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Abstract
The solution structure of the d(T-C-G-A) sequence at acidic pH has been
determined by a combination of NMR and molecular dynamics calculations including
NOE intensity based refinements. This sequence forms a right-handed
parallel-stranded duplex with C+ .C (three hydrogen bonds along Watson-Crick
edge), G.G (two symmetry related N2-H.. N3 hydrogen bonds) and A.A (two symmetry
related N6-H..N7 hydrogen bonds) homo base-pair formation at acidic pH. The
duplex is stabilized by intra-strand base stacking at the C2-G3 step and
cross-strand base stacking at the G3-A4 step. The thymine residues on partner
strands are directed towards each other and are positioned over the C+ .C
base-pair. All four residues adopt anti glycosidic torsion angles and C2'-endo
type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which
exhibits large changes in twist angles between adjacent steps along the duplex.
This study rules out previously proposed models for the structure of the
d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions,
which established that d(C-G) and d(C-G-A) containing sequences at acidic pH
pair through parallel-stranded alignment. We have also monitored hydration
patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A)
duplex.
