title: Design, synthesis, and application of Spinach molecular beacons triggered by strand displacement.
abstract: We describe design parameters for the synthesis and analytical application of a label-free RNA molecular beacon, termed Spinach.ST. The RNA aptamer Spinach fluoresces upon binding the small-molecule fluorophore DFHBI ((Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one). Spinach has been reengineered by extending its 5'- and 3'-ends to create Spinach.ST, which is predicted to fold into an inactive conformation that fails to bind DHFBI. Hybridization of a trigger oligonucleotide to a designed toehold on Spinach.ST initiates toehold-mediated strand displacement and restores the DFHBI-binding, fluorescence-enhancing conformation of Spinach. The versatile Spinach.ST sensor can detect DNA or RNA trigger sequences and can readily distinguish single-nucleotide mismatches in the trigger toehold. Primer design techniques are described that augment amplicons produced by enzymatic amplification with Spinach.ST triggers. Interaction between these triggers and Spinach.ST molecular beacons leads to the real-time, sequence-specific quantitation of these amplicons. The use of Spinach.ST with isothermal amplification reactions such as nucleic acid sequence-based amplification (NASBA) may enable point-of-care applications. The same design principles could also be used to adapt Spinach reporters to the assay of nonnucleic acid analytes in trans.
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, Texas, USA.
authors.forename: Sanchita
authors.initials: S
authors.lastname: Bhadra
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, Texas, USA. Electronic address: ellingtonlab@gmail.com.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
mesh_terms: D005818:Genetic Engineering / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics*; D018724:Spinacia oleracea / Q000235:genetics*
chemical_list: D012313:RNA
keywords: Aptamer; Aptamer beacon; Fluorescent RNA; Molecular beacon; Nucleic acid diagnostics; Nucleic acid engineering; Strand displacement