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A novel form of RNA double helix based on G{middle dot}U and C{middle dot}A+ wobble base pairing [ARTICLE]

Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double-helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A+ wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A+ base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson–Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A+ base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.

Authors:   Ankur Garg; Udo Heinemann
Journal:   RNA
Volume:   24
edition:   2
Year:   2018
Pages:   209
DOI:   10.1261/rna.064048.117
Publication date:   01-Feb-2018
Facts, background information, dossiers
  • nucleic acids
  • hydrogen bonds
  • DNA nanotechnology
More about Cold Spring Harbor Laboratory Press
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