Homogeneous and Universal Detection of Various Targets with a Dual‐Step Transduced Toehold Switch Sensor

Toehold switch sensors represent a class of new advances that allow specific targets to trigger in situ expression of a protein reporter. Although they offer unique advantages of a label‐free nature and high portability, they generally require repeated sequence design, high expenditure, and laborious optimization of toehold switch sequences according to different targets. To simplify the sensing process further and to improve its practicability, we innovatively introduce a dual‐step pre‐transduction upon traditional toehold switch sensor. Through two successive toehold‐mediated strand‐displacement reactions that are initiated, respectively, by a linear and an associative trigger, different DNAs, RNAs, or ligands of functional nucleic acids can be generally transduced into the input of one high‐performance toehold switch sensor. This advance greatly increases the target range. Furthermore, the whole process is signal‐on, homogeneous, and free of any requirements for complicated operations such as probe labeling, separation, and reconstruction of the toehold switch, being promising and practical even in portable or point‐of‐care assays.

[1]  Heinz Koeppl,et al.  Cell-free prototyping of AND-logic gates based on heterogeneous RNA activators , 2019, bioRxiv.

[2]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[3]  Kaixiang Zhang,et al.  Isothermal Amplification for MicroRNA Detection: From the Test Tube to the Cell. , 2017, Accounts of chemical research.

[4]  Xi Chen,et al.  Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. , 2012, Journal of the American Chemical Society.

[5]  Andrea Ventura,et al.  MicroRNAs and Cancer: Short RNAs Go a Long Way , 2009, Cell.

[6]  Yingfu Li,et al.  Structure-switching signaling aptamers. , 2003, Journal of the American Chemical Society.

[7]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[8]  Margaret L. Rodgers,et al.  A newborn RNA switches its fate , 2019, Nature Chemical Biology.

[9]  P. Gill,et al.  Nucleic Acid Isothermal Amplification Technologies—A Review , 2008, Nucleosides, nucleotides & nucleic acids.

[10]  Sai Bi,et al.  Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. , 2017, Chemical Society reviews.

[11]  Andrew D. Ellington,et al.  Diagnostic Applications of Nucleic Acid Circuits , 2014, Accounts of chemical research.

[12]  Xi Chen,et al.  Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods , 2011, Nucleic acids research.

[13]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[14]  Michael C. Jewett,et al.  BioBits™ Explorer: A modular synthetic biology education kit , 2018, Science Advances.

[15]  Fuan Wang,et al.  A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging , 2019, Chemical science.

[16]  R. Micura,et al.  The dynamic nature of RNA as key to understanding riboswitch mechanisms. , 2011, Accounts of chemical research.

[17]  Guillaume Lambert,et al.  Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components , 2016, Cell.

[18]  X Chris Le,et al.  Universal strategy to engineer catalytic DNA hairpin assemblies for protein analysis. , 2015, Analytical chemistry.

[19]  Juewen Liu,et al.  Functional nucleic acid sensors. , 2009, Chemical reviews.

[20]  Young Je Lee,et al.  Modulating Responses of Toehold Switches by an Inhibitory Hairpin. , 2019, ACS synthetic biology.

[21]  Itamar Willner,et al.  Amplified fluorescence aptamer-based sensors using exonuclease III for the regeneration of the analyte. , 2012, Chemistry.

[22]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[23]  Monica P. McNerney,et al.  Point-of-care biomarker quantification enabled by sample-specific calibration , 2019, Science Advances.

[24]  Feika Bian,et al.  Hybridization chain reactions on silica coated Qbeads for the colorimetric detection of multiplex microRNAs. , 2017, Chemical communications.

[25]  Katherine E Deigan,et al.  Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. , 2011, Accounts of chemical research.

[26]  Jay D Keasling,et al.  Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression , 2011, Science.

[27]  N. Colburn,et al.  MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene , 2008, Oncogene.

[28]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[29]  J. Collins,et al.  Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.

[30]  C. Fan,et al.  Isothermal Amplification of Nucleic Acids. , 2015, Chemical reviews.

[31]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[32]  James J Collins,et al.  A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers , 2018, Nature Communications.

[33]  Bingling Li,et al.  Establishment of a universal and rational gene detection strategy through three-way junction-based remote transduction† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc03190d , 2017, Chemical science.