RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA

Base-pairing interactions between nucleic acids mediate target recognition in many biological processes. We developed a super-resolution imaging and modeling platform that enabled the in vivo determination of base pairing-mediated target recognition kinetics. We examined a stress-induced bacterial s...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 2015-03, Vol.347 (6228), p.1371-1374
Main Authors: Fei, Jingyi, Singh, Digvijay, Zhang, Qiucen, Park, Seongjin, Balasubramanian, Divya, Golding, Ido, Vanderpool, Carin K, Ha, Taekjip
Format: Article
Language:English
Subjects:
Base Pairing
Endoribonucleases - chemistry
Endoribonucleases - genetics
Escherichia coli - genetics
Escherichia coli - metabolism
Kinetics
Molecular Imaging - methods
Mutation
Phosphoenolpyruvate Sugar Phosphotransferase System - genetics
RNA Stability
RNA, Messenger - chemistry
RNA, Small Untranslated - chemistry
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Summary:Base-pairing interactions between nucleic acids mediate target recognition in many biological processes. We developed a super-resolution imaging and modeling platform that enabled the in vivo determination of base pairing-mediated target recognition kinetics. We examined a stress-induced bacterial small RNA, SgrS, which induces the degradation of target messenger RNAs (mRNAs). SgrS binds to a primary target mRNA in a reversible and dynamic fashion, and formation of SgrS-mRNA complexes is rate-limiting, dictating the overall regulation efficiency in vivo. Examination of a secondary target indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other small RNA systems and other target search processes.
ISSN:1095-9203
DOI:10.1126/science.1258849