Determination of the residence time of water molecules hydrating B ′ -DNA and B -DNA, by one-dimensional zero-enhancement nuclear overhauser effect spectroscopy

Abstract

The residence time of water in the minor groove of the d(CGCGAATTCGCG) duplex has been determined by a recent measurement combining nuclear Overhauser enhancements (NOE, ROE) and 17O relaxation dispersion. The time is in the range of nanoseconds, so that it may be measured by a rather simple method proposed here, namely the choice of conditions such that the NOE between the observed DNA proton and a nearby water proton is zero. This condition is realized when the residence time of the water molecule is 0.178 times the nuclear magnetic resonance period (e.g. 0.297 ns at 600 MHz). It may be achieved by varying the magnetic field and/or the temperature.The zero-NOE measurement may be performed by one-dimensional NMR, and has therefore good sensitivity. We have developed excitation sequences which suppress two spurious contributions to the NOE: from neighboring exchangeable protons and from H3′ protons whose chemical shift is close to that of water. The method is applied here to the comparison of residence times of water next to B -DNA and next to B′-DNA, the latter corresponding to better stacked, propeller-twisted base-pairs and a correspondingly narrower minor groove.In the minor groove of [d(CGCGAATTCGCG)]2, a B′-DNA duplex, the residence time of the water molecule next to H2 of adenine(6) (underlined), is 0.6 ns at 10 °C, in good agreement with the value obtained previously. The residence time is slightly but distinctly shorter for the water next to A5, suggesting non-cooperative departure of these two molecules which are presumed to be part of the hydration spine. Near A5 and A4 of [d(AAAAATTTTT)]2, another B′-DNA duplex, the residence times are approximately twice as long, but the activation enthalpies are about the same, ca. 38 kJ/mol.The residence time in the minor groove of the regular B -DNA sequence d(CGCGATCGCG) was 0.3 ns at 10 °C, shorter than in the case of the B′-DNA sequences by factors of 2 and 4, respectively. The temperature dependence is less, with an activation enthalpy of 27 kJ/mol.The major groove residence times are comparable for the three sequences, and a few times shorter than those of minor groove water. A value of 0.36 ns, or even more in case of rotation of water, is obtained around −8 °C.The most striking aspect of these results is the relatively small difference in the residence times of reputedly fast and slow-exchanging water molecules bound to DNA in biological conditions. This suggests that the spine of hydration is perhaps not a major stabilizer of the B′-DNA structure as compared with B -DNA.