Molecular Dynamics of Hemiprotonated Intercalated Four-Stranded i-DNA:  Stable Trajectories on a Nanosecond Scale

Molecular dynamics (MD) simulations are presented of hemiprotonated four-stranded intercalated d(CCCC) 4 and d(CCCA) 4, utilizing crystal coordinates as starting models. The central core region of these i-DNA molecules, 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 Å. 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. In the course of the simulation of d(CCCA) 4, the adenine·adenine (A·A) base pairs that extend the four-stranded intercalated cytosine motif are disrupted, providing further evidence that the stability of i-DNA originates primarily in the hemiprotonated C·CH + core region. All simulations were carried out with the AMBER4.1 force field, using the particle mesh-Ewald technique for electrostatic interactions, with total length close to 15 ns. The maintenance of a stable structure in the simulations challenges the traditional views on the role of base stacking in stabilizing nucleic acid conformation and illustrates the complexity of interactions in biomolecules.