The EcoRI DNA dodecamer d(CGCGAATTCGCG)2 is investigated by state-of-the-art molecular dynamics simulations. The BI → BII transition is shown to be a consequence of destacking processes of adjacent base pairs and is coupled with migration of water from ionic phosphate to the sugar oxygen. Two-thirds of the double-helical base steps temporarily are in the BII substate. The time-averaged BI/BII population ratio is 9.2, but at a given time, it can be as low as 2.7. Observed changes in the solvation properties closely match recently reported spectroscopic features. The different time scales of all processes involved are discussed with respect to experimental results. Formation of contact ion-pairs is demonstrated to be independent of substate transitions.

Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)2 dodecamer have the same BI and BII substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated unoriented films to 200 K, and isothermal structural relaxation toward equilibrium by interconversion of substates was followed by Fourier transform infrared spectroscopy. BI interconverts into BII on isothermal relaxation at 200 K, whereas on slow cooling from ambient temperature, BII interconverts into BI. Our estimation of the dodecamer's BI-to-BII conformer substate population by curve resolution of the symmetrical stretching vibration of the ionic phosphate is 2.4 +/- 0.5 to 1 at 200 K, and it is 1.3 +/- 0.5 to 1 between 270 and 290 K. Pronounced spectral changes upon BI-to-BII interconversion are consistent with base destacking coupled with migration of water from ionic phosphate toward the phosphodiester and sugar moieties. Nonspecific interaction of proteins with the DNA backbone could become specific by induced-fit-type interactions with either BI or BII backbone conformations. This suggests that the BI-to-BII substate interconversion could be a major contributor to the protein recognition process.

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The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta-Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5'-GTACT-3'), and it was investigated recently by X-ray crystallography. On one hand we are able to reproduce X-ray-determined DNA--drug contacts, and on the other hand we provide new contact information which is important for the development of potential ligands. The new insights show how the beta-tail of the polyamide ligands contributes to binding. Our simulations also indicate that complexation freezes the DNA backbone in a specific B(I) or B(II) substate conformation and thus optimizes nonbonded contacts. The existence of this distinct B(I)/B(II) substate pattern also allows the formation of water-mediated contacts. Thus, we suggest the B(I) <==> B(II) substate behavior to be an important part of the indirect readout of DNA.

Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations. Analysis of the resulting transition processes with respect to the backbone angles reveals concerted changes not only for backbone angles epsilon, zeta, and beta, but also for the 5'-delta and 5'-chi angles. For alpha and delta inside the interconverting base step, a change is seen in short lived B(II) conformers. With respect to base morphology distinct changes are observed for buckle, propeller twist, shift, roll and twist, as well as x-displacement and tip. The base mainly involved in the changes is identified as the base preceding the interconverting phosphate. Altogether single B(I)<==>B(II) interconversions result only in local distortions represented by the larger spread of most parameters. Comparison of the atomic positional fluctuations derived from the simulation with those obtained from the static X-ray structure results in striking similarities.