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Nucleic Acids Research, 2003, Vol. 31, No. 21 e135
© 2003 Oxford University Press

Rapid purification of RNA secondary structures

Stacy L. Gelhaus, William R. LaCourse*, Nathan A. Hagan, Gaya K. Amarasinghe and Daniele Fabris

Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA

*To whom correspondence should be addressed. Tel: +1 410 455 2105; Fax: +1 410 455 2608; Email: lacourse{at}umbc.edu
Present address:
Gaya Amarasinghe, Department of Biochemistry, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

A new method for rapid purification and structural analysis of oligoribonucleotides of 19 and 20 nt is applied to RNA hairpins SL3 and SL2, which are stable secondary structures present on the {psi} recognition element of HIV-1. This approach uses ion-pairing reversed-phase liquid chromatography (IP-RPLC) to achieve the separation of the stem–loop from the transcription mix. Evidence is presented that IP-RPLC is sensitive to the different conformers of these secondary structures. The purity of each stem–loop was confirmed by mass spectrometry and PAGE. IP-RPLC purification was found to be superior to PAGE in terms of time, safety and, most importantly, purity.


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[Abstract] [Full Text] [PDF]


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