1b6y

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{{STRUCTURE_1b6y| PDB=1b6y | SCENE= }}
{{STRUCTURE_1b6y| PDB=1b6y | SCENE= }}
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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'''
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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===
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==Overview==
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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.
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{{ABSTRACT_PUBMED_8873597}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA].
==Reference==
==Reference==
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[[Category: Ethenodc]]
[[Category: Ethenodc]]
[[Category: Exocyclic lesion]]
[[Category: Exocyclic lesion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:24:51 2008''

Revision as of 15:24, 30 June 2008

Image:1b6y.png

Template:STRUCTURE 1b6y

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

Template:ABSTRACT PUBMED 8873597

About this Structure

Full experimental 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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