Combinatorial selection of a small RNA that induces amplification of IncFII plasmids in Escherichia coli

Matthew J. Ferber, L. James Maher

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Cellular RNAs play fundamental roles as genetic messages, structural components and, in some cases, as catalytic agents. The ability to create vast combinatorial libraries of random RNA sequences has previously been exploited in vivo to identify RNA aptamers with desirable binding specificities, and to isolate RNAs with novel catalytic properties. Despite the advantages of in vitro selections from RNA libraries, there is no way to predict if the identified RNAs can function in living cells. We are therefore exploring random RNA expression libraries in Escherichia coli to search for small RNAs with novel functions. Here we describe selections that identified a small RNA (~260 nucleotides) capable of altering the copy-number control circuitry of IncFII plasmids. The novel RNA appears to function by annealing to a region of the mRNA encoding the plasmid replicator protein. The resulting RNA-RNA hybrid permits translation of the replicator protein, but blocks base-pairing with a natural negative regulatory RNA. Implications of this in vivo selection strategy are discussed.

Original languageEnglish (US)
Pages (from-to)565-576
Number of pages12
JournalJournal of Molecular Biology
Issue number3
StatePublished - Jun 12 1998


  • Antisense
  • Combinatorial
  • IncFII
  • Plasmid
  • Selection

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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