5NXT

Wobble base paired RNA double helix

Summary for 5NXT

• Entry DOI: 10.2210/pdb5nxt/pdb
• Descriptor: RNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3') (2 entities in total)
• Functional Keywords: double helix, wobble pairs, n1-adenine protonation, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 5717.45

Authors

Garg, A.,Heinemann, U. (deposition date: 2017-05-10, release date: 2017-11-29, Last modification date: 2024-01-17)

Primary citation

Garg, A.,Heinemann, U.
A novel form of RNA double helix based on G·U and C·A+ wobble base pairing.
RNA, 24:209-218, 2018

PubMed 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 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.

PubMed: 29122970
DOI: 10.1261/rna.064048.117

Experimental method

X-RAY DIFFRACTION (1.379 Å)