The Conformer Substates of Nonoriented B-type DNA in Double Helical Poly(dG-dC)

Abstract

A nonoriented hydrated film of poly(dG-dC) with ≈20 water molecules per nucleotide (called B by Loprete and Hartman (Biochem. 32, 4077–4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra. Comparison with difference curves obtained in the same manner from two classical B-DNA forms, namely the d(CGCGAATTCGCG)₂ dodecamer and polymeric NaDNA from salmon testes, revealed that the spectral changes on B_Ito-B_II interconversion in the classical B-DNA forms are very similar to those in the B-form, and that the spectroscopic differences between the B_I and B_II features from classical B-DNA and those from the modified B-form are minor. Nonexponential kinetics of the B_I→B_II transition in the B-form of poly(dG-dC) at 200 K showed that the structural relaxation time is about three times of that in the classical B-DNA forms (≈30 versus ≈10 min at 200 K). The unexpected reversal of conformer substates interconversion (that is B_II→B_I transition on cooling from 290 K and B_I→B_II transition on isothermal relaxation at 200 K) observed for classical B-DNA occurs also in the modified B-form. We therefore conclude that restructuring of hydration shells rules the low-temperature dynamics of the B-form via its two conformer substates in the same manner reported for classical B-DNA by Pichler et al. (J. Phys. Chem. B 106, 3263–3274 (2002)).