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'''13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure''' | '''13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure''' | ||
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==About this Structure== | ==About this Structure== | ||
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPX OCA]. | |||
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/17323932 17323932] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17323932 17323932] | ||
[[Category: Case, D A.]] | [[Category: Case, D A.]] | ||
[[Category: Chen, J.]] | [[Category: Chen, J.]] | ||
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[[Category: Stubbe, J.]] | [[Category: Stubbe, J.]] | ||
[[Category: Turner, C J.]] | [[Category: Turner, C J.]] | ||
[[Category: | [[Category: Abasic site]] | ||
[[Category: | [[Category: Bleomycin]] | ||
[[Category: | [[Category: Dna damage]] | ||
[[Category: | [[Category: Molecular dynamic]] | ||
[[Category: | [[Category: Nmr]] | ||
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Revision as of 06:33, 4 May 2008
13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure
OverviewOverview
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.
About this StructureAbout this Structure
Full crystallographic information is available from OCA.
ReferenceReference
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 Page seeded by OCA on Sun May 4 06:33:53 2008