Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

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 B-I and B-II 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. B-I interconverts into B-II on isothermal relaxation at 200 K, whereas on slow cooling from ambient temperature, B-II interconverts into B-I. Our estimation of the dodecamer's B-I-to-B-II 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 B-I-to-B-II 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 B-I or B-II backbone conformations. This suggests that the B-I-to-B-II substate interconversion could be a major contributor to the protein recognition process.