1b5k

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{{STRUCTURE_1b5k| PDB=1b5k | SCENE= }}
{{STRUCTURE_1b5k| PDB=1b5k | SCENE= }}
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'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS'''
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===3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS===
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==Overview==
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The exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27 degrees bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T (N3H) and epsilon C(N4) stabilizes the epsilon C(syn).T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the epsilon C(syn).T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the epsilon C.dA and epsilon C.T duplexes.
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{{ABSTRACT_PUBMED_8873598}}
==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=1B5K OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5K 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 18:18:53 2008''

Revision as of 15:18, 30 June 2008

Image:1b5k.png

Template:STRUCTURE 1b5k

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

Template:ABSTRACT PUBMED 8873598

About this Structure

Full experimental information is available from OCA.

Reference

NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct., Cullinan D, Korobka A, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13319-27. PMID:8873598

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