In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity

Laura Martini; Adam J Meyer; Jared W Ellefson; John N Milligan; Michele Forlin; Andrew D Ellington; Sheref S Mansy

doi:10.1021/acssynbio.5b00054

In Vitro Selection for Small-Molecule-Triggered Strand Displacement and Riboswitch Activity

ACS Synth Biol. 2015 Oct 16;4(10):1144-50. doi: 10.1021/acssynbio.5b00054. Epub 2015 May 22.

Authors

Laura Martini¹, Adam J Meyer², Jared W Ellefson², John N Milligan², Michele Forlin¹, Andrew D Ellington², Sheref S Mansy¹

Affiliations

¹ CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy.
² Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin , Austin, Texas 78712, United States.

PMID: 25978303
DOI: 10.1021/acssynbio.5b00054

Abstract

An in vitro selection method for ligand-responsive RNA sensors was developed that exploited strand displacement reactions. The RNA library was based on the thiamine pyrophosphate (TPP) riboswitch, and RNA sequences capable of hybridizing to a target duplex DNA in a TPP regulated manner were identified. After three rounds of selection, RNA molecules that mediated a strand exchange reaction upon TPP binding were enriched. The enriched sequences also showed riboswitch activity. Our results demonstrated that small-molecule-responsive nucleic acid sensors can be selected to control the activity of target nucleic acid circuitry.

Keywords: SELEX; aptamer; in vitro selection; riboswitch; strand displacement.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Aptamers, Nucleotide / chemistry*
Biosensing Techniques
Nucleic Acid Conformation
Riboswitch / genetics*

Substances

Aptamers, Nucleotide
Riboswitch