Protocol abstract
Nature Protocols 2, - 1954 - 1962 (2007)
Published online: 9 August 2007 | doi:10.1038/nprot.2007.273
Subject Categories: Isolation, purification and separation | Chemical modification | Nucleic acid based molecular biology | Synthetic chemistry | Spectroscopy and structural analysis
Site-specific incorporation of nitroxide spin-labels into 2'-positions of nucleic acids
Thomas E Edwards1 & Snorri Th Sigurdsson1
Abstract
A protocol is described for the incorporation of nitroxide spin-labels into specific 2'-sites within nucleic acids. This labeling strategy facilitates the investigation of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) spectroscopy and macromolecular complex formation using paramagnetic relaxation enhancement NMR spectroscopy. A spin-labeling reagent, 4-isocyanato TEMPO, which can be prepared in one facile step or obtained commercially, is used for postsynthetic modification of site-specifically 2'-amino-modified nucleic acids. This spin-labeling protocol has been applied primarily to RNA, but is also applicable to DNA. Subsequently, EPR spectroscopic analysis of the spin-labeled nucleic acids allows for the measurements of distances, solvent accessibilities and conformation dynamics. Using the spin-labeling strategy described here, spin-labeled samples can be prepared in 2–4 d.
- University of Iceland, Science Institute, Dunhaga 3, IS-107 Reykjavik, Iceland.
Correspondence to: Snorri Th Sigurdsson1 e-mail: snorrisi@hi.is
nature-products
A-Z product listing
- 0.1-ml Hamilton glass syringe(Fisher Scientific)
- 0.8
1.0 mm2 Quartz capillary tubes(VitroCom, Inc) - 1.5-ml microtubes(Fisher Scientific)
- 2'-amino uridine phosphoramidite(Chemgenes)
- 4-Amino-2,2,6,6-tetramethylpiperidine-1-oxyl (4-amino TEMPO(Sigma-Aldrich)
- 4-isocyanato TEMPO(Toronto Research Chemicals)
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