Water at DNA surfaces: Ultrafast dynamics in minor groove recognition

Abstract

Water molecules at the surface of DNA are critical to its equilibrium structure, DNA-protein function, and DNA-ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them (Ϸ20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the ''ordered'' water molecules are the most weakly bound and are accordingly involved in the entropic (hydration͞dehydration) process of recognition. H ydration of DNA plays important role in its structure, conformation, and function. Of significance to the function is the selective recognition by DNA of small molecules (ref. 1 and references therein). X-ray crystallography, NMR, dielectric relaxation, and molecular dynamics simulation studies have shown that a significant amount of water molecules are bound to DNA (for reviews, see refs. 2-6). For example, measurements of dielectric relaxation caused by water molecules bound to DNA in mixed water-ethanol solutions have found that 18-19 water molecules per nucleotide are present in B-DNA, but only 13-14 water molecules are bound in A-DNA (5). The study also suggested that a structural transition of poly(dG-dC)⅐poly(dGdC) DNA from its B to Z form takes place on the removal of the bound water molecules, preferentially from the phosphate groups.The molecular picture of hydration in the minor groove of B-DNA is unique. An x-ray crystallographic investigation (7) followed by solution NMR study (8) on a model dodecamer B-DNA duplex (for the sequence of A͞T tracts, CGCGAAT-TCGCG) showed that the minor groove is hydrated in an extensive and regular manner, with a zigzag ''spine'' of firstand second-shell hydration along the f loor of the groove. In contrast, hydration within the major groove is principally confined to a monolayer of water molecules. The conformational energy calculation suggested that the presence of the spine of hydration is the prime reason for the further narrowing of minor groove (9).The influence of drug binding on DNA hydration is striking. Acoustic and densimetric studies have shown that a fraction (not total) of the water molecules is released on recognition (10, 11). Hence, the balance between enthalpic and entr...

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