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| - | [[Image:1s37.gif|left|200px]]<br /><applet load="1s37" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1s37" /> | |
| - | '''Accomodation of Mispair-Aligned N3T-Ethyl-N3T DNA Interstrand Crosslink'''<br /> | |
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| - | ==Overview== | + | ==Accomodation of Mispair-Aligned N3T-Ethyl-N3T DNA Interstrand Crosslink== |
| - | The solution structure of the undecamer d(CGAAATTTTCG)(2), where T represents a N(3)T-ethyl-N(3)T interstrand cross link, was elucidated using molecular dynamics calculations restrained by NOE and dihedral data obtained from NMR spectroscopy. The ethyl moiety is particularly well-accommodated between the minor and major grooves. This is an exceptional example of the plasticity along the axis defined by the stem and a unique finding of an interstrand cross link occupying the area associating minor and major grooves. The mismatch-aligned tethered bases preserve good intrastrand stacking with flanking bases. Base-pair steps adjacent to the lesion site are overwound. Accommodation of the lesion also results in an increase in mispair staggering alignment modulated by flexibility because of the tetrahedral geometry of the exocyclic ethyl carbon atoms. This is mechanically coupled with a small measure of concomitant propeller twisting without an increase in intrastrand base-step distance. Both x displacement and sugar puckering are indicative of canonical B DNA throughout the stem. We have thus established that the lesion defined by mismatch-aligned minor groove N(3)T-ethyl-N(3)T cross-linked thymine bases produces very localized distortions in a DNA stem that may be difficult to recognize by repair mechanisms that are not transcription- or replication-coupled. Thus, this synthetic DNA is a valuable structural probe to study mechanisms of repair.
| + | <StructureSection load='1s37' size='340' side='right'caption='[[1s37]]' scene=''> |
| - | | + | == Structural highlights == |
| - | ==About this Structure== | + | <table><tr><td colspan='2'>[[1s37]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S37 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S37 FirstGlance]. <br> |
| - | 1S37 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=EHN:'>EHN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S37 OCA].
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TTM:N3-ETHYL-THYMIDINE-5-MONOPHOSPHATE'>TTM</scene></td></tr> |
| - | ==Reference==
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s37 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s37 OCA], [https://pdbe.org/1s37 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s37 RCSB], [https://www.ebi.ac.uk/pdbsum/1s37 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s37 ProSAT]</span></td></tr> |
| - | Accommodation of mispair aligned N3T-ethyl-N3T DNA interstrand cross link., da Silva MW, Wilds CJ, Noronha AM, Colvin OM, Miller PS, Gamcsik MP, Biochemistry. 2004 Oct 5;43(39):12549-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15449944 15449944]
| + | </table> |
| - | [[Category: Protein complex]] | + | __TOC__ |
| - | [[Category: Colvin, O M.]] | + | </StructureSection> |
| - | [[Category: Gamcsik, M P.]] | + | [[Category: Large Structures]] |
| - | [[Category: Miller, P S.]] | + | [[Category: Colvin OM]] |
| - | [[Category: Noll, D M.]] | + | [[Category: Gamcsik MP]] |
| - | [[Category: Noronha, A M.]] | + | [[Category: Miller PS]] |
| - | [[Category: Silva, M W.da.]] | + | [[Category: Noll DM]] |
| - | [[Category: EHN]]
| + | [[Category: Noronha AM]] |
| - | [[Category: dna interstrand cross-link]]
| + | [[Category: Da Silva MW]] |
| - | [[Category: interstrand crosslink]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:57:25 2008''
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