1coc

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{{Seed}}
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{{STRUCTURE_1coc| PDB=1coc | SCENE= }}
{{STRUCTURE_1coc| PDB=1coc | SCENE= }}
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'''SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER.'''
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===SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER.===
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==Overview==
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The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed.
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The line below this paragraph, {{ABSTRACT_PUBMED_9753551}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 9753551 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9753551}}
==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=1COC OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1COC OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Uv-photoproduct]]
[[Category: Uv-photoproduct]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 12:56:38 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 21:00:58 2008''

Revision as of 18:01, 30 June 2008

Image:1coc.png

Template:STRUCTURE 1coc

SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER.

Template:ABSTRACT PUBMED 9753551

About this Structure

Full experimental information is available from OCA.

Reference

Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA., McAteer K, Jing Y, Kao J, Taylor JS, Kennedy MA, J Mol Biol. 1998 Oct 9;282(5):1013-32. PMID:9753551

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