NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Yelena V. Lerman; Scott D. Kennedy; Neelaabh Shankar; Marc Parisien; Francois Major; Douglas H. Turner

doi:10.1261/rna.2641911

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

¹Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
²Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
³Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec H3C CJ7, Canada

Abstract

The NMR solution structure is reported of a duplex, 5′GUGAAGCCCGU/3′UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine–purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5′GAA/3′AGG, 5′GAG/3′AGG, 5′GAA/3′AAG, and 5′AAG/3′AGG. The structural information is compared with predictions made with the MC-Sym program.

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↵4 Corresponding author.

E-mail turner{at}chem.rochester.edu.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2641911.