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A novel form of RNA double helix based on G·U and C·A(+) wobble base pairing

Item Type:Article
Title:A novel form of RNA double helix based on G·U and C·A(+) wobble base pairing
Creators Name:Garg, A. and Heinemann, U.
Abstract: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 GvU 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.
Keywords:RNA Double Helix, Wobble Base Pairing, Wobble Helix, Adenine N1 Protonation, pH Dependent Structural Variation
Publisher:Cold Spring Harbor Laboratory Press (U.S.A.)
Page Range:209-218
Date:February 2018
Official Publication:https://doi.org/10.1261/rna.064048.117
External Fulltext:View full text on PubMed Central
PubMed:View item in PubMed

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