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1qe7

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[[Image:1qe7.gif|left|200px]]
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{{Seed}}
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[[Image:1qe7.png|left|200px]]
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{{STRUCTURE_1qe7| PDB=1qe7 | SCENE= }}
{{STRUCTURE_1qe7| PDB=1qe7 | SCENE= }}
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'''SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA'''
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===SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA===
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==Overview==
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Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The(1)H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T(12)and U(15)nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T(14)stacks upon both T(12)and U(15)while T(13)partially stacks upon T(14). Very weak stacking interaction is observed between T(13)and T(12). All the individual nucleotide bases adopt ' anti ' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T(13)and T(14). The stereochemistry of U(15)mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.
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The line below this paragraph, {{ABSTRACT_PUBMED_10481034}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 10481034 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10481034}}
==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=1QE7 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QE7 OCA].
==Reference==
==Reference==
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[[Category: Hairpin loop]]
[[Category: Hairpin loop]]
[[Category: Uracil]]
[[Category: Uracil]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 06:10:48 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:17:51 2008''

Revision as of 14:17, 28 July 2008

Image:1qe7.png

Template:STRUCTURE 1qe7

SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA

Template:ABSTRACT PUBMED 10481034

About this Structure

Full experimental information is available from OCA.

Reference

Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics., Ghosh M, Kumar NV, Varshney U, Chary KV, Nucleic Acids Res. 1999 Oct 1;27(19):3938-44. PMID:10481034

Page seeded by OCA on Mon Jul 28 17:17:51 2008

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