2o4y: Difference between revisions

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[[Image:2o4y.gif|left|200px]]
{{Seed}}
[[Image:2o4y.png|left|200px]]


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{{STRUCTURE_2o4y|  PDB=2o4y  |  SCENE=  }}  
{{STRUCTURE_2o4y|  PDB=2o4y  |  SCENE=  }}  


'''Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide'''
===Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide===




==Overview==
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Universal bases hybridize with all other natural DNA or RNA bases, and have applications in PCR and sequencing. We have analysed by nuclear magnetic resonance spectroscopy the structure and dynamics of three DNA oligonucleotides containing the universal base analogues 5-nitroindole and 5-nitroindole-3-carboxamide. In all systems studied, both the 5-nitroindole nucleotide and the opposing nucleotide adopt a standard anti conformation and are fully stacked within the DNA duplex. The 5-nitroindole bases do not base pair with the nucleotide opposite them, but intercalate between this base and an adjacent Watson-Crick pair. In spite of their smooth accommodation within the DNA double-helix, the 5-nitroindole-containing duplexes exist as a dynamic mixture of two different stacking configurations exchanging fast on the chemical shift timescale. These configurations depend on the relative intercalating positions of the universal base and the opposing base, and their exchange implies nucleotide opening motions on the millisecond time range. The structure of these nitroindole-containing duplexes explains the mechanism by which these artificial moieties behave as universal bases.
The line below this paragraph, {{ABSTRACT_PUBMED_17438041}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 17438041 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17438041}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O4Y OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O4Y OCA].  


==Reference==
==Reference==
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[[Category: Loakes, D.]]
[[Category: Loakes, D.]]
[[Category: Dna universal base nitroindole intercalation dynamic]]
[[Category: Dna universal base nitroindole intercalation dynamic]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 10:19:58 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:37:21 2008''

Revision as of 16:37, 27 July 2008

File:2o4y.png

Template:STRUCTURE 2o4y

Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide

Template:ABSTRACT PUBMED 17438041

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide., Gallego J, Loakes D, Nucleic Acids Res. 2007;35(9):2904-12. Epub 2007 Apr 16. PMID:17438041

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