MOLECULAR DYNAMICS OF HEMIPROTONATED INTERCALATED FOUR-STRANDED I-DNA AND GUANINE QUARTETS. STABLE TRAJECTORIES ON A NANOSECOND SCALE

Naďa Spackova^1,2, Imre Berger ³, Martin Egli ⁴, Jiri Sponer ⁵

¹Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
²Department of Physical Electronics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
³Institute for Molecular Biology and Biophysics, ETH-Hoenggerberg, CH-8093 Zürich, Switzerland
⁴Drug Discovery Program and Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, IL 60611-3008 U.S.A.
⁵J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Prague, Czech Republic

Molecular dynamics (MD) simulations are presented of hemiprotonated four-stranded intercalated d(CCCC)4 and quadruplex d(GGGG)4 structures using crystal coordinates as starting models. The central core region of the i-DNA molecule, consisting of consecutive layers of hemiprotonated cytosine.cytosine+ (C.CH+) base pairs, is exceptionally stable in all simulations, with root mean square deviations (RMSd) between theoretical and crystal structures around 1 \AA. This result is surprising, as consecutive layers of hemiprotonated C.CH+ base pairs are characterized by highly unfavorable base stacking interactions due to electrostatic repulsion between base pairs that carry a positive charge. In addition, MD simulations have been carried out of theoretical d(CCCC)4 structures with alternating protonated C.CH+ and neutral C.imC base pairs utilizing the imino cytosine tautomer to eliminate the electrostatic repulsion between consecutive protonated bases. These simulations yield again stable structures with only slightly higher deviations from the crystal data compared to the protonated structures, hinting at the possibility of some involvement of the imino cytosine tautomer in stabilizing i-DNA molecules. The theoretical guanine tetrad structure stabilized by a string of monovalent cations in the channel is also very rigid and and stays close to the crystal geometry. Removal of the cations leads to a substantial destabilization of the quartet. The electrostatic repulsion between cations is eliminated by the presence of guanine-tetrads. Therefore, in contrast to i-DNA, G-tetrad structure is characterized by attractive vertical interactions along the helix. Simulation of both i-DNA and G-tetrads revealed oscillatory movements of some phosphate groups which did not propagate to the rest of the structures. Also this observation is in agreement with experimental data.

All simulations were carried out with the AMBER 4.1 force field, using the particle mesh Ewald technique for electrostatic interactions, with total length of all simulations close to 25 ns. The maintenance of a stable structure in the i-DNA simulations challenges the traditional views on the role of base stacking in stabilizing nucleic acid conformation and illustrates the complexity of interactions in biomolecules.

Spacková, N.,Berger, I., Egli, M., Sponer, J., J. Am. Chem. Soc. (in press).