Conversion of stable RNA hairpin to a metastable dimer in frozen solution
Abstract
Previous studies employing a 79-nucleotide (nt) RNA indicated that this RNA could form two bands in a native polyacrylamide gel while one band was observed in a denaturing gel. This report describes an investigation on the nature of the two corresponding structures and the segment responsible for forming the slower mobility band. Sedimentation equilibrium of the 79-nt RNA was consistent with the two gel bands corresponding to monomer and dimer forms. The portion of the RNA required for dimer formation was explored using a secondary structure prediction algorithm of two 79-nt RNAs linked in a head-to-tail fashion. The predicted structure suggested that the first 21-nt at the 5′ end of each RNA formed a self-complementary duplex. A ribonuclease H assay carried out with RNA prepared as monomer (M), or a mixture of monomer and dimer (M/D), gave results consistent with the predicted M and D structures. Gel mobility experiments on 5′ and 3′ segments of the 79-nt RNA also indicated that dimer formation was due to the 21-nt 5′ end. Studies on the 21-nt RNA molecule and sequence variants showed that this sequence can form a hairpin and a dimer complex. Unexpectedly, the hairpin to dimer conversion was shown to occur at high efficiency in frozen solution, although little or no conversion was observed above 0°C. The results indicate that a freezing environment can promote formation of intermolecular RNA complexes from stable RNA hairpins, supporting the notion that this environment could have played a role in the evolution of RNA complexity.
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Footnotes
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Reprint requests to: Roger M. Wartell, School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332, USA; e-mail: roger.wartell{at}biology.gatech.edu; fax: (404) 894-0519.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.433307.
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- Received December 14, 2006.
- Accepted August 29, 2007.
- Copyright © 2007 RNA Society