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| - | [[Image:1xci.gif|left|200px]] | |
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| - | {{Structure
| + | ==Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink== |
| - | |PDB= 1xci |SIZE=350|CAPTION= <scene name='initialview01'>1xci</scene>
| + | <StructureSection load='1xci' size='340' side='right'caption='[[1xci]]' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TTM:N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE'>TTM</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xci OCA], [http://www.ebi.ac.uk/pdbsum/1xci PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xci RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink'''
| + | [[Category: Synthetic construct]] |
| - | | + | [[Category: Bierbryer RG]] |
| - | | + | [[Category: Colvin OM]] |
| - | ==Overview==
| + | [[Category: Gamcsik MP]] |
| - | 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: Miller PS]] |
| - | | + | [[Category: Noronha AM]] |
| - | ==About this Structure==
| + | [[Category: Wilds CJ]] |
| - | 1XCI is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XCI OCA].
| + | [[Category: Da Silva MW]] |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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: Protein complex]] | + | |
| - | [[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 Mon Mar 31 00:47:42 2008''
| + | |
