2o4y
From Proteopedia
(New page: 200px<br /><applet load="2o4y" size="350" color="white" frame="true" align="right" spinBox="true" caption="2o4y" /> '''Solution structure of a DNA duplex containin...) |
|||
| Line 4: | Line 4: | ||
==Overview== | ==Overview== | ||
| - | Universal bases hybridize with all other natural DNA or RNA bases, and | + | 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== | ==About this Structure== | ||
| Line 16: | Line 16: | ||
[[Category: dna universal base nitroindole intercalation dynamics]] | [[Category: dna universal base nitroindole intercalation dynamics]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:14:28 2008'' |
Revision as of 16:14, 21 February 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
2O4Y is a Protein complex structure of sequences from [1]. 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 Thu Feb 21 18:14:28 2008
