1
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Kachwala MJ, Hamdard F, Cicek D, Dagci H, Smith CW, Kalla N, Yigit MV. Universal CRISPR-Cas12a and Toehold RNA Cascade Reaction on Paper Substrate for Visual Salmonella Genome Detection. Adv Healthc Mater 2024:e2400508. [PMID: 38683016 DOI: 10.1002/adhm.202400508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/12/2024] [Indexed: 05/01/2024]
Abstract
Salmonella, the most prevalent food-borne pathogen, poses significant medical and economic threats. Swift and accurate on-site identification and serotyping of Salmonella is crucial to curb its spread and contamination. Here, a synthetic biology cascade reaction is presented on a paper substrate using CRISPR-Cas12a and recombinase polymerase amplification (RPA), enabling the programming of a standard toehold RNA switch for a genome of choice. This approach employs just one toehold RNA switch design to differentiate between two different Salmonella serotypes, i.e., S. Typhimurium and S. Enteritidis, without the need for reengineering the toehold RNA switch. The sensor exhibits high sensitivity, capable of visually detecting as few as 100 copies of the whole genome from a model Salmonella pathogen on a paper substrate. Furthermore, this robust assay is successfully applied to detect whole genomes in contaminated milk and lettuce samples, demonstrating its potential in real sample analysis. Due to its versatility and practical features, genomes from different organisms can be detected by merely changing a single RNA element in this universal cell-free cascade reaction.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Farishta Hamdard
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Damla Cicek
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Hilal Dagci
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Nabeel Kalla
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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2
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Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023; 14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.
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Affiliation(s)
- Chenggang Xi
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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3
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Phillips EA, Silverman AD, Joneja A, Liu M, Brown C, Carlson P, Coticchia C, Shytle K, Larsen A, Goyal N, Cai V, Huang J, Hickey JE, Ryan E, Acheampong J, Ramesh P, Collins JJ, Blake WJ. Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes. Nat Biomed Eng 2023; 7:1571-1582. [PMID: 37142844 PMCID: PMC10727988 DOI: 10.1038/s41551-023-01028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/25/2023] [Indexed: 05/06/2023]
Abstract
Nucleic acid assays are not typically deployable in point-of-care settings because they require costly and sophisticated equipment for the control of the reaction temperature and for the detection of the signal. Here we report an instrument-free assay for the accurate and multiplexed detection of nucleic acids at ambient temperature. The assay, which we named INSPECTR (for internal splint-pairing expression-cassette translation reaction), leverages the target-specific splinted ligation of DNA probes to generate expression cassettes that can be flexibly designed for the cell-free synthesis of reporter proteins, with enzymatic reporters allowing for a linear detection range spanning four orders of magnitude and peptide reporters (which can be mapped to unique targets) enabling highly multiplexed visual detection. We used INSPECTR to detect a panel of five respiratory viral targets in a single reaction via a lateral-flow readout and ~4,000 copies of viral RNA via additional ambient-temperature rolling circle amplification of the expression cassette. Leveraging synthetic biology to simplify workflows for nucleic acid diagnostics may facilitate their broader applicability at the point of care.
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Affiliation(s)
| | | | | | | | - Carl Brown
- Sherlock Biosciences, Watertown, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | | | | | | | | | | | | | | | - Emily Ryan
- Sherlock Biosciences, Watertown, MA, USA
| | | | | | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA, USA
- College of Arts and Sciences, Harvard University, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William J Blake
- Sherlock Biosciences, Watertown, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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4
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Zhang C, Li Z, Liu J, Liu C, Zhang H, Lee WG, Yao C, Guo H, Xu F. Synthetic Gene Circuit-Based Assay with Multilevel Switch Enables Background-Free and Absolute Quantification of Circulating Tumor DNA. Research (Wash D C) 2023; 6:0217. [PMID: 37789988 PMCID: PMC10543738 DOI: 10.34133/research.0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023]
Abstract
Circulating tumor DNA (ctDNA) detection has found widespread applications in tumor diagnostics and treatment, where the key is to obtain accurate quantification of ctDNA. However, this remains challenging due to the issue of background noise associated with existing assays. In this work, we developed a synthetic gene circuit-based assay with multilevel switch (termed CATCH) for background-free and absolute quantification of ctDNA. The multilevel switch combining a small transcription activating RNA and a toehold switch was designed to simultaneously regulate transcription and translation processes in gene circuit to eliminate background noise. Moreover, such a multilevel switch-based gene circuit was integrated with a Cas9 nickase H840A (Cas9n) recognizer and a molecular beacon reporter to form CATCH for ctDNA detection. The CATCH can be implemented in one-pot reaction at 35 °C with virtually no background noise, and achieve robust absolute quantification of ctDNA when integrated with a digital chip (i.e., digital CATCH). Finally, we validated the clinical capability of CATCH by detecting drug-resistant ctDNA mutations from the plasma of 76 non-small cell lung cancer (NSCLC) patients, showing satisfying clinical sensitivity and specificity. We envision that the simple and robust CATCH would be a powerful tool for next-generation ctDNA detection.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
- TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China
| | - Jie Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Won Gu Lee
- Department of Mechanical Engineering,
Kyung Hee University, Yongin 17104, Republic of Korea
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital,
Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
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5
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Yang YJ, Fu H, Li XL, Yang HY, Zhou EC, Xie CY, Wu SW, He F, Zhang Y, Zhang XH. A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes. Nucleic Acids Res 2023; 51:e90. [PMID: 37562941 PMCID: PMC10516651 DOI: 10.1093/nar/gkad601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
The detection of nucleic acid sequences in parallel with the discrimination of single nucleotide variations (SNVs) is critical for research and clinical applications. A few limitations make the detection technically challenging, such as too small variation in probe-hybridization energy caused by SNVs, the non-specific amplification of false nucleic acid fragments and the few options of dyes limited by spectral overlaps. To circumvent these limitations, we developed a single-molecule nucleic acid detection assay without amplification or fluorescence termed THREF (hybridization-induced tandem DNA hairpin refolding failure) based on multiplexed magnetic tweezers. THREF can detect DNA and RNA sequences at femtomolar concentrations within 30 min, monitor multiple probes in parallel, quantify the expression level of miR-122 in patient tissues, discriminate SNVs including the hard-to-detect G-U or T-G wobble mutations and reuse the probes to save the cost. In our demonstrative detections using mock clinic samples, we profiled the let-7 family microRNAs in serum and genotyped SARS-CoV-2 strains in saliva. Overall, the THREF assay can discriminate SNVs with the advantages of high sensitivity, ultra-specificity, multiplexing, reusability, sample hands-free and robustness.
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Affiliation(s)
- Ya-Jun Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Hang Fu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
- School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Lu Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Hong-Yu Yang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Cheng-Yu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Shu-Wen Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Fan He
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
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6
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Liu Z, Zhang R, Jiang X, Ji L, Sun P, Ji Y, Zhang Y, Ding Y, Li K, Pu Z, Zhou F, Zou J. Highly Sensitive Enrichment of Low-Frequency Variants by Hairpin Competition Amplification. Anal Chem 2023; 95:12015-12023. [PMID: 37527514 DOI: 10.1021/acs.analchem.3c01803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Gene mutations are inevitably accumulated in cells of the human body. It is of great significance to detect mutations at the earliest possible time in physiological and pathological processes. However, genotyping low-copy tumor DNA (ctDNA) in patients is challenging due to abundant wild DNA backgrounds. One novel strategy to enrich rare mutations at low variant allele fractions (VAFs) with quantitative polymerase chain reaction (qPCR) and Sanger sequencing was contrived by introducing artificial hairpins into amplicons to compete with primers, coined as the hairpin competition amplification (HCA) system. The influence imposed by artificial hairpins on primer-binding in a high-temperature PCR system was investigated for the first time in this work, paving the way for the optimization of HCA. HCA differs from the previously reported work in which hairpins are formed to inhibit extension of wild-type DNA using 5-exonuclease-negative polymerase, where the readout is dependent on melting curve analysis after asymmetric PCR. Targeted at six different variants, HCA qPCR and HCA Sanger-enriched mutant DNA at VAFs as low as 0.1 or 0.01% were performed. HCA demonstrated advantages in multiplex reaction and temperature robustness. In profiling gene status from 12 lung cancer ctDNA samples and 16 thyroid cancer FNA DNA samples, HCA demonstrated a 100% concordance rate compared to ddPCR and commercial ARMS kit. HCA qPCR and Sanger sequencing can enrich low-abundance variants with high sensitivity and temperature robustness, presenting a novel and effective tool for precision diagnosis and treatment of rare variant diseases.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Xixi Jiang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yu Zhang
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yan Ding
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
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7
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Yan Z, Tang AA, Eshed A, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches. medRxiv 2023:2023.06.02.23290873. [PMID: 37333364 PMCID: PMC10275000 DOI: 10.1101/2023.06.02.23290873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Zackary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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8
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Schaffter SW, Wintenberg ME, Murphy TM, Strychalski EA. Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits. ACS Synth Biol 2023; 12:1546-1561. [PMID: 37134273 DOI: 10.1021/acssynbio.3c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.
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Affiliation(s)
- Samuel W Schaffter
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Molly E Wintenberg
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Terence M Murphy
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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9
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McSweeney MA, Zhang Y, Styczynski MP. Short Activators and Repressors of RNA Toehold Switches. ACS Synth Biol 2023; 12:681-688. [PMID: 36802167 PMCID: PMC10028691 DOI: 10.1021/acssynbio.2c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
RNA toehold switches are a widely used class of molecule to detect specific RNA "trigger" sequences, but their design, intended function, and characterization to date leave it unclear whether they can function properly with triggers shorter than 36 nucleotides. Here, we explore the feasibility of using standard toehold switches with 23-nucleotide truncated triggers. We assess the crosstalk of different triggers with significant homology and identify a highly sensitive trigger region where just one mutation from the consensus trigger sequence can reduce switch activation by 98.6%. However, we also find that triggers with as many as seven mutations outside of this region can still lead to 5-fold induction of the switch. We also present a new approach using 18- to 22-nucleotide triggers as translational repressors for toehold switches and assess the off-target regulation for this strategy as well. The development and characterization of these strategies could help enable applications like microRNA sensors, where well-characterized crosstalk between sensors and detection of short target sequences are critical.
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Affiliation(s)
- Megan A McSweeney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yan Zhang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Yu H, Weng Z, Zhou X, Bai D, Luo W, Han X, Song L, Liu Q, Li J, Yang Y, Guo Y, Lv K, Xie G. A hairpin probe-mediated exponential amplification reaction for highly sensitive and specific detection of microRNAs. Chem Commun (Camb) 2023; 59:4158-4161. [PMID: 36880314 DOI: 10.1039/d3cc00241a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
In this work, we propose a hairpin probe-mediated exponential amplification reaction (HEAR) strategy that combines DNA strand displacement with a "who triggers, who gets generated" mode, providing excellent single-base discrimination and a reduced background signal. The detection limit is 19 aM, which is reduced by 3 orders of magnitude compared to traditional exponential amplification approaches. This one-pot strategy also exhibits a wide dynamic range, high specificity and short detection time. It is expected to become a powerful tool for clinical diagnosis.
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Affiliation(s)
- Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Qian Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Junjie Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, LuZhou Key Laboratory of Nanobiosensing and Microfluidic Point-of-Care Testing, Luzhou 646000, P. R. China.
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Chongqing 40016, P. R. China.
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, P. R. China.
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11
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Han YH, Kim G, Seo SW. Programmable synthetic biology tools for developing microbial cell factories. Curr Opin Biotechnol 2023; 79:102874. [PMID: 36610368 DOI: 10.1016/j.copbio.2022.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Microbial conversion to generate value-added chemicals from diverse biomass is one of the keystones of energy biotechnology. Programmable synthetic biology tools offer versatile, standardized options for developing microbial cell factories. These tools thus can be reprogrammed in a user-defined manner for flexible wiring of stimuli and response, highly efficient genome engineering, and extensive perturbation of metabolic flux and genetic circuits. They also can be modularly assembled to construct elaborate and unprecedented biological systems with unique features. This review highlights recent advances in programmable synthetic biology tools based on biosensors, CRISPR-Cas, and RNA devices for developing microbial cell factories that have the potential to be utilized for energy biotechnology.
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Affiliation(s)
- Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Giho Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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12
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Wang T, Hellmer H, Simmel FC. Genetic switches based on nucleic acid strand displacement. Curr Opin Biotechnol 2023; 79:102867. [PMID: 36535150 DOI: 10.1016/j.copbio.2022.102867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Toehold-mediated strand displacement (TMSD) is an isothermal switching process that enables the sequence-programmable and reversible conversion of DNA or RNA strands between single- and double-stranded conformations or other secondary structures. TMSD processes have already found widespread application in DNA nanotechnology, where they are used to drive DNA-based molecular devices or for the realization of synthetic biochemical computing circuits. Recently, researchers have started to employ TMSD also for the control of RNA-based gene regulatory processes in vivo, in particular in the context of synthetic riboregulators and conditional guide RNAs for CRISPR/Cas. Here, we provide a review over recent developments in this emerging field and discuss the opportunities and challenges for such systems in in vivo applications.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Henning Hellmer
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.
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13
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Jung KJ, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring. bioRxiv 2023:2023.01.09.523248. [PMID: 36711593 PMCID: PMC9881948 DOI: 10.1101/2023.01.09.523248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts of Escherichia coli . We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a 'build-your-own' activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms - and at home - without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Kirsten J. Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Blake J. Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Grant A. Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | | | - Robert Kuhn
- Centennial High School, Roswell, GA 30076, USA
- Fulton County Schools Innovation Academy, Alpharetta, GA 30009, USA
| | | | - Holly M. Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Brenda M. Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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14
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Abstract
Nucleic acid strand displacement reactions involve the competition of two or more DNA or RNA strands of similar sequence for binding to a complementary strand, and facilitate the isothermal replacement of an incumbent strand by an invader. The process can be biased by augmenting the duplex comprising the incumbent with a single-stranded extension, which can act as a toehold for a complementary invader. The toehold gives the invader a thermodynamic advantage over the incumbent, and can be programmed as a unique label to activate a specific strand displacement process. Toehold-mediated strand displacement processes have been extensively utilized for the operation of DNA-based molecular machines and devices as well as for the design of DNA-based chemical reaction networks. More recently, principles developed initially in the context of DNA nanotechnology have been applied for the de novo design of gene regulatory switches that can operate inside living cells. The article specifically focuses on the design of RNA-based translational regulators termed toehold switches. Toehold switches utilize toehold-mediated strand invasion to either activate or repress translation of an mRNA in response to the binding of a trigger RNA molecule. The basic operation principles of toehold switches will be discussed as well as their applications in sensing and biocomputing. Finally, strategies for their optimization will be described as well as challenges for their operation in vivo.
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Affiliation(s)
- Friedrich C Simmel
- TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany
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15
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Zhou C, Yang D, Sensale S, Sharma P, Wang D, Yu L, Arya G, Ke Y, Wang P. A bistable and reconfigurable molecular system with encodable bonds. Sci Adv 2022; 8:eade3003. [PMID: 36399380 PMCID: PMC9674029 DOI: 10.1126/sciadv.ade3003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ's conformation and transformation is realized by programming the stacking bonds (quasi-blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms. A specific DOJ conformation may be achieved by encoding the stacking bonds with binary stacking sequences based on thermodynamic calculations. Dynamic transformations of DOJ between various conformations are achieved by using specific environmental and molecular stimulations to reprogram the stacking codes. This work provides a useful platform for constructing self-assembled DNA nanostructures and nanomachines and insights for future design of artificial molecular systems with increasing complexity and reconfigurability.
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Affiliation(s)
- Chunyang Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- College of Life Sciences and Technology, Changchun University of Science and Technology, Changchun 130013, Jilin, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sebastian Sensale
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Pranav Sharma
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Lei Yu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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16
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Bai D, Zhou X, Luo W, Yu H, Bai S, Wu Y, Song L, Chen K, Xie Y, Chen X, Zhao J, Fu Y, Yang Y, Li J, Xie G. Cooperative strand displacement circuit with dual-toehold and bulge-loop structure for single-nucleotide variations discrimination. Biosens Bioelectron 2022; 216:114677. [PMID: 36087401 DOI: 10.1016/j.bios.2022.114677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022]
Abstract
Nucleic acid nanotechnologies based on toehold-mediated strand displacement are ideally suited for single-nucleotide variations (SNVs) detection. But only a limited number of means could be used to construct selective hybridization probes via finely designed toehold and regulation of branching migration. Herein, we present a cooperative hybridization strategy relying on a dual-toehold and bulge-loop (DT&BL) probe, coupled with the strand displacement catalytic (SDC) cycle to identify SNVs. The dual-toehold can simultaneously hybridize the 5' and 3' ends of the target, so that it possessed the mutual correction function for improving the specificity in comparison with the single target-binding domain. Insertion of BLs into the dual-toehold probe allows tuning of Gibbs free energy change (ΔG) and control of the reaction rate during branching migration. Using the SDC cycle, the reactivity and selectivity of the DT&BL probe were increased drastically without elaborate competitive sequences. The feasibilities of this platform were demonstrated by the identification of three cancer-related genes. Moreover, the applicability of this biosensor to detect clinical samples showed satisfactory accuracy and reliability. We envision it would offer a new perspective for the construction of highly specific probes based on dynamic DNA nanotechnology, and serves as a promising tool for clinical diagnostics.
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17
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Zhai T, Wei Y, Wang L, Li J, Fan C. Advancing pathogen detection for airborne diseases. Fundamental Research 2022. [PMCID: PMC9618456 DOI: 10.1016/j.fmre.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Airborne diseases including SARS, bird flu, and the ongoing Coronavirus Disease 2019 (COVID-19) have stimulated the demand for developing novel bioassay methods competent for early-stage diagnosis and large-scale screening. Here, we briefly summarize the state-of-the-art methods for the detection of infectious pathogens and discuss key challenges. We highlight the trend for next-generation technologies benefiting from multidisciplinary advances in microfabrication, nanotechnology and synthetic biology, which allow sensitive, rapid yet inexpensive pathogen assays with portable intelligent device.
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Affiliation(s)
- Tingting Zhai
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhan Wei
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China,Corresponding authors: Prof. Jiang Li, Shanghai Jiao Tong University, The Interdisciplinary Research Center, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China,Corresponding authors: Prof. Jiang Li, Shanghai Jiao Tong University, The Interdisciplinary Research Center, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai 200240, China
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18
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Wu Y, Tang M, Wang Z, Yang Y, Li Z, Liang S, Yin P, Qi H. Efficient In Vitro Full-Sense-Codons Protein Synthesis. Adv Biol (Weinh) 2022; 6:e2200023. [PMID: 35676219 DOI: 10.1002/adbi.202200023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/14/2022] [Indexed: 01/28/2023]
Abstract
Termination of translation is essential but hinders applications of genetic code engineering, e.g., unnatural amino acids incorporation and codon randomization mediated saturation mutagenesis. Here, for the first time, it is demonstrated that E. coli Pth and ArfB together play an efficient translation termination without codon preference in the absence of class-I release factors. By degradation of the targeted protein, both essential and alternative termination types of machinery are completely removed to disable codon-dependent termination in cell extract. Moreover, a total of 153 engineered tRNAs are screened for efficient all stop-codons decoding to construct a codon-dependent termination defect in vitro protein synthesis with all 64 sense-codons, iPSSC. Finally, this full sense genetic code achieves significant improvement in the incorporation of distinct unnatural amino acids at up to 12 positions and synthesis of protein encoding consecutive NNN codons. By decoding all information in nucleotides to amino acids, iPSSC may hold great potential in building artificial protein synthesis beyond the cell.
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Affiliation(s)
- Yang Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China.,College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
| | - Mengtong Tang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Youhui Yang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Zhong Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Shurui Liang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China.,Zhejiang Institute of Tianjin University, Shaoxing, Zhejiang, China
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19
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20
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Zhang T, Deng R, Wang Y, Wu C, Zhang K, Wang C, Gong N, Ledesma-Amaro R, Teng X, Yang C, Xue T, Zhang Y, Hu Y, He Q, Li W, Li J. A paper-based assay for the colorimetric detection of SARS-CoV-2 variants at single-nucleotide resolution. Nat Biomed Eng 2022. [PMID: 35835993 DOI: 10.1038/s41551-022-00907-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 05/29/2022] [Indexed: 02/05/2023]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for versatile diagnostic assays that can discriminate among emerging variants of the virus. Here we report the development and performance benchmarking of an inexpensive (approximately US$0.30 per test) assay for the rapid (sample-to-answer time within 30 min) colorimetric detection of SARS-CoV-2 variants. The assay, which we integrated into foldable paper strips, leverages nucleic acid strand-displacement reactions, the thermodynamic energy penalty associated with single-base-pair mismatches and the metal-ion-controlled enzymatic cleavage of urea to amplify the recognition of viral RNAs for the colorimetric readout of changes in pH via a smartphone. For 50 throat swab samples, the assay simultaneously detected the presence of SARS-CoV-2 and mutations specific to the SARS-CoV-2 variants Alpha, Beta and Gamma, with 100% concordance with real-time quantitative polymerase chain reaction and RNA sequencing. Customizable and inexpensive paper-based assays for the detection of viruses and their variants may facilitate viral surveillance.
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21
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Harbaugh SV, Silverman AD, Chushak YG, Zimlich K, Wolfe M, Thavarajah W, Jewett MC, Lucks JB, Chávez JL. Engineering a Synthetic Dopamine-Responsive Riboswitch for In Vitro Biosensing. ACS Synth Biol 2022; 11:2275-2283. [PMID: 35775197 DOI: 10.1021/acssynbio.1c00560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The detection of chemicals using natural allosteric transcription factors is a powerful strategy for point-of-use molecular sensing, particularly using fieldable cell-free gene expression (CFE) systems. However, the reliance of detection schemes on characterized protein-based sensors limits the number of measurable analytes. One alternative solution to this issue is to develop new sensors by generating RNA aptamers against the target analyte and then incorporating them directly into a riboswitch scaffold for ligand-inducible genetic control of a reporter protein. However, this strategy has not generated more than a handful of successful portable cell-free molecular sensors. To address this gap, here we convert dopamine-binding aptamers into functional dopamine-sensing riboswitches that regulate gene expression in a freeze-dried CFE reaction. We then develop an assay for direct detection and semi-quantification of dopamine in human urine. We anticipate that this work will be broadly applicable for converting many in vitro-generated RNA aptamers into fieldable molecular diagnostics.
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Affiliation(s)
- Svetlana V Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Adam D Silverman
- Sherlock Biosciences, Boston, Massachusetts 02135, United States
| | - Yaroslav G Chushak
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,Henry M. Jackson Foundation, Dayton, Ohio 45433, United States
| | - Kathryn Zimlich
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,Henry M. Jackson Foundation, Dayton, Ohio 45433, United States
| | - Monica Wolfe
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,UES, Inc., Dayton, Ohio 45432, United States
| | - Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Jorge L Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
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22
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Ekdahl AM, Rojano-Nisimura AM, Contreras LM. Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022;:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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23
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Mu K, Ren X, Yang H, Zhang T, Yan W, Yuan F, Wu J, Kang Z, Han D, Deng R, Zeng Q. CRISPR-Cas12a-Based Diagnostics of Wheat Fungal Diseases. J Agric Food Chem 2022; 70:7240-7247. [PMID: 35578739 DOI: 10.1021/acs.jafc.1c08391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fusarium head blight (FHB) of wheat, mainly caused by Fusarium graminearum (F. graminearum) infection, reduces crop yield and contaminates grain with mycotoxins. We report a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based nucleic acid assay for an early and rapid diagnosis of wheat FHB. Guide RNA (gRNA) was screened for highly specific recognition of polymerase chain reaction (PCR) amplicon of the internal transcribed spacer (ITS) region and the transcription elongation factor 1α (EF1α) of F. graminearum. The trans-activation of Cas12a protein cleaves the single-stranded DNA probes with the terminal fluorophore and quencher groups, thus allowing us to report the presence of ITS and EF1α of F. graminearum. Owing to the dual recognition process through PCR primers and gRNA hybridization, the approach realized specific discrimination of F. graminearum from other pathogenic fungi. It also allowed us to detect as low as 1 fg/μL total DNA from F. graminearum, which is sufficient to diagnose a 4 day F. graminearum infection. CRISPR-Cas12a-based nucleic acid assay promises the molecular diagnosis of crop diseases and broadens the application of CRISPR tools.
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Affiliation(s)
- Keqing Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Weiyi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
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24
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Soudier P, Rodriguez Pinzon D, Reif-Trauttmansdorff T, Hijazi H, Cherrière M, Goncalves Pereira C, Blaise D, Pispisa M, Saint-Julien A, Hamlet W, Nguevo M, Gomes E, Belkhelfa S, Niarakis A, Kushwaha M, Grigoras I. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima. Synth Syst Biotechnol 2022; 7:791-801. [PMID: 35415278 PMCID: PMC8976095 DOI: 10.1016/j.synbio.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods’ limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.
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25
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Wang T, Simmel FC. Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli. Nucleic Acids Res 2022; 50:4784-4798. [PMID: 35446427 PMCID: PMC9071393 DOI: 10.1093/nar/gkac275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
Regulatory RNA molecules have been widely investigated as components for synthetic gene circuits, complementing the use of protein-based transcription factors. Among the potential advantages of RNA-based gene regulators are their comparatively simple design, sequence-programmability, orthogonality, and their relatively low metabolic burden. In this work, we developed a set of riboswitch-inspired riboregulators in Escherichia coli that combine the concept of toehold-mediated strand displacement (TMSD) with the switching principles of naturally occurring transcriptional and translational riboswitches. Specifically, for translational activation and repression, we sequestered anti-anti-RBS or anti-RBS sequences, respectively, inside the loop of a stable hairpin domain, which is equipped with a single-stranded toehold region at its 5' end and is followed by regulated sequences on its 3' side. A trigger RNA binding to the toehold region can invade the hairpin, inducing a structural rearrangement that results in translational activation or deactivation. We also demonstrate that TMSD can be applied in the context of transcriptional regulation by switching RNA secondary structure involved in Rho-dependent termination. Our designs expand the repertoire of available synthetic riboregulators by a set of RNA switches with no sequence limitation, which should prove useful for the development of robust genetic sensors and circuits.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems – E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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26
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Carr AR, Dopp JL, Wu K, Sadat Mousavi P, Jo YR, McNeley CE, Lynch ZT, Pardee K, Green AA, Reuel NF. Toward Mail-in-Sensors for SARS-CoV-2 Detection: Interfacing Gel Switch Resonators with Cell-Free Toehold Switches. ACS Sens 2022; 7:806-815. [PMID: 35254055 DOI: 10.1021/acssensors.1c02450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The COVID-19 pandemic has emphasized the importance of widespread testing to control the spread of infectious diseases. The rapid development, scale-up, and deployment of viral and antibody detection methods since the beginning of the pandemic have greatly increased testing capacity. Desirable attributes of detection methods are low product costs, self-administered protocols, and the ability to be mailed in sealed envelopes for the safe analysis and subsequent logging to public health databases. Herein, such a platform is demonstrated with a screen-printed, inductor-capacitor (LC) resonator as a transducer and a toehold switch coupled with cell-free expression as the biological selective recognition element. In the presence of the N-gene from SARS-CoV-2, the toehold switch relaxes, protease enzyme is expressed, and it degrades a gelatin switch that ultimately shifts the resonant frequency of the planar resonant sensor. The gelatin switch resonator (GSR) can be analyzed through a sealed envelope allowing for assessment without the need for careful sample handling with personal protective equipment or the need for workup with other reagents. The toehold switch used in this sensor demonstrated selectivity to SARS-CoV-2 virus over three seasonal coronaviruses and SARS-CoV-1, with a limit of detection of 100 copies/μL. The functionality of the platform and assessment in a sealed envelope with an automated scanner is shown with overnight shipment, and further improvements are discussed to increase signal stability and further simplify user protocols toward a mail-in platform.
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Affiliation(s)
- Adam R. Carr
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Dopp
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Kaiyue Wu
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | | | - Yeong Ran Jo
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Ciara E. McNeley
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Zachary T. Lynch
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Keith Pardee
- University of Toronto, Leslie Dan Faculty of Pharmacy, Toronto, ON M5S 1A1, Canada
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Nigel F. Reuel
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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27
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Ma D, Li Y, Wu K, Yan Z, Tang AA, Chaudhary S, Ticktin ZM, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Green AA. Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics. Nat Biomed Eng 2022. [PMID: 35288660 DOI: 10.1038/s41551-022-00857-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
Applications of RNA-based molecular logic have been hampered by sequence constraints imposed on the input and output of the circuits. Here we show that the sequence constraints can be substantially reduced by appropriately encoded multi-arm junctions of single-stranded RNA structures. To conditionally activate RNA translation, we integrated multi-arm junctions, self-assembled upstream of a regulated gene and designed to unfold sequentially in response to different RNA inputs, with motifs of loop-initiated RNA activators that function independently of the sequence of the input RNAs and that reduce interference with the output gene. We used the integrated RNA system and sequence-independent input RNAs to execute two-input and three-input OR and AND logic in Escherichia coli, and designed paper-based cell-free colourimetric assays that accurately identified two human immunodeficiency virus (HIV) subtypes (by executing OR logic) in amplified synthetic HIV RNA as well as severe acute respiratory syndrome coronavirus-2 (via two-input AND logic) in amplified RNA from saliva samples. The sequence-independent molecular logic enabled by the integration of multi-arm junction RNAs with motifs for loop-initiated RNA activators may be broadly applicable in biotechnology.
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28
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Weng Z, Yu H, Luo W, Guo Y, Liu Q, Zhang L, Zhang Z, Wang T, Dai L, Zhou X, Han X, Wang L, Li J, Yang Y, Xie G. Cooperative Branch Migration: A Mechanism for Flexible Control of DNA Strand Displacement. ACS Nano 2022; 16:3135-3144. [PMID: 35113525 DOI: 10.1021/acsnano.1c10797] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA strand displacement plays an essential role in the field of dynamic DNA nanotechnology. However, flexible regulation of strand displacement remains a significant challenge. Most previous regulatory tools focused on controllable activation of toehold and thus limited the design flexibility. Here, we introduce a regulatory tool termed cooperative branch migration (CBM), through which DNA strand displacement can be controlled by regulating the complementarity of branch migration domains. CBM shows perfect compatibility with the majority of existing regulatory tools, and when combined with forked toehold, it permits continuous fine-tuning of the strand displacement rate spanning 5 orders of magnitude. CBM manifests multifunctional regulation ability, including rate fine-tuning, continuous dynamic regulation, reaction resetting, and selective activation. To exemplify the powerful function, we also constructed a nested if-function signal processing system on the basis of cascading CBM reactions. We believe that the proposed regulatory strategy would effectively enrich the DNA strand displacement toolbox and ultimately promote the construction of DNA machines of higher complexity in nucleic acid research and biomedical applications.
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Affiliation(s)
- Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, 646000, PR China
| | - Qian Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ting Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junjie Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
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29
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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30
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Wu K, Yan Z, Green AA. Computational Design of RNA Toehold-Mediated Translation Activators. Methods Mol Biol 2022; 2518:33-47. [PMID: 35666437 DOI: 10.1007/978-1-0716-2421-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Translation activators are an important class of riboregulators that respond to nucleic acid signals by activating gene expression. Toehold switches and single-nucleotide-specific programmable riboregulators (SNIPRs) are two types of translation activators that can detect nearly any nucleic acid sequence using interactions initiated by single-stranded domains known as toeholds. Toehold switches operate with high dynamic range, orthogonality, and programmability, making them capable of detecting a variety of pathogens in paper-based cell-free diagnostic assays. SNIPRs are designed to enable the accurate detection of single-nucleotide mutations, making them valuable tools for mutation and drug-resistance assays. Here we describe the computational design process for generating toehold switches and SNIPRs active against different pathogens and mutations of interest. Such riboregulators can be deployed in paper-based diagnostic assays to enable rapid and low-cost disease detection.
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Affiliation(s)
- Kaiyue Wu
- Molecular Biology, Cell Biology and Biochemistry Graduate Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Zhaoqing Yan
- Molecular Biology, Cell Biology and Biochemistry Graduate Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Alexander A Green
- Molecular Biology, Cell Biology and Biochemistry Graduate Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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31
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Zambrano RAI, Hernandez-Perez C, Takahashi MK. RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools. Methods Mol Biol 2022; 2518:253-269. [PMID: 35666450 DOI: 10.1007/978-1-0716-2421-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding RNA structure has become critical in the study of RNA in their roles as mediators of biological processes. To aid in these studies, computational algorithms that utilize thermodynamics have been developed to predict RNA secondary structure. Due to the importance of intermolecular interactions, the algorithms have been expanded to determine and predict RNA-RNA hybridization. This chapter discusses popular webservers with the tools for RNA secondary structure prediction, RNA-RNA hybridization, and design. We address key features that distinguish common-functioning programs and their purposes for the interests of the user. Ultimately, we hope this review elucidates web-based tools researchers may take advantage of in their investigations of RNA structure and function.
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Affiliation(s)
| | | | - Melissa K Takahashi
- Department of Biology, California State University Northridge, Northridge, CA, USA.
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32
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Wu K, Green AA. Detection of Norovirus Using Paper-Based Cell-Free Systems. Methods Mol Biol 2022; 2433:375-390. [PMID: 34985757 DOI: 10.1007/978-1-0716-1998-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Norovirus infections are the leading cause of foodborne illness and human gastroenteritis, afflicting hundreds of millions of people each year. Molecular assays with the capacity to detect norovirus without expensive equipment and with high sensitivity and specificity represent useful tools to track and contain future outbreaks. Here we describe how norovirus can be detected in low-cost paper-based cell-free reactions. These assays combine freeze-dried, thermostable cell-free transcription-translation reactions with toehold switch riboregulators designed to target the norovirus genome, enabling convenient colorimetric assay readouts. Coupling cell-free reactions with synbody-based viral enrichment and isothermal amplification enables detection of norovirus from clinical samples down to concentrations as low as 270 zM. These diagnostic tests are promising assays for confronting norovirus outbreaks and can be adapted to a variety of other human pathogens.
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Affiliation(s)
- Kaiyue Wu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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33
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Chakravarthy A, Nandakumar A, George G, Ranganathan S, Umashankar S, Shettigar N, Palakodeti D, Gulyani A, Ramesh A. Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay. Life Sci Alliance 2021; 4:4/12/e202101213. [PMID: 34593555 PMCID: PMC8500229 DOI: 10.26508/lsa.202101213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/11/2021] [Accepted: 09/20/2021] [Indexed: 12/26/2022] Open
Abstract
This work reports engineered toehold RNA–based biosensors for COVID-19 diagnostics, with a simple color or luminescence readout that makes it easily deployable in both well-equipped labs as well as low resource settings. The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostics that are adaptable to the virus. We have developed toehold RNA–based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. Here, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter protein, for example, LacZ or nano-lantern that is easily detected using color/luminescence. By optimizing RNA amplification and biosensor design, we have generated a highly sensitive diagnostic assay that is capable of detecting as low as 100 copies of viral RNA with development of bright color. This is easily visualized by the human eye and quantifiable using spectrophotometry. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects viral RNA in patient samples. This work presents a powerful and universally accessible strategy for detecting COVID-19 and variants. This strategy is adaptable to further viral evolution and brings RNA bioengineering center-stage.
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Affiliation(s)
- Anirudh Chakravarthy
- InStem-Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,SASTRA University, Tirumalaisamudram, Thanjavur, India
| | - Anirudh Nandakumar
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India.,Trans-Disciplinary Health Sciences and Technology, Bangalore, India
| | - Geen George
- InStem-Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | | | | - Nishan Shettigar
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
| | - Dasaradhi Palakodeti
- InStem-Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Akash Gulyani
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arati Ramesh
- National Centre for Biological Sciences, GKVK Campus, Bangalore, India
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34
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Song F, Shen Y, Wei Y, Yang C, Ge X, Wang A, Li C, Wan Y, Li J. Botulinum toxin as an ultrasensitive reporter for bacterial and SARS-CoV-2 nucleic acid diagnostics. Biosens Bioelectron 2021; 176:112953. [PMID: 33418182 PMCID: PMC7836976 DOI: 10.1016/j.bios.2020.112953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 01/18/2023]
Abstract
The rapid identification of pathogenic microorganisms plays a crucial role in the timely diagnosis and treatment strategies during a global pandemic, especially in resource-limited area. Herein, we present a sensitive biosensor strategy depended on botulinum neurotoxin type A light chain (BoNT/A LC) activated complex assay (BACA). BoNT/A LC, the surrogate of BoNT/A which embodying the most potent biological poisons, could serve as an ultrasensitive signal reporter with high signal-to-noise ratio to avoid common strong background response, poor stability and low intensity of current biosensor methods. A nanoparticle hybridization system, involving specific binding probes that recognize pathogenic 16S rRNAs or SARS-CoV-2 gene site, was developed to measure double-stranded biotinylated target DNA containing a single-stranded overhang using Fluorescence Resonance Energy Transfer (FRET)-based assay and colorimetric method. The method is validated widely by six different bacteria strains and severe acute respiratory related coronavirus 2 (SARS-CoV-2) nucleic acid, demonstrating a single cell or 1 aM nucleic acid detecting sensitivity. This detection strategy offers a solution for general applications and has a great prospect to be a simple instrument-free colorimetric tool, especially when facing public health emergency.
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Affiliation(s)
- Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yuanyuan Shen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yangdao Wei
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Chunrong Yang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Xiaolin Ge
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Chaoyang Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China; Shandong Key Laboratory of Corrosion Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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35
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Tan X, Letendre JH, Collins JJ, Wong WW. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021; 184:881-898. [PMID: 33571426 PMCID: PMC7897318 DOI: 10.1016/j.cell.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.
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Affiliation(s)
- Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Justin H Letendre
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, 77 Massachusetts Ave., Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
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36
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Park S, Lee JW. Detection of Coronaviruses Using RNA Toehold Switch Sensors. Int J Mol Sci 2021; 22:1772. [PMID: 33578973 DOI: 10.3390/ijms22041772] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/13/2022] Open
Abstract
A rapid, sensitive and simple point-of-care (POC) nucleic acid diagnostic test is needed to prevent spread of infectious diseases. Paper-based toehold reaction, a recently emerged colorimetric POC nucleic acid diagnostic test, has been widely used for pathogen detection and microbiome profiling. Here, we introduce an amplification method called reverse transcription loop-mediated amplification (RT-LAMP) prior to the toehold reaction and modify it to enable more sensitive and faster colorimetric detection of RNA viruses. We show that incorporating the modified RT-LAMP to the toehold reaction detects as few as 120 copies of coronavirus RNA in 70 min. Cross-reactivity test against other coronaviruses indicates this toehold reaction with the modified RT-LAMP is highly specific to the target RNA. Overall, the paper-based toehold switch sensors with the modified RT-LAMP allow fast, sensitive, specific and colorimetric coronavirus detection.
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Suea-Ngam A, Bezinge L, Mateescu B, Howes PD, deMello AJ, Richards DA. Enzyme-Assisted Nucleic Acid Detection for Infectious Disease Diagnostics: Moving toward the Point-of-Care. ACS Sens 2020; 5:2701-2723. [PMID: 32838523 PMCID: PMC7485284 DOI: 10.1021/acssensors.0c01488] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023]
Abstract
Driven by complex and interconnected factors, including population growth, climate change, and geopolitics, infectious diseases represent one of the greatest healthcare challenges of the 21st century. Diagnostic technologies are the first line of defense in the fight against infectious disease, providing critical information to inform epidemiological models, track diseases, decide treatment choices, and ultimately prevent epidemics. The diagnosis of infectious disease at the genomic level using nucleic acid disease biomarkers has proven to be the most effective approach to date. Such methods rely heavily on enzymes to specifically amplify or detect nucleic acids in complex samples, and significant effort has been exerted to harness the power of enzymes for in vitro nucleic acid diagnostics. Unfortunately, significant challenges limit the potential of enzyme-assisted nucleic acid diagnostics, particularly when translating diagnostic technologies from the lab toward the point-of-use or point-of-care. Herein, we discuss the current state of the field and highlight cross-disciplinary efforts to solve the challenges associated with the successful deployment of this important class of diagnostics at or near the point-of-care.
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Affiliation(s)
- Akkapol Suea-Ngam
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Léonard Bezinge
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Bogdan Mateescu
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
- Brain Research Institute,
Medical Faculty of the University of
Zürich, Winterthurerstrasse 190, 8057
Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Andrew J. deMello
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Daniel A. Richards
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
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Li S, Li S, Disoma C, Zheng R, Zhou M, Razzaq A, Liu P, Zhou Y, Dong Z, Du A, Peng J, Hu L, Huang J, Feng P, Jiang T, Xia Z. SARS‐CoV‐2: Mechanism of infection and emerging technologies for future prospects. Rev Med Virol 2020; 31:e2168. [DOI: 10.1002/rmv.2168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/23/2020] [Accepted: 08/30/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Shiqin Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Sijia Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Cyrollah Disoma
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Rong Zheng
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Mei Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Aroona Razzaq
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Pinjia Liu
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Yuzheng Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Zijun Dong
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Ashuai Du
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Jian Peng
- Department of General Surgery Xiangya Hospital Central South University Changsha China
| | - Liqiang Hu
- The First Hospital of Changsha University of South China Changsha China
| | - Jufang Huang
- Department of Anatomy and Neurobiology School of Basic Medical Sciences Central South University Changsha China
- School of Life Sciences Central South University Changsha China
| | - Pinghui Feng
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Taijiao Jiang
- Center for Systems Medicine Institute of Basic Medical Sciences Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China
- Suzhou Institute of Systems Medicine Suzhou Jiangsu China
| | - Zanxian Xia
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics School of Life Sciences Hunan Key Laboratory of Animal Models for Human Diseases Central South University Changsha China
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Jiao K, Zhu B, Guo L, Zhou H, Wang F, Zhang X, Shi J, Li Q, Wang L, Li J, Fan C. Programming Switchable Transcription of Topologically Constrained DNA. J Am Chem Soc 2020; 142:10739-10746. [DOI: 10.1021/jacs.0c01962] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kai Jiao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Bing Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Linjie Guo
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Haibin Zhou
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Fei Wang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201499, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201499, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lihua Wang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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40
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Hoang Trung Chau T, Hoang Anh Mai D, Ngoc Pham D, Thi Quynh Le H, Yeol Lee E. Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics. Int J Mol Sci 2020; 21:E3192. [PMID: 32366036 PMCID: PMC7247568 DOI: 10.3390/ijms21093192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Riboswitches and toehold switches are considered to have potential for implementation in various fields, i.e., biosensing, metabolic engineering, and molecular diagnostics. The specific binding, programmability, and manipulability of these RNA-based molecules enable their intensive deployments in molecular detection as biosensors for regulating gene expressions, tracking metabolites, or detecting RNA sequences of pathogenic microorganisms. In this review, we will focus on the development of riboswitches and toehold switches in biosensing and molecular diagnostics. This review introduces the operating principles and the notable design features of riboswitches as well as toehold switches. Moreover, we will describe the advances and future directions of riboswitches and toehold switches in biosensing and molecular diagnostics.
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Affiliation(s)
| | | | | | | | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (T.H.T.C.); (D.H.A.M.); (D.N.P.); (H.T.Q.L.)
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41
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Tang L. Pinpointing RNA mutations. Nat Methods 2020; 17:365-365. [DOI: 10.1038/s41592-020-0805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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