Altered stoichiometry of an evolved RNA aptamer

RNA. 2018 Apr;24(4):480-485. doi: 10.1261/rna.063610.117. Epub 2017 Dec 28.


Inhibitory aptamers against a protein are promising as antagonistic reagents and repressive genetic components. Typically, improvement of such aptamers is achieved by acquiring higher binding affinity. Here, we report an alternative mechanism for the improvement of aptamer activity. Recently, we reported a transcriptional activator based on an inhibitory RNA aptamer against lambda cI repressor. We improved the aptamer through in vitro selection (SELEX) from a randomly mutagenized aptamer pool, followed by in vivo screening and truncation. Biochemical analyses indicated that the activity improvement was achieved by alteration of the complex formation stoichiometry, rather than by higher affinity or expression. Our results suggest an alternative strategy for improving aptamer activity.

Keywords: aptamer; directed evolution; repressor; stoichiometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / genetics
  • Aptamers, Nucleotide / metabolism*
  • Base Sequence
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli / virology*
  • RNA / genetics
  • Repressor Proteins / antagonists & inhibitors*
  • Repressor Proteins / genetics
  • SELEX Aptamer Technique / methods*
  • Transcriptional Activation / genetics
  • Viral Regulatory and Accessory Proteins / antagonists & inhibitors*
  • Viral Regulatory and Accessory Proteins / genetics


  • Aptamers, Nucleotide
  • Repressor Proteins
  • Viral Regulatory and Accessory Proteins
  • phage repressor proteins
  • RNA