2o4y
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:2o4y.gif|left|200px]] | [[Image:2o4y.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_2o4y", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{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''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O4Y OCA]. | |
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/17438041 17438041] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17438041 17438041] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Gallego, J.]] | [[Category: Gallego, J.]] | ||
[[Category: Loakes, D.]] | [[Category: Loakes, D.]] | ||
| - | [[Category: | + | [[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 | + | |
Revision as of 07:20, 4 May 2008
Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide
Overview
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.
About this Structure
Full crystallographic 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 Page seeded by OCA on Sun May 4 10:19:58 2008
