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| {{STRUCTURE_2hsl| PDB=2hsl | SCENE= }} | | {{STRUCTURE_2hsl| PDB=2hsl | SCENE= }} |
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| '''NMR structure of 13mer duplex DNA containing an abasic site, averaged structure (alpha anomer)'''
| | ===NMR structure of 13mer duplex DNA containing an abasic site, averaged structure (alpha anomer)=== |
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| ==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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_17323932}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 17323932 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_17323932}} |
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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=2HSL OCA]. | | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSL OCA]. |
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| ==Reference== | | ==Reference== |
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| [[Category: Base excision repair]] | | [[Category: Base excision repair]] |
| [[Category: Dna lesion]] | | [[Category: Dna lesion]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 06:39:40 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 03:49:30 2008'' |
