MINOR-GROOVE HYDRATION OF DNA IN AQUEOUS-SOLUTION - SEQUENCE-DEPENDENT NEXT NEIGHBOR EFFECT OF THE HYDRATION LIFETIMES IN D(TTAA)(2) SEGMENTS MEASURED BY NMR-SPECTROSCOPY

The hydration in the minor groove of double stranded DNA fragments con taining the sequences 5'-dTTAAT, 5'-dTTAAC, 5'-dTTAAA and 5'-dTTAAG wa s investigated by studying the decanucleotide duplex d(GCATTAATGC)(2) and the singly cross-linked decameric duplexes 5'-d(GCATTAACGC)-3'-lin ker-5'-d(GCGTTAATGC)-3' and 5'-d(GCCTTAAAGC)-3'-linker-5'-d(GCTTTAAGGC )-3' by NMR spectroscopy. The linker employed consisted of six ethylen eglycol units. The hydration water was detected by NOEs between water and DNA protons in NOESY and ROESY spectra. NOE-NOESY and ROE-NOESY ex periments were used to filter out intense exchange cross-peaks and to observe water-DNA NOEs with sugar 1' protons, Positive NOESY cross-pea ks corresponding to residence times longer than similar to 0.5 ns were observed for 2H resonances of the central adenine residues in the dup lex containing the sequences 5'-dTTAAT and 5'-dTTAAC, but not in the d uplex containing the sequences 5'-dTTAAA and 5'-dTTAAG. In all nucleot ide sequences studied here, the hydration water in the minor groove is significantly more mobile at both ends of the AT-rich inner segments, as indicated by very weak or negative water-A 2H NOESY cross-peaks, N o positive NOESY cross-peaks were detected with the G 1'H and C 1'H re sonances, indicating that the minor groove hydration water near GC bas e pairs is kinetically less restrained than for AT-rich DNA segments, Kinetically stabilized minor groove hydration water was manifested by positive NOESY cross-peaks with both A 2H and 1'H signals of the 5'-dT TAA segment in d(GCATTAATGC)(2). More rigid hydration water was detect ed near T4 in d(GCATTAATGC)(2) as compared with 5'-d(GCATTAACGC)-3'-li nker-5'-d(GCGTTAATGC)-3', although the sequences differ only in a sing le base pair. This illustrates the high sensitivity of water-DNA NOEs towards small conformational differences.