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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: 3] [Impact Index Per Article: 3.0] [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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2
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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3
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Zhao R, Yu C, Lu B, Li B. Coupling nucleic acid circuitry with the CRISPR-Cas12a system for universal and signal-on detection. RSC Adv 2022; 12:10374-10378. [PMID: 35425009 PMCID: PMC8977996 DOI: 10.1039/d2ra01332k] [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: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
We report a universal and signal-on HCR based detection platform via innovatively coupling the CRISPR-Cas12a system with HCR. By using this CRISPR-HCR pathway, we can detect different targets by only changing the crRNA. The CRISPR-HCR platform coupling with an upstream amplifier can achieve a practical sensitivity as low as ∼aM of ASFV gene in serum.
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Affiliation(s)
- Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
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4
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Borum RM, Jokerst JV. Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging. Biomater Sci 2021; 9:347-366. [PMID: 32734995 PMCID: PMC7855509 DOI: 10.1039/d0bm00931h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.
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Affiliation(s)
- Raina M Borum
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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6
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Zeng C, Gao J, Lou Y, Cui L. Enzyme-free and protein-assisted dual-amplified fluorescence anisotropy for sensitive miRNA detection in tumor cells. Talanta 2020; 218:121179. [PMID: 32797926 DOI: 10.1016/j.talanta.2020.121179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023]
Abstract
We here report a double amplification strategy to construct a fluorescence anisotropy sensor for microRNA analysis in practical biological samples. In this strategy, one target can trigger cyclic catalyzed hairpin assembly (CHA), with streptavidin incorporated as an amplifier of molar mass to enhance the signal intensity. The proposed strategy has a good linearity in the range of 5 pM - 0.5 nM with a detection limit down to 2.3 pM. More importantly, by using fluorescence anisotropy as the signal output, the strategy can be used directly for detection of miRNA in practical samples without any tedious sample pretreatment, holding the practical value in real biological systems.
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Affiliation(s)
- Chaofei Zeng
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Jiafeng Gao
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Yifei Lou
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Liang Cui
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
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7
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Zhu Z, Duan X, Li Q, Wu R, Wang Y, Li B. Low-Noise Nanopore Enables In-Situ and Label-Free Tracking of a Trigger-Induced DNA Molecular Machine at the Single-Molecular Level. J Am Chem Soc 2020; 142:4481-4492. [PMID: 32069050 DOI: 10.1021/jacs.0c00029] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Solid-state nanopores have shown special high potential in a label-free molecular assay, structure identification, and target-index at the single-molecular level, even though frustrating electrical baseline noise is still one of the major factors that limit the spatial resolution and signaling reliability of solid-state nanopores, especially in small target detection. Here we develop a significant and easy-operating noise-reduction approach via mixing organic solvents with high dielectric constants into a traditional aqueous electrolyte. The strategy is generally effective for pores made of different materials, such as the most commonly used conical glass (CGN) or SiNx. While the mechanism should be multisourced, MD simulations suggest the noise reduction may partially arise from the even ionic distribution caused by the addition of higher dielectric species. Among all solvents experimentally tested, the two with the highest dielectric constants, formamide and methylformamide, exhibit the best noise reduction effect for target detection of CGN. The power spectral density at the low-frequency limit is reduced by nearly 3 orders with the addition of 20% formamide. Our work qualifies the reliability of solid-state nanopores into much subtler scales of detection, such as dsDNAs under 100 bp. As a practical example, bare CGN is innovatively employed to perform in-situ tracking of trigger-responsive DNA machine forming oligomers.
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Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiaozheng Duan
- State Key Lab of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Qiao Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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8
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One-tube smart genetic testing via coupling isothermal amplification and three-way nucleic acid circuit to glucometers. Anal Chim Acta 2020; 1106:191-198. [PMID: 32145848 PMCID: PMC7094703 DOI: 10.1016/j.aca.2020.01.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 11/23/2022]
Abstract
Urgent demand for portable diagnosis has promoted a new sensing strategy that uses personal glucometer (PGM) to detect non-glucose targets. Even though great progresses have been achieved in terms of target range and sensing principle, issues such as low final signal-to-background ratio and hard-to-realize one-tube smart analysis still exist and challenge real-world applications in gene detection. Here we propose a practical solution via coupling isothermal amplification (i.e. LAMP) and three-way amplifiable catalytic hairpin assembly (i.e. CHA) to a PGM. It allows direct transduction from genomic information to commercial portable devices with all of ultra-high sensitivity, specificity and enhanced signal-to-noise ratio. Compared with previous report without signal amplification, the introduction of CHA has successfully improved the signal amplitude by at least 12.5 folds. More importantly, through importing an effective three-way junction based transduction, we also innovatively develop a one-tube logical or multiplex analysis strategy in PGM based detection. Totally four situations of two foodborne bacteria genes, in Cronobacter sakazakii (ompA) and Escherichia coli (malB), could be directly readout using the final PGM signals, with the lowest detection amount down to less than 100 molecular copies (6.6 × 10-18 M). It is believed such a LAMP-CHA-PGM method has been already sensitive, specific, and of great potential for practically portable gene diagnostics.
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9
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A rapid, adaptative DNA biosensor based on molecular beacon-concatenated dual signal amplification strategies for ultrasensitive detection of p53 gene and cancer cells. Talanta 2019; 210:120638. [PMID: 31987215 DOI: 10.1016/j.talanta.2019.120638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 11/23/2022]
Abstract
The cancer diagnosis with single level of biomarkers suffers from limitation of insufficient accuracy. Hence, developing sensitive, rapid and adaptative analytical strategies for double-level biomarkers are essential for improving the accuracy of clinical cancer diagnosis at early stage. Herein, a DNA biosensor was established based on the catalytic hairpin assembly-mediated Y-junction nicking enzyme assisted signal amplification (CHA-YNEASA) circuits, where the two circuits were concatenated by molecular beacon (MB). In absence of target, both the CHA and YNEASA circuits were effectively hindered because of MB's outstanding ability to control signal background. In presence of target, the initiated CHA circuits made enzyme recognition sequences in close proximity to the assisted sequences to open MB, leading to further trigger the YNEASA circuits. Due to the unique design of dual signal amplification strategies, CHA-YNEASA circuits significantly shorten the reaction time, and improve signal-to-background ratio as well as facilitate the analysis process. It was demonstrated that a high sensitivity with limit of detection (LOD) of 0.9 pM for p53 gene detection was obtained just within 23 min by the proposed DNA biosensor. Moreover, mismatched p53 gene at nucleic acid level was effectively discriminated and strong anti-interference capability was achieved. Noticeably, the DNA biosensor was adaptative for designing a cytosensor at cell level using hairpin DNA, containing MUC1 aptamer and initiation strand of CHA-YNEASA circuits, as switch based on modularity principle. The cytosensor is able to measure MUC1 positive breast cancer cells (MCF-7) with the LOD as low as 100 cells/mL. Excellent specificity for MUC1 negative cells, and good anti-interference capability in 10% fetal bovine serum (FBS) were observed by the cytosensor. Therefore, the proposed DNA biosensor is a sensitive, rapid, adaptative platform for detection of double-level biomarkers, offering novel strategy applied for clinical cancer diagnosis.
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10
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Xiong E, Zhen D, Jiang L, Zhou X. Binding-Induced 3D-Bipedal DNA Walker for Cascade Signal Amplification Detection of Thrombin Combined with Catalytic Hairpin Assembly Strategy. Anal Chem 2019; 91:15317-15324. [PMID: 31710462 DOI: 10.1021/acs.analchem.9b04987] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As an important biomarker, thrombin (TB) is a major player in thrombosis and hemostasis and has attracted increasing attention involving its determination. Herein a universal and ultrasensitive fluorescence biosensor based on a binding-induced 3D-bipedal DNA walker and catalytic hairpin assembly (CHA) strategy has been proposed for cascade signal amplification detection of thrombin. In this study, we designed two proximity probes (foot 1 and foot 2) which include a specific affinity ligand for TB binding and a Pb2+-dependent DNAzyme tail sequence. In the presence of TB, the simultaneous binding of TB to foot 1 (F1) and foot 2 (F2) via TB aptamer (TBA) brings the tail sequences into close proximity and the melting temperature for tail sequences and track DNA is increased, allowing the Pb2+-dependent DNAzyme to cleave the track DNA into two short fragments which have lower affinities for the DNAzyme and, finally, leading to the release of trigger DNA (T-DNA) for subsequent CHA reaction. In the meantime, the dissociated DNA walkers (F1 and F2) explore adjacent unwound track DNA, and the walking procedure is conducted. Unlike the conventional unipedal DNA walkers that anchor foot DNA and track DNA on the same sensing surface, the proposed 3D-bipedal DNA walking machine can not only increase the local concentration of track DNA but can also improve the walking efficiency and expand the range of the walkers to some extent due to the two free feet. Moreover, with the advantages of superior sensitivity and excellent specificity, this biosensing platform exhibits a huge potential in practical application in biomedical research and clinical diagnosis.
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Affiliation(s)
- Erhu Xiong
- School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Deshuai Zhen
- College of Chemistry and Chemical Engineering , Qiannan Normal University for Nationalities , Duyun 558000 , China.,State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082 , China
| | - Ling Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082 , China
| | - Xiaoming Zhou
- School of Life Sciences , South China Normal University , Guangzhou 510631 , China
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11
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Zhu Z, Wu R, Li B. Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit. Chem Sci 2019; 10:1953-1961. [PMID: 30881624 PMCID: PMC6385554 DOI: 10.1039/c8sc04875d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022] Open
Abstract
Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the "base-pair distribution" of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.
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Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
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12
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Wang B, Thachuk C, Ellington AD, Winfree E, Soloveichik D. Effective design principles for leakless strand displacement systems. Proc Natl Acad Sci U S A 2018; 115:E12182-E12191. [PMID: 30545914 PMCID: PMC6310779 DOI: 10.1073/pnas.1806859115] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Artificially designed molecular systems with programmable behaviors have become a valuable tool in chemistry, biology, material science, and medicine. Although information processing in biological regulatory pathways is remarkably robust to error, it remains a challenge to design molecular systems that are similarly robust. With functionality determined entirely by secondary structure of DNA, strand displacement has emerged as a uniquely versatile building block for cell-free biochemical networks. Here, we experimentally investigate a design principle to reduce undesired triggering in the absence of input (leak), a side reaction that critically reduces sensitivity and disrupts the behavior of strand displacement cascades. Inspired by error correction methods exploiting redundancy in electrical engineering, we ensure a higher-energy penalty to leak via logical redundancy. Our design strategy is, in principle, capable of reducing leak to arbitrarily low levels, and we experimentally test two levels of leak reduction for a core "translator" component that converts a signal of one sequence into that of another. We show that the leak was not measurable in the high-redundancy scheme, even for concentrations that are up to 100 times larger than typical. Beyond a single translator, we constructed a fast and low-leak translator cascade of nine strand displacement steps and a logic OR gate circuit consisting of 10 translators, showing that our design principle can be used to effectively reduce leak in more complex chemical systems.
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Affiliation(s)
- Boya Wang
- Electrical and Computer Engineering, University of Texas at Austin, Austin, TX 78712
| | - Chris Thachuk
- Computer Science, California Institute of Technology, Pasadena, CA 91125
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Erik Winfree
- Computer Science, California Institute of Technology, Pasadena, CA 91125
- Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125
- Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - David Soloveichik
- Electrical and Computer Engineering, University of Texas at Austin, Austin, TX 78712;
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13
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Xiong E, Zhen D, Jiang L. Homogeneous enzyme-free and entropy-driven isothermal fluorescent assay for nucleic acids based on a dual-signal output amplification strategy. Chem Commun (Camb) 2018; 54:12594-12597. [DOI: 10.1039/c8cc07508e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proposed fluorescent biosensor improves the reaction rate, has excellent analytical performance (LOD 15.6 fM) and shows outstanding recognition toward mismatched DNA strands. This approach provides a potential universal platform for the determination of other nucleic acids.
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Affiliation(s)
- Erhu Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Deshuai Zhen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Ling Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
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14
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Tang Y, Lu B, Zhu Z, Li B. Establishment of a universal and rational gene detection strategy through three-way junction-based remote transduction. Chem Sci 2017; 9:760-769. [PMID: 29629146 PMCID: PMC5872807 DOI: 10.1039/c7sc03190d] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/18/2017] [Indexed: 01/19/2023] Open
Abstract
The polymerase chain reaction and many isothermal amplifications are able to achieve super gene amplification. Unfortunately, most commonly-used transduction methods, such as dye staining and Taqman-like probing, still suffer from shortcomings including false signals or difficult probe design, or are incompatible with multi-analysis. Here a universal and rational gene detection strategy has been established by translating isothermal amplicons to enzyme-free strand displacement circuits via three-way junction-based remote transduction. An assistant transduction probe was imported to form a partial hybrid with the target single-stranded nucleic acid. After systematic optimization the hybrid could serve as an associative trigger to activate a downstream circuit detector via a strand displacement reaction across the three-way junction. By doing so, the detection selectivity can be double-guaranteed through both amplicon-transducer recognition and the amplicon-circuit reaction. A well-optimized circuit can be immediately applied to a new target detection through simply displacing only 10-12 nt on only one component, according to the target. More importantly, this property for the first time enables multi-analysis and logic-analysis in a single reaction, sharing a single fluorescence reporter. In an applicable model, trace amounts of Cronobacter and Enterobacteria genes have been clearly distinguished from samples with no bacteria or one bacterium, with ultra-high sensitivity and selectivity.
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Affiliation(s)
- Yidan Tang
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , 130022 , Jilin , China . .,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Baiyang Lu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , 130022 , Jilin , China .
| | - Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , 130022 , Jilin , China . .,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , 130022 , Jilin , China .
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Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation. Sci Rep 2017; 7:15191. [PMID: 29123195 PMCID: PMC5680199 DOI: 10.1038/s41598-017-15697-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022] Open
Abstract
Gene regulation systems are mimicked by simple quantitative detection of non-nucleic acid molecular targets such as protein and metabolite. Here, we describe a one-tube, one-step real-time quantitative detection methodology for isothermal signal amplification of those targets. Using this system, real-time quantitative detection of thrombin and streptomycin, which were used as examples for protein and metabolite targets, was successfully demonstrated with detection limits of at most 50 pM and 75 nM, respectively. Notably, the dynamic range of target concentrations could be obtained for over four orders of magnitude. Thus, our method is expected to serve as a point-of-care or on-site test for medical diagnosis and food and environmental hygiene.
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