Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex

Chien Chung Cheng; Kuo Chan Hung; Wei Chun Huang-Fu

doi:10.1002/jccs.200500186

Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex

Chien Chung Cheng, Kuo Chan Hung, Wei Chun Huang-Fu

Research output: Contribution to journal › Article › peer-review

Abstract

Single-stranded RNA molecules usually include secondary structural elements such as bulges, internal loops, and hairpin loops. These RNA secondary structural elements are often essential for the biological activity and functions of the RNA molecule. Chemical probe Co¹¹(HAPP)(TFA) ₂ in the presence of H₂O₂ is found to differentiate single-stranded RNA from branched structures and hairpin loops. This study uses Co¹¹(HAPP)(TFA)₂ to analyze the structures of two RNA molecules: a fragment of HIV TAR RNA (TAR-27) and the catalytic domain 5 of group II intron (D5-29). The electrophoretic mobility of TAR-27 does not shift in the presence of Co¹¹(HAPP)(TFA)₂, suggesting that the reagent does not change the conformation of RNA substrate. Cleavage of the RNA substrates by Co¹¹(HAPP)(TFA)₂ unambiguously differentiated RNA internal looped structures from hairpin loops. The results show that Co¹¹(HAPP)(TFA)₂ is a sensitive, informative and convenient tool for analysis of RNA secondary structures.

Original language	English
Pages (from-to)	1291-1297
Number of pages	7
Journal	Journal of the Chinese Chemical Society
Volume	52
Issue number	6
DOIs	https://doi.org/10.1002/jccs.200500186
Publication status	Published - 2005
Externally published	Yes

Keywords

Bulge
Cobalt
Hairpin loop
Internal loop
RNA cleavage

ASJC Scopus subject areas

General Chemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1002/jccs.200500186

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title = "Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex",

abstract = "Single-stranded RNA molecules usually include secondary structural elements such as bulges, internal loops, and hairpin loops. These RNA secondary structural elements are often essential for the biological activity and functions of the RNA molecule. Chemical probe Co11(HAPP)(TFA) 2 in the presence of H2O2 is found to differentiate single-stranded RNA from branched structures and hairpin loops. This study uses Co11(HAPP)(TFA)2 to analyze the structures of two RNA molecules: a fragment of HIV TAR RNA (TAR-27) and the catalytic domain 5 of group II intron (D5-29). The electrophoretic mobility of TAR-27 does not shift in the presence of Co11(HAPP)(TFA)2, suggesting that the reagent does not change the conformation of RNA substrate. Cleavage of the RNA substrates by Co11(HAPP)(TFA)2 unambiguously differentiated RNA internal looped structures from hairpin loops. The results show that Co11(HAPP)(TFA)2 is a sensitive, informative and convenient tool for analysis of RNA secondary structures.",

keywords = "Bulge, Cobalt, Hairpin loop, Internal loop, RNA cleavage",

author = "Cheng, {Chien Chung} and Hung, {Kuo Chan} and Huang-Fu, {Wei Chun}",

year = "2005",

doi = "10.1002/jccs.200500186",

language = "English",

volume = "52",

pages = "1291--1297",

journal = "Journal of the Chinese Chemical Society",

issn = "0009-4536",

publisher = "John Wiley and Sons Inc.",

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TY - JOUR

T1 - Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex

AU - Cheng, Chien Chung

AU - Hung, Kuo Chan

AU - Huang-Fu, Wei Chun

PY - 2005

Y1 - 2005

N2 - Single-stranded RNA molecules usually include secondary structural elements such as bulges, internal loops, and hairpin loops. These RNA secondary structural elements are often essential for the biological activity and functions of the RNA molecule. Chemical probe Co11(HAPP)(TFA) 2 in the presence of H2O2 is found to differentiate single-stranded RNA from branched structures and hairpin loops. This study uses Co11(HAPP)(TFA)2 to analyze the structures of two RNA molecules: a fragment of HIV TAR RNA (TAR-27) and the catalytic domain 5 of group II intron (D5-29). The electrophoretic mobility of TAR-27 does not shift in the presence of Co11(HAPP)(TFA)2, suggesting that the reagent does not change the conformation of RNA substrate. Cleavage of the RNA substrates by Co11(HAPP)(TFA)2 unambiguously differentiated RNA internal looped structures from hairpin loops. The results show that Co11(HAPP)(TFA)2 is a sensitive, informative and convenient tool for analysis of RNA secondary structures.

AB - Single-stranded RNA molecules usually include secondary structural elements such as bulges, internal loops, and hairpin loops. These RNA secondary structural elements are often essential for the biological activity and functions of the RNA molecule. Chemical probe Co11(HAPP)(TFA) 2 in the presence of H2O2 is found to differentiate single-stranded RNA from branched structures and hairpin loops. This study uses Co11(HAPP)(TFA)2 to analyze the structures of two RNA molecules: a fragment of HIV TAR RNA (TAR-27) and the catalytic domain 5 of group II intron (D5-29). The electrophoretic mobility of TAR-27 does not shift in the presence of Co11(HAPP)(TFA)2, suggesting that the reagent does not change the conformation of RNA substrate. Cleavage of the RNA substrates by Co11(HAPP)(TFA)2 unambiguously differentiated RNA internal looped structures from hairpin loops. The results show that Co11(HAPP)(TFA)2 is a sensitive, informative and convenient tool for analysis of RNA secondary structures.

KW - Bulge

KW - Cobalt

KW - Hairpin loop

KW - Internal loop

KW - RNA cleavage

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DO - 10.1002/jccs.200500186

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VL - 52

SP - 1291

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JO - Journal of the Chinese Chemical Society

JF - Journal of the Chinese Chemical Society

IS - 6

ER -

Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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