179d
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SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS
OverviewOverview
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.
About this StructureAbout this Structure
179D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs., Wang Y, Patel DJ, J Mol Biol. 1994 Sep 30;242(4):508-26. PMID:7932707
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