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| - | [[Image:1n4b.gif|left|200px]] | |
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| - | <!--
| + | ==Solution Structure of the undecamer CGAAAC*TTTCG== |
| - | The line below this paragraph, containing "STRUCTURE_1n4b", creates the "Structure Box" on the page.
| + | <StructureSection load='1n4b' size='340' side='right'caption='[[1n4b]]' 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'>[[1n4b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N4B 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=D00:2-DEOXY-N-ETHYLCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>D00</scene></td></tr> |
| - | {{STRUCTURE_1n4b| PDB=1n4b | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n4b OCA], [https://pdbe.org/1n4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n4b RCSB], [https://www.ebi.ac.uk/pdbsum/1n4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n4b ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Solution Structure of the undecamer CGAAAC*TTTCG'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Colvin OM]] |
| - | The solution structure of an interstrand cross-linked self-complementary oligodeoxynucleotide containing directly opposed alkylated N(4)C-ethyl-N(4)C cytosine bases was determined by molecular dynamics calculations guided by NMR-derived restraints. The undecamer d(CGAAACTTTCG)(2), where C represents directly opposed alkylated N(4)C-ethyl-N(4)C cytosine bases, serves as model for the cytotoxic cross-links formed by bifunctional alkylating agents used in cancer therapy. The structure of the duplex shows the cross-link protruding into the major groove. An increase in the diameter of the DNA at the pseudoplatform formed by the cross-linked residues creates an A-DNA characteristic hole in the central portion of the DNA. This results in a centrally underwound base step and a number of subsequent overwinding steps leading to an overall axis bend toward the major groove. The structure shows narrowing of both minor and major grooves in the proximity of the cross-link. The perturbation leads to preferential intrastrand base stacking, disruption of adjacent canonical (A.T) base pairing, and buckling of base pairs, the extent of which diminishes with progression away from the lesion site. Overall, the distortion induced by the cross-link spreads over three base pairs on the 5'- and 3'-sides of the cross-link.
| + | [[Category: Gamcsik MP]] |
| - | | + | [[Category: Miller PS]] |
| - | ==About this Structure== | + | [[Category: Noll DM]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4B OCA]. | + | [[Category: Noronha AM]] |
| - | | + | [[Category: Webba da Silva M]] |
| - | ==Reference== | + | |
| - | Solution structure of a DNA duplex containing mispair-aligned N4C-ethyl-N4C interstrand cross-linked cytosines., Webba da Silva M, Noronha AM, Noll DM, Miller PS, Colvin OM, Gamcsik MP, Biochemistry. 2002 Dec 24;41(51):15181-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12484755 12484755] | + | |
| - | [[Category: Colvin, O M.]]
| + | |
| - | [[Category: Gamcsik, M P.]] | + | |
| - | [[Category: Miller, P S.]] | + | |
| - | [[Category: Noll, D M.]] | + | |
| - | [[Category: Noronha, A M.]] | + | |
| - | [[Category: Silva, M Webba da.]] | + | |
| - | [[Category: Alkylated cytosine]] | + | |
| - | [[Category: Alkylated dna]] | + | |
| - | [[Category: Interstrand cross-link]] | + | |
| - | [[Category: Modified cytosine]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:04:33 2008''
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