys. 1985 Mar;31(3):1695-1697
9895674
Phys Rev Lett. 2000 Dec 25;85(26 Pt 1):5651-4
11136069
Genome Res. 2008 Nov;18(11):1851-8
18714091