The role of water in B-DNAs BI to BII conformer substates interconversion: a combined study by calorimetry, FT-IR spectroscopy and computer simulation Original Research Article

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 nonoriented films or fibers into the glassy state, and isothermal structural relaxation towards equilibrium by interconversion of substates was followed either by differential scanning calorimetry or by Fourier transform infrared spectroscopy. BI converts to BII on isothermal relaxation between 180 and 220 K, whereas on slow cooling from ambient temperature, BII converts to BI. State-of-the-art molecular dynamics simulation of the d(CGCGAATTCGCG)2 dodecamer revealed that the BI→BII transition involves not only destacking of adjacent base pairs, but is coupled with migration of water from ionic phosphate to the sugar oxygen. These results are consistent with pronounced infrared spectral changes observed upon BI→BII interconversion. The BII substate is stabilized in comparison to BI by enhanced hydrogen-bond interaction with the migrating water. Curve resolution of infrared spectra showed that in hydrated nonoriented films of the d(CGCGAATTCGCG)2 dodecamer, the BII population is enhanced in comparison to that in single crystals. Thus, the BII substate could be of biological relevance, and the BI to BII substate interconversion could be a major contributor to the protein recognition process.