Key result
The nuclear magnetic resonance structure of an 8 × 8 nucleotide RNA internal loop was determined and compared to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
The study provides a high-resolution NMR structure of a complex RNA internal loop to aid in the development of 3D structure prediction programs.
Benchmarks RNA 3D prediction tools; leaves open their accuracy for in vivo or therapeutic applications.
The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the nuclear magnetic resonance structure of the (5′CCA GAAACGGA UGG A ) 2 duplex, which contains an 8 × 8 nucleotide internal loop flanked by three Watson–Crick pairs on each side. The loop is comprised of a central 5′AC/3′CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
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Kauffmann et al. (2017) studied this question. Nuclear magnetic resonance structure determination vs. Automated predictions by MC-sym, RNA FARFAR, and RNAComposer was evaluated on Hydrogen bonding patterns, all-atom root-mean-square deviation, and deformation index. The nuclear magnetic resonance structure of an 8 × 8 nucleotide RNA internal loop was determined and compared to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
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