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

The residence time of water in the minor groove of the d(CGCGAATTCGCG) dupl ex has been determined by a recent measurement combining nuclear Overhauser enhancements (NOE, ROE) and O-17 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 t he 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 ach ieved by varying the magnetic field and/or the temperature. The zero-NOE measurement may be performed by one-dimensional NMR, and has t herefore good sensitivity. We have developed excitation sequences which sup press 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 stacke d, propeller-twisted base-pairs and a correspondingly narrower minor groove . In the minor groove of [d(CGCGA (A) under bar TTCGCG)](2), a B'-DNA duplex, the residence time of the water molecule next to H2 of adenine(6) (underli ned), is 0.6 ns at 10 degrees C, in good agreement with the value obtained previously. The residence time is slightly but distinctly shorter for the w ater next to A5, suggesting noncooperative departure of these two molecules which are presumed to be part of the hydration spine. Near A5 and A4 of [d (AAA<(AA)under bar>TTTTT)](2), another B'-DNA duplex, the residence times a re 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(CGCG (A) under bar TCGCG) was 0.3 ns at 10 degrees C, shorter than in the case of the B'-DNA sequences by factors of 2 and 4, respectively. The temperatur e dependence is less, with an activation enthalpy of 27 kJ/mol. The major groove residence times are comparable for the three sequences, an d 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 degrees C . The most striking aspect of these results is the relatively small differenc e in the residence times of reputedly fast and slow-exchanging water molecu les 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 comp ared with B-DNA. (C) 1999 Academic Press.