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2hpx

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{{STRUCTURE_2hpx| PDB=2hpx | SCENE= }}
{{STRUCTURE_2hpx| PDB=2hpx | SCENE= }}
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'''13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure'''
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===13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure===
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 17323932 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17323932}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPX OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPX OCA].
==Reference==
==Reference==
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[[Category: Molecular dynamic]]
[[Category: Molecular dynamic]]
[[Category: Nmr]]
[[Category: Nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:47:12 2008''

Revision as of 21:47, 27 July 2008

Image:2hpx.png

Template:STRUCTURE 2hpx

13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure

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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