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

作者：Lerman Yelena V; Kennedy Scott D; Shankar Neelaabh; Parisien Marc; Major Francois; Turner Douglas H^*

来源：RNA-A Publication of the RNA Society, 2011, 17(9): 1664-1677.

DOI：10.1261/rna.2641911

• retrotransposon
• RNA structure
• RNA motif
• NMR
• internal loop

The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 x 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 degrees 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.

• 出版日期2011-9