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Biochemistry. 2017 Jul 25;56(29):3733-3744. doi: 10.1021/acs.biochem.7b00201. Epub 2017 Jul 12.

Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.

Author information

1
Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.
2
Center for RNA Biology, University of Rochester , Rochester, New York 14627, United States.
3
Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester , Rochester, New York 14642, United States.

Abstract

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 × 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.

PMID:
28700212
PMCID:
PMC5609818
DOI:
10.1021/acs.biochem.7b00201
[Indexed for MEDLINE]
Free PMC Article

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