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Science. 2015 Mar 20;347(6228):1371-4. doi: 10.1126/science.1258849.

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

Author information

1
Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA.
2
Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA.
3
Department of Microbiology, University of Illinois, Urbana, IL, USA.
4
Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
5
Department of Microbiology, University of Illinois, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.
6
Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. Carl R. Woese Institute for Genomic Biology, Howard Hughes Medical Institute, Urbana, IL, USA. Howard Hughes Medical Institute, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.

Abstract

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.

PMID:
25792329
PMCID:
PMC4410144
DOI:
10.1126/science.1258849
[Indexed for MEDLINE]
Free PMC Article

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