1B6Y

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES

Summary for 1B6Y

• Entry DOI: 10.2210/pdb1b6y/pdb
• Descriptor: 5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3', 5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3' (2 entities in total)
• Functional Keywords: deoxyribonucleic acid, ethenodc, edc, exocyclic lesion, dna
• Total number of polymer chains: 2
• Total formula weight: 6716.42

Authors

Korobka, A.,Cullinan, D.,Cosman, M.,Grollman, A.P.,Patel, D.J.,Eisenberg, M.,De Los Santos, C. (deposition date: 1999-01-19, release date: 1999-01-27, Last modification date: 2024-04-10)

Primary citation

Korobka, A.,Cullinan, D.,Cosman, M.,Grollman, A.P.,Patel, D.J.,Eisenberg, M.,de los Santos, C.
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.
Biochemistry, 35:13310-13318, 1996

PubMed Abstract: 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.

PubMed: 8873597
DOI: 10.1021/bi9605696

Experimental method

SOLUTION NMR