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[[Image:2hsk.gif|left|200px]]
{{Seed}}
[[Image:2hsk.png|left|200px]]


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{{STRUCTURE_2hsk|  PDB=2hsk  |  SCENE=  }}  
{{STRUCTURE_2hsk|  PDB=2hsk  |  SCENE=  }}  


'''NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)'''
===NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)===




==Overview==
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A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
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{{ABSTRACT_PUBMED_17323932}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA].  


==Reference==
==Reference==
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[[Category: Base excision repair]]
[[Category: Base excision repair]]
[[Category: Dna lesion]]
[[Category: Dna lesion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:06:52 2008''

Revision as of 03:06, 29 July 2008

File:2hsk.png

Template:STRUCTURE 2hsk

NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)

Template:ABSTRACT PUBMED 17323932

About this Structure

Full experimental information is available from OCA.

Reference

Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites., Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J, Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932

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