NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes

Hammerhead ribozymes are a model system for studying molecular mechanism of RNA catalysis. Physicochemical data-driven mechanistic studies are an indispensable step towards understanding the catalysis of hammerhead ribozymes. Here we characterized a model RNA duplex with catalytically important shea...

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Bibliographic Details
Published in:Nucleosides, nucleotides & nucleic acids nucleotides & nucleic acids, 2018-01, Vol.37 (7), p.383-396
Main Authors: Hattori, Yoshikazu, Yamanaka, Daichi, Morioka, Saori, Yamaguchi, Taishi, Tomonari, Honoka, Kojima, Chojiro, Tanaka, Yoshiyuki
Format: Article
Language:English
Subjects:
Binding Sites
Catalysis
Catalytic Domain
core sequence
Magnetic Resonance Spectroscopy
Metal ions
NMR
Nuclear magnetic resonance
Nucleic Acid Conformation
Nucleic Acid Heteroduplexes
Nucleotide sequence
Physicochemical properties
Ribonucleic acid
Ribozymes
RNA
RNA, Catalytic - chemistry
RNA, Catalytic - metabolism
spectroscopic characterization
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Summary:Hammerhead ribozymes are a model system for studying molecular mechanism of RNA catalysis. Physicochemical data-driven mechanistic studies are an indispensable step towards understanding the catalysis of hammerhead ribozymes. Here we characterized a model RNA duplex with catalytically important sheared-type G12-A9 base pair and A9-G10.1 metal ion-binding motif in hammerhead ribozymes. By using high magnetic field NMR, all base proton signals, including catalytic residues, were unambiguously assigned. We further characterized structural features of this RNA molecule and found that it reflects the structural features of the A9-G10.1 motif of hammerhead ribozymes. Therefore, this RNA molecule is suitable for extracting an intrinsic physicochemical properties of catalytically important residues.
ISSN:1525-7770
1532-2335
DOI:10.1080/15257770.2018.1473877