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1n4b

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(New page: 200px<br /><applet load="1n4b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n4b" /> '''Solution Structure of the undecamer CGAAAC*T...)
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[[Image:1n4b.gif|left|200px]]<br /><applet load="1n4b" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1n4b" />
 
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'''Solution Structure of the undecamer CGAAAC*TTTCG'''<br />
 
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==Overview==
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==Solution Structure of the undecamer CGAAAC*TTTCG==
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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.
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<StructureSection load='1n4b' size='340' side='right'caption='[[1n4b]]' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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1N4B is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with EHN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N4B OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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==Reference==
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<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>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12484755 12484755]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Colvin, O.M.]]
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</StructureSection>
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[[Category: Gamcsik, M.P.]]
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[[Category: Large Structures]]
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[[Category: Miller, P.S.]]
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[[Category: Colvin OM]]
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[[Category: Noll, D.M.]]
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[[Category: Gamcsik MP]]
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[[Category: Noronha, A.M.]]
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[[Category: Miller PS]]
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[[Category: Silva, M.Webba.da.]]
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[[Category: Noll DM]]
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[[Category: EHN]]
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[[Category: Noronha AM]]
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[[Category: alkylated cytosine]]
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[[Category: Webba da Silva M]]
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[[Category: alkylated dna]]
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[[Category: interstrand cross-link]]
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[[Category: modified cytosine]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:32:32 2007''
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Current revision

Solution Structure of the undecamer CGAAAC*TTTCG

PDB ID 1n4b

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