1n4b: Difference between revisions

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[[Image:1n4b.gif|left|200px]]
{{Seed}}
[[Image:1n4b.png|left|200px]]


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{{STRUCTURE_1n4b|  PDB=1n4b  |  SCENE=  }}  
{{STRUCTURE_1n4b|  PDB=1n4b  |  SCENE=  }}  


'''Solution Structure of the undecamer CGAAAC*TTTCG'''
===Solution Structure of the undecamer CGAAAC*TTTCG===




==Overview==
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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.
The line below this paragraph, {{ABSTRACT_PUBMED_12484755}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 12484755 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12484755}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4B OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N4B OCA].  


==Reference==
==Reference==
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[[Category: Interstrand cross-link]]
[[Category: Interstrand cross-link]]
[[Category: Modified cytosine]]
[[Category: Modified cytosine]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:04:33 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:17:57 2008''

Revision as of 17:18, 28 July 2008

File:1n4b.png

Template:STRUCTURE 1n4b

Solution Structure of the undecamer CGAAAC*TTTCG

Template:ABSTRACT PUBMED 12484755

About this Structure

Full experimental information is available from OCA.

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:12484755

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