2hsr
From Proteopedia
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13mer duplex DNA containing an abasic site with beta anomer
Overview
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 Structure
2HSR is a Protein complex structure of sequences from [1]. Full crystallographic 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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