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| - | [[Image:1xci.gif|left|200px]] | |
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| - | <!--
| + | ==Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink== |
| - | The line below this paragraph, containing "STRUCTURE_1xci", creates the "Structure Box" on the page.
| + | <StructureSection load='1xci' size='340' side='right'caption='[[1xci]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1xci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XCI FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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> |
| - | {{STRUCTURE_1xci| PDB=1xci | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xci OCA], [https://pdbe.org/1xci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xci RCSB], [https://www.ebi.ac.uk/pdbsum/1xci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xci ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Synthetic construct]] |
| - | The introduction of a covalent interstrand cross-link induces changes in the intrinsic structure and deformability of the DNA helix that are recognized by elements of the DNA repair apparatus. In this context, the solution structure of the undecamer d(CGAAAT*TTTCG)2, where T* represents a N3T-butyl-N3T interstrand cross-link, was determined using molecular dynamics calculations restrained by NOE and dihedral angle data obtained from NMR spectroscopy. The structure of this cross-linked undecamer shows dramatic widening of the major groove of the B-DNA stem without disruption of Watson-Crick base pairing. This change in tertiary structure illustrates the cumulative effect of cooperativity in intrastrand base stacking of an A-tract of three adenines. Further, it is the direct result from the imposition of geometric angular constraints by the cross-link chain on an ApT* and T*pT steps in the segment AAAT*T. The widening of the major groove is due to the dominant contribution of base stacking to the stability of the ApT compared to the TpT step suggesting that the latter is more deformable within a DNA stem. Compared to earlier structures of ethyl cross-linked oligonucleotides, this unique perturbation induced by the butyl moiety offers a new probe for systematic studies of DNA repair mechanisms.
| + | [[Category: Bierbryer RG]] |
| - | | + | [[Category: Colvin OM]] |
| - | ==About this Structure==
| + | [[Category: Gamcsik MP]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XCI OCA]. | + | [[Category: Miller PS]] |
| - | | + | [[Category: Noronha AM]] |
| - | ==Reference== | + | [[Category: Wilds CJ]] |
| - | Intrastrand base-stacking buttresses widening of major groove in interstrand cross-linked B-DNA., da Silva MW, Bierbryer RG, Wilds CJ, Noronha AM, Colvin OM, Miller PS, Gamcsik MP, Bioorg Med Chem. 2005 Jul 15;13(14):4580-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15953553 15953553]
| + | [[Category: Da Silva MW]] |
| - | [[Category: Bierbryer, R G.]] | + | |
| - | [[Category: Colvin, O M.]] | + | |
| - | [[Category: Gamcsik, M P.]] | + | |
| - | [[Category: Miller, P S.]] | + | |
| - | [[Category: Noronha, A M.]] | + | |
| - | [[Category: Silva, M W.da.]] | + | |
| - | [[Category: Wilds, C J.]] | + | |
| - | [[Category: Double helix]] | + | |
| - | [[Category: Interstrand cross-link]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:51:19 2008''
| + | |
