Key result
The NMR solution structure of a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA reveals a 3RRs motif that is 1.6 kcal/mol more stable at 37°C than predicted.
Identifies the 3RRs motif as a common structural element in RNA that can facilitate 3D structure prediction.
Improves RNA 3D structure prediction models; leaves open whether targeting this highly.
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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Lerman et al. (2011) studied this question. The NMR solution structure of a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA reveals a 3RRs motif that is 1.6 kcal/mol more stable at 37°C than predicted.
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