Comparison of a left-handed Z-DNA molecular structure determined by X-rays with that simulated by a molecular...

The 1.0 A resolution X-ray crystal structures of the left-handed Z-DNA(Z-I and Z-II conformations) were compared with that of the simulated molecular dynamics(MD) structure both in vacuo and in solution. Whilst the X-ray structure showed a tendency for the d(CG)3 molecule to take on a Z-II conformation in high salt solution or in strongly ionized conditions, the MD simulation with Na ion for 30 ps revealed that the left-handed d(CG)3 structure with the Z-I conformation was transformed into the Z-II conformation in the torsion angles of the C3, G4 and C5 phosphate groups, and furthermore, when K+ ion was used as the counterion instead of Na+ ion, the torsion angles in almost the entire d(CG)3 molecule were preserved. On the other hand, the MD calculation resulted in some very important changes on the sugar puckerings; the simulation with Na+ ion indicated that all the sugar puckerings of cytosine residues were changed from C2'-endo to C3'-endo, while those for guanosine residues tended to keep unchanged (C3'-endo) except for a terminal residue (G6).