Journal
BIOCHEMISTRY
Volume 56, Issue 29, Pages 3733-3744Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.biochem.7b00201
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Funding
- National Institutes of Health [GM22939]
- National Institutes of Health Shared Instrumentation Grant [1S10 OD012254]
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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'CCAGAAACGGAUGGA)(2) duplex, which contains an 8 x 8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central S'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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