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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 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*


  • RNA, Messenger
  • RNA, Small Untranslated
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphoenolpyruvate-glucose phosphotransferase
  • Endoribonucleases
  • ribonuclease E