Published online 10 August 2004
Nucleic Acids Research, Vol. 32 No. 14 © Oxford University Press 2004; all rights reserved
DNA and its counterions: a molecular dynamics study
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
* To whom correspondence should be addressed. Tel: +33 1 58415174; Fax: +33 1 58415026; Email: krystyna{at}ibpc.fr
Present address: Péter Várnai, University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
Received April 7, 2004; Revised June 15, 2004; Accepted July 26, 2004
The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of <13%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive 
/
transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Curuksu, M. Zacharias, R. Lavery, and K. Zakrzewska Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res., June 1, 2009; 37(11): 3766 - 3773. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Jiranusornkul and C. A Laughton Destabilization of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair J R Soc Interface, December 6, 2008; 5(Suppl_3): 191 - 198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Khalid, P. J Bond, J. Holyoake, R. W Hawtin, and M. S.P Sansom DNA and lipid bilayers: self-assembly and insertion J R Soc Interface, December 6, 2008; 5(Suppl_3): 241 - 250. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Mura and J. A. McCammon Molecular dynamics of a {kappa}B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation Nucleic Acids Res., September 1, 2008; 36(15): 4941 - 4955. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Perez, F. Lankas, F. J. Luque, and M. Orozco Towards a molecular dynamics consensus view of B-DNA flexibility Nucleic Acids Res., April 1, 2008; 36(7): 2379 - 2394. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Timsit and S. Bombard The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction RNA, December 1, 2007; 13(12): 2098 - 2107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Fujii, H. Kono, S. Takenaka, N. Go, and A. Sarai Sequence-dependent DNA deformability studied using molecular dynamics simulations Nucleic Acids Res., September 25, 2007; 35(18): 6063 - 6074. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Sefcikova, M. V. Krasovska, J. Sponer, and N. G. Walter The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis Nucleic Acids Res., March 19, 2007; 35(6): 1933 - 1946. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Spackova and J. Sponer Molecular dynamics simulations of sarcin-ricin rRNA motif Nucleic Acids Res., February 2, 2006; 34(2): 697 - 708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Cheng, N. Korolev, and L. Nordenskiold Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study Nucleic Acids Res., January 30, 2006; 34(2): 686 - 696. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zhou, S. Krueger, and S. K. Gregurick A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution Nucleic Acids Res., November 10, 2005; 33(19): 6361 - 6371. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Range, E. Mayaan, L. J. Maher III, and D. M. York The contribution of phosphate-phosphate repulsions to the free energy of DNA bending Nucleic Acids Res., March 1, 2005; 33(4): 1257 - 1268. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Y. Ponomarev, K. M. Thayer, and D. L. Beveridge Ion motions in molecular dynamics simulations on DNA PNAS, October 12, 2004; 101(41): 14771 - 14775. [Abstract] [Full Text] [PDF]
|
|