Nucleic Acids Research, Vol 24, Issue 15 2911-2918, Copyright © 1996 by Oxford University Press
A Jacobson, W Leupin, E Liepinsh and F Otting
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(GCATTAATGC)2 and the
singly cross-linked decameric duplexes 5'-d(GCATTAACGC)-3'-
linker-5'-d(GCGTTAATGC)-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 approximately 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 conformational differences.
ARTICLES
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
Department of Medical Biochemisry and Biophysics, Karolinska Institute, S-171 77 Stockholm, Sweden.
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