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

摘要

The hydration in the minor groove of double stranded DNA fragments containing the sequences 5′-dTTAAT, 5′-dTTAAC, 5′-dTTAAA and 5′-dTTAAG was investigated by studying the decanucleotide duplex d(GCAT-TAATGC)₂ and the singly cross-linked decameric duplexes 5′-d(GCATTAACGC)-3′-linker-5′-d(GCGTT-AATGC)-3′ and 5′-d(GCCTTAAAGC)-3′-linker-5′-d(GCTTTAAGGC)-3′ by NMR spectroscopy. The linker employed consisted of six ethyleneglycol units. The hydration water was detected by NOEs between water and DNA protons in NOESY and ROESY spectra. NOE-NOESY and ROE-NOESY experiments were used to filter out intense exchange cross-peaks and to observe water-DNA NOEs with sugar 1′ protons. Positive NOESY cross-peaks corresponding to residence times longer than ～0.5 ns were observed for 2H resonances of the central adenine residues in the duplex containing the sequences 5′-dTTAAT and 5′-dTTAAC, but not in the duplex containing the sequences 5′-dTTAAA and 5′-dTTAAG. In all nucleotide 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. No positive NOESY cross-peaks were detected with the G 1′H and C 1′H resonances, indicating that the minor groove hydration water near GC base 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′-dTTAA segment in d(GCATTAATGC)₂. More rigid hydration water was detected near T4 in d(GCATTAATGC)₂ as compared with 5′-d(GCATTAACGC)-3′-linker-5′-d(GCGTTAATGC)-3′, although the sequences differ only in a single base pair. This illustrates the high sensitivity of water-DNA NOEs towards small con-formational differences.