N. Špačková,1 R. Štefl,2 E. Fadrná,3 T.E. Cheatham,4 and J. Šponer 1


1 National Centre for Biomolecular Research and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.

2 Institute of Molecular Biology and Biophysics, CH-8093 Zurich, Switzerland

3 National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.

4 Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, 30 South 2000 East, Salt Lake City, Utah 84112-5820, USA.


Molecular dynamics (MD) simulations with explicit solvent represent very powerful tools for detailed insights into the structure and dynamics of various systems. Unfortunately, MD simulations are limited to the nanosecond timescale leading to impossibility to observe slower processes. An example of such process is the formation of a cation-stabilized guanine quadruplex (G-DNA) stem. It is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. The formation of a parallel stranded G-DNA stem consisting of four strands of d(GGGG) has been investigated using MD simulations [1]. Rather than watching for the spontaneous formation of G-DNA, our approach probed the stability of possible supramolecular intermediates (including two-, three-, and four-stranded assemblies with out-of-register basepairing between guanines) on the formation pathway. To supplement the analysis, approximate free energies of the models have been calculated using Molecular–Mechanics-Poisson Boltzmann-Surface Area (MM-PBSA) method.

Similar approach has been applied in the study of various DNA duplex sequences interacting with the minor groove binding drug 4’,6-diamidino-2-phenylindole (DAPI) [2]. Sequences investigated include the binding modes observed experimentally, that is, AATT in d(CGCGAATTCGCG)2 and ATTG in d(GGCCAATTGG)2 and alternative shifted binding modes ATTC and AATT, respectively. The simulations also suggest that the DAPI molecule is able to adopt different conformational substates accompanied by specific hydration patterns that include long residing waters. The MM-PBSA technology has been utilized to compare free energies of different binding modes. It is demonstrated that explicit inclusion of a subset of bound water molecules shifts the calculated relative binding free energies in favor of both crystallographically observed binding modes, underlining the importance of structured hydration.

The approach applied here serves as a prototype for qualitatively investigating other molecules using molecular dynamics simulation and free-energy analysis.


1. R. Štefl, T.E. Cheatham, N. Špačková, E. Fadrná, I. Berger, J. Koča & J. Šponer, Biophysical Journal, 85 (2003) 1787-1804.

2. N. Špačková, T.E. Cheatham III, F. Ryjáček, F. Lankaš, L. van Meervelt, P. Hobza & J. Šponer, Journal of the American Chemical Society, 125 (2003) 1759-1769.