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Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Molecular Dynamics of Guanine Quadruplex Molecules

Thorough insight into the structure and dynamics of guanine quadruplex molecules (G-DNA) has been obtained by state of the art molecular dynamics (MD) simulations with explicit representation of solvent and counterions and a correct treatment of long-range electrostatic interactions. We will summarize our latest results in this area. For example, we have investigated the formation process of guanine quadruplex stem using explicit solvent simulations and MM_PBSA thermodynamics calculations with explicit inclusion of monovalent cations. Attention has also been paid to interactions between monovalent cations and the loops. Force field approximations and limitations will be discussed.

N. Spackova1
R. Stefl2,3
I. Berger3
E. Fadrna2
J. Koca2
T. E. Cheatham, III4
J. Sponer1

1Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
612 65 Brno, Czech Republic
Phone: (420) 5415 17109
Fax: (420) 5412 11293
spackova@ibp.cz
2National Centre for Biomolecular Research
Masaryk University
Kotlarska 2
611 37 Brno, Czech Republic
3Institute for Molecular Biology and Biophysics
CH-8093 Zurich, Switzerland
4Department of Medicinal Chemistry
University of Utah
30 South 2000 East
Salt Lake City, Utah 84112-5820, USA
tec3@utah.edu

References and Footnotes
  1. N. Spackova, I. Berger, J. Sponer, J. Am. Chem. Soc. 121, 5519 (1999).
  2. R. Stefl, N. Spackova, I. Berger, J. Koca, J. Sponer, Biophys. J. 80, 455 (2001).
  3. N. Spackova, I. Berger, J. Sponer, J. Am. Chem. Soc. 123, 3295 (2001).
  4. R. Stefl, T. E. Cheatham, III, N. Spackova, I. Berger, E. Fadrna, J. Koca, J. Sponer, submitted.