1b6y
From Proteopedia
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3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES
Overview
The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G), oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine, adduct positioned opposite 2'-deoxyadenosine in the center of the helix, has been analyzed by proton NMR spectroscopy and restrained molecular, dynamics. The spectroscopic data establish a right-handed duplex, with, sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti, conformation around the glycosidic torsion angle and, with the exception, of epsilon C.dA, Watson-Crick hydrogen bond alignment for all base pairs., Molecular dynamics simulations, restrained by the full relaxation matrix, approach, produced a three-dimensional model with an NMR R-factor of 7%., The duplex structure shows no significant perturbation of the, sugar-phosphate backbone, which remains in B-form. The exocyclic adduct, and its partner dA are incorporated into the helix without producing a, noticeable kink. The epsilon C.dA alignment adopts a staggered, conformation with each residue displaced toward the 5'-terminus and, intercalated between bases on the opposite strand, without increase of, inter-phosphate distances. The partial intercalation of the epsilon C, (anti).dA(anti) alignment allows stacking between the aromatic rings of, epsilon C and dA and with base pairs adjacent to the lesion, suggesting an, important role played by hydrophobic forces in the stabilization of the, solution structure.
About this Structure
1B6Y is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics., Korobka A, Cullinan D, Cosman M, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13310-8. PMID:8873597
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