1ttd: Difference between revisions
New page: left|200px<br /> <applet load="1ttd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ttd" /> '''SOLUTION-STATE STRUCTURE OF A DNA DODECAMER... |
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'''SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER'''<br /> | '''SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER'''<br /> | ||
==Overview== | ==Overview== | ||
The solution structures of a duplex DNA dodecamer containing a cis-syn | 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. | ||
==About this Structure== | ==About this Structure== | ||
1TTD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. The following page contains interesting information on the relation of 1TTD with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. Full crystallographic information is available from [http:// | 1TTD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. The following page contains interesting information on the relation of 1TTD with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TTD OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Jing, Y.]] | [[Category: Jing, Y.]] | ||
[[Category: Kao, J.]] | [[Category: Kao, J.]] | ||
[[Category: Kennedy, M | [[Category: Kennedy, M A.]] | ||
[[Category: Mcateer, K.]] | [[Category: Mcateer, K.]] | ||
[[Category: Taylor, J | [[Category: Taylor, J S.]] | ||
[[Category: bii backbone]] | [[Category: bii backbone]] | ||
[[Category: dna structure]] | [[Category: dna structure]] | ||
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[[Category: uv-photoproducts]] | [[Category: uv-photoproducts]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:17:10 2008'' | ||
Revision as of 16:17, 21 February 2008
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SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER
OverviewOverview
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.
About this StructureAbout this Structure
1TTD is a Protein complex structure of sequences from [1]. The following page contains interesting information on the relation of 1TTD with [Thymine Dimers]. Full crystallographic information is available from OCA.
ReferenceReference
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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