The role of water in B-DNAs B-I to B-II conformer substates interconversion: a combined study by calorimetry, FT-IR spectroscopy and computer simulation

Conformational substates of B-DNA had been observed so far in synthetic oli gonucleotides but not in naturally occurring highly polymeric B-DNA. Our lo w-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)(2) dodecamer have the same B-I and B-II substates. Nonequi librium distribution of conformer population was generated by quenching hyd rated nonoriented films or fibers into the glassy state, and isothermal str uctural relaxation towards equilibrium by interconversion of substates was followed either by differential scanning calorimetry or by Fourier transfor m infrared spectroscopy. B-I converts to B-II on isothermal relaxation betw een 180 and 220 K, whereas on slow cooling from ambient temperature, B-II c onverts to B-I. State-of-the-art molecular dynamics simulation of the d(CGC GAATTCGCG)(2) dodecamer revealed that the B-I --> B-II transition involves not only destacking of adjacent base pairs, but is coupled with migration o f water from ionic phosphate to the sugar oxygen. These results are consist ent with pronounced infrared spectral changes observed upon B-I --> B-II in terconversion. The B-II substate is stabilized in comparison to B-I by enha nced hydrogen-bond interaction with the migrating water. Curve resolution o f infrared spectra showed that in hydrated nonoriented films of the d(CGCGA ATTCGCG)(2) dodecamer, the B-II population is enhanced in comparison to tha t in single crystals. Thus, the B-II substate could be of biological releva nce, and the B-I to B-II substate interconversion could be a major contribu tor to the protein recognition process. (C) 2000 Elsevier Science B.V. All rights reserved.