title: An in vitro selection for small molecule induced switching RNA molecules.
abstract: The selection of RNA and DNA aptamers now has a long history. However, the ability to directly select for conformational changes upon ligand binding has remained elusive. These difficulties have stymied attempts at making small molecule responsive strand displacement circuitry as well as synthetic riboswitches. Herein we present a detailed strand displacement based selection protocol to directly select for RNA molecules with switching activity. The library was based on a previously selected thiamine pyrophosphate riboswitch. The fully in vitro methodology gave sequences that showed strong strand displacement activity in the presence of thiamine pyrophosphate. Further, the selected sequences possessed riboswitch activity similar to that of natural riboswitches. The presented methodology should aid in the design of more complex, environmentally responsive strand displacement circuitry and in the selection of riboswitches responsive to toxic ligands.
authors.affiliation: CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Martini
authors.affiliation: Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: ellingtonlab@gmail.com.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
authors.affiliation: CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy. Electronic address: sheref.mansy@unitn.it.
authors.forename: Sheref S
authors.initials: SS
authors.lastname: Mansy
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics*; D008024:Ligands; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D058928:Riboswitch / Q000235:genetics*; D054852:Small Molecule Libraries / Q000737:chemistry; D013835:Thiamine Pyrophosphate / Q000235:genetics
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D058928:Riboswitch; D054852:Small Molecule Libraries; D012313:RNA; D013835:Thiamine Pyrophosphate
keywords: In vitro selection; Riboswitch; SELEX; Stand displacement