179D

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

Summary for 179D

• Entry DOI: 10.2210/pdb179d/pdb
• Descriptor: DNA (5'-D(*TP*CP*GP*A)-3') (1 entity in total)
• Functional Keywords: dna
• Total number of polymer chains: 2
• Total formula weight: 2381.66

Authors

Wang, Y.,Patel, D.J. (deposition date: 1994-06-15, release date: 1994-07-31, Last modification date: 2024-05-22)

Primary citation

Wang, Y.,Patel, D.J.
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.
J.Mol.Biol., 242:508-526, 1994

PubMed 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.

PubMed: 7932707

Experimental method

SOLUTION NMR