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1xcy

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[[Image:1xcy.gif|left|200px]]
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{{STRUCTURE_1xcy| PDB=1xcy | SCENE= }}
{{STRUCTURE_1xcy| PDB=1xcy | SCENE= }}
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'''Structure of DNA containing the alpha-anomer of a carbocyclic abasic site'''
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===Structure of DNA containing the alpha-anomer of a carbocyclic abasic site===
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==Overview==
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Naturally occurring abasic sites in DNA exist as an equilibrium mixture of the aldehyde, the hydrated aldehyde, and the hemiacetal forms (dominant). The influence of the configuration of the C1' hydroxyl group of the hemiacetal form on duplex structure and abasic site repair has been examined using novel carbocyclic analogues. Both the alpha- and beta-forms of this novel abasic site were introduced into oligomeric DNA using the standard DMT-phosphoramidite approach in an automated solid-phase synthesizer. Solution structures of the d(CGTACXCATGC).d(GCATGAGTACG) duplex (where X is the alpha- or beta-anomer of the carbocyclic abasic site analogue) were determined by NMR spectroscopy and restrained molecular dynamics simulations. The structures were only minimally perturbed by the presence of either anomer of the abasic site. All residues adopted an anti conformation, and Watson-Crick alignments were observed on all base pairs of the duplexes. At the lesion site, the abasic residues and their partner adenines showed increased dynamic behavior but adopted intrahelical positions in the final refined structures. Incision of duplexes having the alpha- or beta-anomer of the carbocyclic abasic site by human AP endonuclease showed that the enzyme recognizes both configurations of the lesion and nicks the DNA backbone with similar efficiency. Our results challenge the suggestion that Ape1 is stereoselective and imply a plasticity at the active site of the enzyme for accommodating either anomer of the lesion.
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The line below this paragraph, {{ABSTRACT_PUBMED_15581347}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 15581347 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15581347}}
==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=1XCY OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XCY OCA].
==Reference==
==Reference==
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[[Category: Abasic site]]
[[Category: Abasic site]]
[[Category: Double helix]]
[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:52:13 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:59:42 2008''

Revision as of 10:59, 28 July 2008

Image:1xcy.png

Template:STRUCTURE 1xcy

Structure of DNA containing the alpha-anomer of a carbocyclic abasic site

Template:ABSTRACT PUBMED 15581347

About this Structure

Full experimental information is available from OCA.

Reference

Impact of the C1' configuration of abasic sites on DNA duplex structure., de Los Santos C, El-Khateeb M, Rege P, Tian K, Johnson F, Biochemistry. 2004 Dec 14;43(49):15349-57. PMID:15581347

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