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Interbase FRET in RNA: from A to Z

Journal article
Authors A. F. Fuchtbauer
M. S. Wranne
Mattias Bood
Erik Weis
P. Pfeiffer
J. R. Nilsson
A. Dahlen
Mårten Grøtli
L. M. Wilhelmsson
Published in Nucleic Acids Research
Volume 47
Issue 19
Pages 9990-9997
ISSN 0305-1048
Publication year 2019
Published at Department of Chemistry and Molecular Biology
Pages 9990-9997
Language en
Keywords z-alpha domain, nucleic-acid, phosphoramidite, visualization, fluorescence, Biochemistry & Molecular Biology
Subject categories Biochemistry and Molecular Biology


Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tC(O) and the non-emissive acceptor tC(nitro). The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.

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