1
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Zhang Q, Wei Z, Jia X. Controllable detection threshold achieved through the toehold switch system in a mercury ion whole-cell biosensor. Biosens Bioelectron 2024; 256:116283. [PMID: 38608495 DOI: 10.1016/j.bios.2024.116283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Due to the toxicity of mercury and its harmful effects on human health, it is essential to establish a low-cost, highly sensitive and highly specific monitoring method with a wide detection range, ideally with a simple visual readout. In this study, a whole-cell biosensor with adjustable detection limits was developed for the detection of mercury ions in water samples, allowing controllable threshold detection with an expanded detection range. Gene circuits were constructed by combining the toehold switch system with lactose operon, mercury-ion-specific operon, and inducible red fluorescent protein gene. Using MATLAB for design and selection, a total of eleven dual-input single-output sensing logic circuits were obtained based on the basic logic of gene circuit construction. Then, biosensor DTS-3 was selected based on its fluorescence response at different isopropyl β-D-Thiogalactoside (IPTG) concentrations, exhibiting the controllable detection threshold. At 5-20 μM IPTG, DTS-3 can achieve variable threshold detection in the range of 0.005-0.0075, 0.06-0.08, 1-2, and 4-6 μM mercury ion concentrations, respectively. Specificity experiments demonstrated that DTS-3 exhibits good specificity, not showing fluorescence response changes compared with other metal ions. Furthermore spiked sample experiments demonstrated its good resistance to interference, allowing it to distinguish mercury ion concentrations as low as 7.5 nM by the naked eye and 5 nM using a microplate reader. This study confirms the feasibility and performance of biosensor with controllable detection threshold, providing a new detection method and new ideas for expanding the detection range of biosensors while ensuring rapid and convenient measurements without compromising sensitivity.
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Affiliation(s)
- Qinglong Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Zixiang Wei
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, PR China.
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2
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Tian Z, Shao D, Tang L, Li Z, Chen Q, Song Y, Li T, Simmel FC, Song J. Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems. Nat Commun 2024; 15:4635. [PMID: 38821953 PMCID: PMC11143192 DOI: 10.1038/s41467-024-49021-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Dandan Shao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Li
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- College of Forestry, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Ningbo institute of Dalian University of Technology, Ningbo, 315016, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technische Universität München, Garching, Germany
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Koksaldi I, Park D, Atilla A, Kang H, Kim J, Seker UOS. RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics. ACS Synth Biol 2024; 13:1026-1037. [PMID: 38588603 PMCID: PMC11036506 DOI: 10.1021/acssynbio.3c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.
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Affiliation(s)
- Ilkay
Cisil Koksaldi
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Dongwon Park
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Abdurahman Atilla
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Hansol Kang
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Jongmin Kim
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Urartu Ozgur Safak Seker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
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4
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Aswathy R, Sumathi S. The Evolving Landscape of Cervical Cancer: Breakthroughs in Screening and Therapy Through Integrating Biotechnology and Artificial Intelligence. Mol Biotechnol 2024:10.1007/s12033-024-01124-7. [PMID: 38573545 DOI: 10.1007/s12033-024-01124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/15/2024] [Indexed: 04/05/2024]
Abstract
Cervical cancer (CC) continues to be a major worldwide health concern, profoundly impacting the lives of countless females worldwide. In low- and middle-income countries (LMICs), where CC prevalence is high, innovative, and cost-effective approaches for prevention, diagnosis, and treatment are vital. These approaches must ensure high response rates with minimal side effects to improve outcomes. The study aims to compile the latest developments in the field of CC, providing insights into the promising future of CC management along with the research gaps and challenges. Integrating biotechnology and artificial intelligence (AI) holds immense potential to revolutionize CC care, from MobileODT screening to precision medicine and innovative therapies. AI enhances healthcare accuracy and improves patient outcomes, especially in CC screening, where its use has increased over the years, showing promising results. Also, combining newly developed strategies with conventional treatment options presents an optimal approach to address the limitations associated with conventional methods. However, further clinical studies are essential for practically implementing these advancements in society. By leveraging these cutting-edge technologies and approaches, there is a substantial opportunity to reduce the global burden of this preventable malignancy, ultimately improving the lives of women in LMICs and beyond.
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Affiliation(s)
- Raghu Aswathy
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Bharathi Park Rd, Near Forest College Campus, Saibaba Colony, Coimbatore, Tamil Nadu, 641043, India
| | - Sundaravadivelu Sumathi
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Bharathi Park Rd, Near Forest College Campus, Saibaba Colony, Coimbatore, Tamil Nadu, 641043, India.
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5
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Santos‐Beneit F. What is the role of microbial biotechnology and genetic engineering in medicine? Microbiologyopen 2024; 13:e1406. [PMID: 38556942 PMCID: PMC10982607 DOI: 10.1002/mbo3.1406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.
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Affiliation(s)
- Fernando Santos‐Beneit
- Institute of Sustainable ProcessesValladolidSpain
- Department of Chemical Engineering and Environmental Technology, School of Industrial EngineeringUniversity of ValladolidValladolidSpain
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6
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Kang X, Zhao C, Chen S, Zhang X, Xue B, Li C, Wang S, Yang X, Xia Z, Xu Y, Huang Y, Qiu Z, Li C, Wang J, Pang J, Shen Z. Development of a cell-free toehold switch for hepatitis A virus type I on-site detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5813-5822. [PMID: 37870419 DOI: 10.1039/d3ay01408h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Picornavirus hepatitis A virus (HAV) is a common cause of hepatitis worldwide. It is spread primarily through contaminated food and water or person-to-person contact. HAV I has been identified as the most common type of human HAV infection. Here, we have developed a cell-free toehold switch sensor for HAV I detection. We screened 10 suitable toehold switch sequences using NUPACK software, and the VP1 gene was used as the target gene. The optimal toehold switch sequence was selected by in vivo expression. The best toehold switch concentration was further found to be 20 nM in a cell-free system. 5 nM trigger RNA activated the toehold switch to generate visible green fluorescence. The minimum detection concentration decreased to 1 pM once combined with NASBA. HAV I trigger RNA could be detected accurately with excellent specificity. In addition, the cell-free toehold switch sensor was verified in HAV I entities. The successful construction of the cell-free toehold switch sensor provided a convenient, rapid, and accurate method for HAV I on-site detection, especially in developing countries, without the involvement of expensive facilities and additional professional operators.
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Affiliation(s)
- Xiaodan Kang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chen Zhao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Shuting Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Xi Zhang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Bin Xue
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chenyu Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Shang Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Xiaobo Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Zhiqiang Xia
- The 908th Hospital of Chinese People's Liberation Army Joint Logistic Support Force, Nanchang, 330000, China
| | - Yongchun Xu
- The 908th Hospital of Chinese People's Liberation Army Joint Logistic Support Force, Nanchang, 330000, China
| | - Yongliang Huang
- The 908th Hospital of Chinese People's Liberation Army Joint Logistic Support Force, Nanchang, 330000, China
| | - Zhigang Qiu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chao Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Jingfeng Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Jian Pang
- The Air Force Hospital of Northern Theater People's Liberation Army, Shenyang 110042, China.
| | - Zhiqiang Shen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
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7
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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8
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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9
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Wang GA, Wu X, Chen F, Shen C, Yang Q, Li F. Toehold-Exchange-Based Activation of Aptamer Switches Enables High Thermal Robustness and Programmability. J Am Chem Soc 2023; 145:2750-2753. [PMID: 36701187 DOI: 10.1021/jacs.2c10928] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aptamer switches are attractive nature-inspired tools for developing smart materials and nanodevices. However, the thermal robustness and programmability of current aptamer switches are often limited by their activation processes that are coupled with high reaction enthalpy. Here, we present an enthalpy-independent activation approach that harnesses toehold-exchange as a general framework to design aptamer switches. We demonstrate mathematically and experimentally that this approach is highly effective in improving thermal robustness and thus leads to better analytical performances of aptamer switches. Enhanced programmability is also demonstrated through fine-grained and dynamic tuning of effective affinities and dynamic ranges, as well as the construction of a synthetic DNA network that resembled biological signaling cascades. Our study not only enriches the current toolbox for engineering and controlling synthetic molecular switches but also offers new insights into their thermodynamic basis, which is critical for diverse synthetic biological designs and applications.
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Affiliation(s)
- Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Xinghong Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Fangfang Chen
- College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, China, 710127
| | - Chenlan Shen
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Qianfan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario, Canada, L2S 3A1.,Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
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10
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Giakountis A, Stylianidou Z, Zaka A, Pappa S, Papa A, Hadjichristodoulou C, Mathiopoulos KD. Development of Toehold Switches as a Novel Ribodiagnostic Method for West Nile Virus. Genes (Basel) 2023; 14:237. [PMID: 36672977 PMCID: PMC9859090 DOI: 10.3390/genes14010237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
West Nile virus (WNV) is an emerging neurotropic RNA virus and a member of the genus Flavivirus. Naturally, the virus is maintained in an enzootic cycle involving mosquitoes as vectors and birds that are the principal amplifying virus hosts. In humans, the incubation period for WNV disease ranges from 3 to 14 days, with an estimated 80% of infected persons being asymptomatic, around 19% developing a mild febrile infection and less than 1% developing neuroinvasive disease. Laboratory diagnosis of WNV infection is generally accomplished by cross-reacting serological methods or highly sensitive yet expensive molecular approaches. Therefore, current diagnostic tools hinder widespread surveillance of WNV in birds and mosquitoes that serve as viral reservoirs for infecting secondary hosts, such as humans and equines. We have developed a synthetic biology-based method for sensitive and low-cost detection of WNV. This method relies on toehold riboswitches designed to detect WNV genomic RNA as transcriptional input and process it to GFP fluorescence as translational output. Our methodology offers a non-invasive tool with reduced operating cost and high diagnostic value that can be used for field surveillance of WNV in humans as well as in bird and mosquito populations.
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Affiliation(s)
- Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Zoe Stylianidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Anxhela Zaka
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
| | - Styliani Pappa
- Department of Microbiology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anna Papa
- Department of Microbiology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Kostas D. Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis-Mezourlo, 41500 Larissa, Greece
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11
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Patterson AT, Styczynski MP. Rapid and Finely-Tuned Expression for Deployable Sensing Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:141-161. [PMID: 37316621 DOI: 10.1007/10_2023_223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Organisms from across the tree of life have evolved highly efficient mechanisms for sensing molecules of interest using biomolecular machinery that can in turn be quite valuable for the development of biosensors. However, purification of such machinery for use in in vitro biosensors is costly, while the use of whole cells as in vivo biosensors often leads to long sensor response times and unacceptable sensitivity to the chemical makeup of the sample. Cell-free expression systems overcome these weaknesses by removing the requirements associated with maintaining living sensor cells, allowing for increased function in toxic environments and rapid sensor readout at a production cost that is often more reasonable than purification. Here, we focus on the challenge of implementing cell-free protein expression systems that meet the stringent criteria required for them to serve as the basis for field-deployable biosensors. Fine-tuning expression to meet these requirements can be achieved through careful selection of the sensing and output elements, as well as through optimization of reaction conditions via tuning of DNA/RNA concentrations, lysate preparation methods, and buffer conditions. Through careful sensor engineering, cell-free systems can continue to be successfully used for the production of tightly regulated, rapidly expressing genetic circuits for biosensors.
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Affiliation(s)
- Alexandra T Patterson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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12
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Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023; 2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the chapter highlights several prominent computational tools applied in the field and their potential use cases. The examples detailed reinforce how ML algorithms can enhance synthetic biology research by providing data-driven insights into the behavior of living systems, even without detailed knowledge of their underlying mechanisms. By doing so, ML promises to increase the efficiency of research projects by modeling hypotheses in silico that can then be tested through experiments. While challenges related to training dataset generation and computational costs remain, ongoing improvements in ML tools are paving the way for smarter and more streamlined synthetic biology workflows that can be readily employed to address grand challenges across manufacturing, medicine, engineering, agriculture, and beyond.
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Affiliation(s)
- Brendan Fu-Long Sieow
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, Singapore
| | - Ryan De Sotto
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhi Ren Darren Seet
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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13
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Transcription Factor-Based Biosensors for Detecting Pathogens. BIOSENSORS 2022; 12:bios12070470. [PMID: 35884273 PMCID: PMC9312912 DOI: 10.3390/bios12070470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 12/23/2022]
Abstract
Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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15
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Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19. J Nucleic Acids 2022; 2022:7130061. [PMID: 35586794 PMCID: PMC9110250 DOI: 10.1155/2022/7130061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.
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16
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Riboswitch RS thiT as a molecular tool in Lactococcus lactis. Appl Environ Microbiol 2021; 88:e0176421. [PMID: 34936833 PMCID: PMC8862789 DOI: 10.1128/aem.01764-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Previous RNA sequencing has allowed the identification of 129 long 5′ untranslated regions (UTRs) in the Lactococcus lactis MG1363 transcriptome. These sequences potentially harbor cis-acting riboswitches. One of the identified extended 5′ UTRs is a putative thiamine pyrophosphate (TPP) riboswitch. It is located immediately upstream of the thiamine transporter gene thiT (llmg_0334). To confirm this assumption, the 5′-UTR sequence was placed upstream of the gene encoding the superfolder green fluorescent protein (sfGFP), sfgfp, allowing the examination of the expression of sfGFP in the presence or absence of thiamine in the medium. The results show that this sequence indeed represents a thiamine-responsive TPP riboswitch. This RNA-based genetic control device was used to successfully restore the mutant phenotype of an L. lactis strain lacking the major autolysin gene, acmA. The L. lactisthiT TPP riboswitch (RSthiT) is a useful molecular genetic tool enabling the gradual downregulation of the expression of genes under its control by adjusting the thiamine concentration. IMPORTANCE The capacity of microbes with biotechnological importance to adapt to and survive under quickly changing industrial conditions depends on their ability to adequately control gene expression. Riboswitches are important RNA-based elements involved in rapid and precise gene regulation. Here, we present the identification of a natural thiamine-responsive riboswitch of Lactococcus lactis, a bacterium used worldwide in the production of dairy products. We used it to restore a genetic defect in an L. lactis mutant and show that it is a valuable addition to the ever-expanding L. lactis genetic toolbox.
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17
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Cai X, Wang Q, Fang Y, Yao D, Zhan Y, An B, Yan B, Cai J. Attenuator LRR - a regulatory tool for modulating gene expression in Gram-positive bacteria. Microb Biotechnol 2021; 14:2538-2551. [PMID: 33720523 PMCID: PMC8601186 DOI: 10.1111/1751-7915.13797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
With the rapid development of synthetic biology in recent years, particular attention has been paid to RNA devices, especially riboswitches, because of their significant and diverse regulatory roles in prokaryotic and eukaryotic cells. Due to the limited performance and context-dependence of riboswitches, only a few of them (such as theophylline, tetracycline and ciprofloxacin riboswitches) have been utilized as regulatory tools in biotechnology. In the present study, we demonstrated that a ribosome-dependent ribo-regulator, LRR, discovered in our previous work, exhibits an attractive regulatory performance. Specifically, it offers a 60-fold change in expression in the presence of retapamulin and a low level of leaky expression of about 1-2% without antibiotics. Moreover, LRR can be combined with different promoters and performs well in Bacillus thuringiensis, B. cereus, B. amyloliquefaciens, and B. subtilis. Additionally, LRR also functions in the Gram-negative bacterium Escherichia coli. Furthermore, we demonstrate its ability to control melanin metabolism in B. thuringiensis BMB171. Our results show that LRR can be applied to regulate gene expression, construct genetic circuits and tune metabolic pathways, and has great potential for many applications in synthetic biology.
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Affiliation(s)
- Xia Cai
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Qian Wang
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Yu Fang
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Die Yao
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Yunda Zhan
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Baoju An
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Bing Yan
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
| | - Jun Cai
- Department of MicrobiologyCollege of Life SciencesNankai UniversityTianjin300071China
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin300071China
- Tianjin Key Laboratory of Microbial Functional GenomicsTianjin300071China
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18
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Koklu A, Ohayon D, Wustoni S, Druet V, Saleh A, Inal S. Organic Bioelectronic Devices for Metabolite Sensing. Chem Rev 2021; 122:4581-4635. [PMID: 34610244 DOI: 10.1021/acs.chemrev.1c00395] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrochemical detection of metabolites is essential for early diagnosis and continuous monitoring of a variety of health conditions. This review focuses on organic electronic material-based metabolite sensors and highlights their potential to tackle critical challenges associated with metabolite detection. We provide an overview of the distinct classes of organic electronic materials and biorecognition units used in metabolite sensors, explain the different detection strategies developed to date, and identify the advantages and drawbacks of each technology. We then benchmark state-of-the-art organic electronic metabolite sensors by categorizing them based on their application area (in vitro, body-interfaced, in vivo, and cell-interfaced). Finally, we share our perspective on using organic bioelectronic materials for metabolite sensing and address the current challenges for the devices and progress to come.
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Affiliation(s)
- Anil Koklu
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - David Ohayon
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Shofarul Wustoni
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Victor Druet
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Abdulelah Saleh
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Sahika Inal
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
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19
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Cao M, Sun Q, Zhang X, Ma Y, Wang J. Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system. Biosens Bioelectron 2021; 182:113173. [PMID: 33773383 DOI: 10.1016/j.bios.2021.113173] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 12/20/2022]
Abstract
Respiratory syncytial virus (RSV) infection is the most common clinical infectious disease threatening the safety of human life. Herein, we provided a sensitive and specific method for detection and differentiation of RSV subgroups A (RSVA) and B (RSVB) with colorimetric toehold switch sensors in a paper-based cell-free system. In this method, we applied the toehold switch, an RNA-based riboswitch, to regulate the translation level of β-galactosidase (lacZ) gene. In the presence of target trigger RNA, the toehold switch sensor was activated and the expressed LacZ hydrolyzed chromogenic substrates to produce a colorimetric result that can be observed directly with the naked eye in a cell-free system. In addition, nucleic acid sequence-based amplification (NASBA) was used to improve the sensitivity by amplifying target trigger RNAs. Under optimal conditions, our method produced a visible result for the detection of RSVA and RSVB with the detection limit of 52 aM and 91 aM, respectively. The cross-reaction of this method was validated with other closely related respiratory viruses, including human coronavirus HKU1 (HCoV-HKU1), and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Furthermore, we used the paper-based carrier material that allows stable storage of our detection elements and rapid detection outside laboratory. In conclusion, this method can sensitively and specifically differentiate RSVA and RSVB and generate a visible colorimetric result without specialized operators and sophisticated equipment. Based on these advantages above, this method serves as a simple and portable detector in resource-poor areas and point-of-care testing (POCT) scenarios.
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Affiliation(s)
- Mengcen Cao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Qiuli Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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20
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Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annu Rev Chem Biomol Eng 2021; 12:263-286. [PMID: 33900805 PMCID: PMC9714562 DOI: 10.1146/annurev-chembioeng-101420-014055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laura M Hertz
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - David Z Bushhouse
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Chloé M Archuleta
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA; .,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA.,Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA.,Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
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21
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Burrington LR, Baryal E, Hui K, Lambert E, Harding ST, Oza JP. The Fold-Illuminator: A low-cost, portable, and disposable incubator-illuminator device. Synth Syst Biotechnol 2021; 6:95-101. [PMID: 33997359 PMCID: PMC8099501 DOI: 10.1016/j.synbio.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 01/08/2023] Open
Abstract
Fluorescent reporters have revolutionized modern applications in the fields of molecular and synthetic biology, enabling applications ranging from education to point-of-care diagnostics. Past advancements in these fields have primarily focused on improving reaction conditions, the development of new applications, and the broad dissemination of these technologies. However, field and classroom-based applications have remained limited in part due to the nature of fluorescent signal detection, which often requires the use of costly lab equipment to observe and quantify fluorescence readouts. Users without access to laboratory equipment rely on qualitative assessments of fluorescence, a process that remains highly variable from user-to-user even within the same classroom. To overcome this challenge, we have developed a foldable illuminator and incubator device to support field-applications of synthetic biology-based biosensors for education and diagnostics. The Fold-Illuminator is an affordable, portable, and recyclable device that allows for the visible detection of fluorescent biomolecules. The Fold-Illuminator's design allows for assembly in under 10 min, a user can then utilize the optional heating element to incubate biochemical reactions and visualize fluorescence outputs in a defined and light-controlled environment. Interchangeable LED strips and light-filtering screens provide modularity to pair with the fluorescence wavelengths of interest. The user can then unfold the device for convenient storage, transport, or even recycling. The cost for the Fold-Illuminator is $5.58 USD and is compatible with an optional heating element for an additional $3.98 cost, with potential for further reductions in cost for larger quantities. Open-source templates for cutting device parts from paper stock are provided for both printing and cutting by hand; cutting can also be achieved with consumer-grade smart cutting machines such as the Cricut®. Combined with the broad applications of fluorescent reporters, the Fold-Illuminator has the potential to improve access to fluorescence visualization and quantification for new users as well as emerging field applications.
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Affiliation(s)
- Logan R Burrington
- Chemistry and Biochemistry Department, College of Science and Math, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Emran Baryal
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Katherine Hui
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Emmett Lambert
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Sarah T Harding
- Mechanical Engineering Department, College of Engineering, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Javin P Oza
- Chemistry and Biochemistry Department, College of Science and Math, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
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22
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Drogalis LK, Batey RT. Requirements for efficient ligand-gated co-transcriptional switching in designed variants of the B. subtilis pbuE adenine-responsive riboswitch in E. coli. PLoS One 2020; 15:e0243155. [PMID: 33259551 PMCID: PMC7707468 DOI: 10.1371/journal.pone.0243155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 11/18/2022] Open
Abstract
Riboswitches, generally located in the 5'-leader of bacterial mRNAs, direct expression via a small molecule-dependent structural switch that informs the transcriptional or translational machinery. While the structure and function of riboswitch effector-binding (aptamer) domains have been intensely studied, only recently have the requirements for efficient linkage between small molecule binding and the structural switch in the cellular and co-transcriptional context begun to be actively explored. To address this aspect of riboswitch function, we have performed a structure-guided mutagenic analysis of the B. subtilis pbuE adenine-responsive riboswitch, one of the simplest riboswitches that employs a strand displacement switching mechanism to regulate transcription. Using a cell-based fluorescent protein reporter assay to assess ligand-dependent regulatory activity in E. coli, these studies revealed previously unrecognized features of the riboswitch. Within the aptamer domain, local and long-range conformational dynamics influenced by sequences within helices have a significant effect upon efficient regulatory switching. Sequence features of the expression platform including the pre-aptamer leader sequence, a toehold helix and an RNA polymerase pause site all serve to promote strong ligand-dependent regulation. By optimizing these features, we were able to improve the performance of the B. subtilis pbuE riboswitch in E. coli from 5.6-fold induction of reporter gene expression by the wild type riboswitch to over 120-fold in the top performing designed variant. Together, these data point to sequence and structural features distributed throughout the riboswitch required to strike a balance between rates of ligand binding, transcription and secondary structural switching via a strand exchange mechanism and yield new insights into the design of artificial riboswitches.
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MESH Headings
- Adenine/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Escherichia coli K12/genetics
- Genes, Reporter
- Genetic Variation
- Ligands
- Models, Genetic
- Models, Molecular
- Mutagenesis
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- Riboswitch/genetics
- Transcription, Genetic
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Affiliation(s)
- Lea K. Drogalis
- Department of Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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23
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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