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Husseini AA, Baydar SY. Optimization of a rapid and sensitive nucleic acid lateral flow biosensor for hepatitis B virus detection. Mol Biol Rep 2023; 50:8329-8336. [PMID: 37592176 DOI: 10.1007/s11033-023-08730-9] [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: 03/15/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND AND OBJECTIVE The utilization of direct amplification of nucleic acid from lysate has attracted interest in the advancement of straightforward and economical point-of-care assays. Consequently, this study primarily focuses on the development of a rapid, precise, and cost-effective lateral flow biosensor for the convenient detection of HBV nucleic acid at the point-of-care. Furthermore, the study evaluates the effectiveness of the direct amplification method in comparison to purified nucleic acid samples within the context of LAMP-LF biosensing approaches. METHODS The experiments conducted in this study utilized clinical serum samples that were confirmed as HBV-positive through real-time PCR assays. Sample preparation involved employing spin column nucleic acid purification and serum heat treatment. To amplify a 250 bp fragment of the HBV polymerase gene, three pairs of specific LAMP primers were utilized, which were biotin-labeled and FITC-labeled for detection purposes. Various incubation temperatures (ranging from 64 to 68 °C) and durations (30 min, 45 min, and 1 h) were investigated to determine the optimal conditions for the LAMP assay. The results were subsequently assessed through fluorometric analysis, white turbidity measurements, and lateral flow assay. Milenia HybriDetect1 strips, designed for immediate use, were employed to visualize the LAMP amplicons. Furthermore, the performance of the lateral flow biosensor was evaluated using 10-fold serial dilutions of a secondary standard containing a viral load of 108 IU/ml. RESULTS The optimization of the LAMP reaction was achieved at a temperature of 67 °C, resulting in significant turbidity after a 30-minute incubation period. When the spin column purification method was employed, varying test bands were observed for templates ranging from 108 IU/ml to 101 IU/ml viral load. However, when serum samples underwent heat treatment and the resulting supernatant was directly used for LAMP, the lateral flow assay was capable of detecting a minimum viral load of 103 IU/ml. CONCLUSION In resource-limited settings, the LAMP-LF assay presents a promising solution for HBV testing. However, it is important to note that direct amplification without DNA purification may diminish the performance of the approach.
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Affiliation(s)
- Abbas Ali Husseini
- Life Sciences and Biomedical Engineering Application and Research Centre, Istanbul Gelisim University, Istanbul, Türkiye.
- Vocational School of health services, Istanbul Gelisim University, 34310, Istanbul, Türkiye.
| | - Serap Yesilkir Baydar
- Life Sciences and Biomedical Engineering Application and Research Centre, Istanbul Gelisim University, Istanbul, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Istanbul Gelisim University, Istanbul, Türkiye
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Mumtaz Z, Rashid Z, Ali A, Arif A, Ameen F, AlTami MS, Yousaf MZ. Prospects of Microfluidic Technology in Nucleic Acid Detection Approaches. BIOSENSORS 2023; 13:584. [PMID: 37366949 DOI: 10.3390/bios13060584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 06/28/2023]
Abstract
Conventional diagnostic techniques are based on the utilization of analyte sampling, sensing and signaling on separate platforms for detection purposes, which must be integrated to a single step procedure in point of care (POC) testing devices. Due to the expeditious nature of microfluidic platforms, the trend has been shifted toward the implementation of these systems for the detection of analytes in biochemical, clinical and food technology. Microfluidic systems molded with substances such as polymers or glass offer the specific and sensitive detection of infectious and noninfectious diseases by providing innumerable benefits, including less cost, good biological affinity, strong capillary action and simple process of fabrication. In the case of nanosensors for nucleic acid detection, some challenges need to be addressed, such as cellular lysis, isolation and amplification of nucleic acid before its detection. To avoid the utilization of laborious steps for executing these processes, advances have been deployed in this perspective for on-chip sample preparation, amplification and detection by the introduction of an emerging field of modular microfluidics that has multiple advantages over integrated microfluidics. This review emphasizes the significance of microfluidic technology for the nucleic acid detection of infectious and non-infectious diseases. The implementation of isothermal amplification in conjunction with the lateral flow assay greatly increases the binding efficiency of nanoparticles and biomolecules and improves the limit of detection and sensitivity. Most importantly, the deployment of paper-based material made of cellulose reduces the overall cost. Microfluidic technology in nucleic acid testing has been discussed by explicating its applications in different fields. Next-generation diagnostic methods can be improved by using CRISPR/Cas technology in microfluidic systems. This review concludes with the comparison and future prospects of various microfluidic systems, detection methods and plasma separation techniques used in microfluidic devices.
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Affiliation(s)
- Zilwa Mumtaz
- KAM School of Life Sciences, Forman Christian College University, Ferozpur Road, Lahore 54600, Pakistan
| | - Zubia Rashid
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi 1227788, United Arab Emirates
| | - Ashaq Ali
- State Key Laboratory of Virology, Center for Biosafety MegaScience, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Afsheen Arif
- Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi 75270, Pakistan
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Suad University, Riyadh 11451, Saudi Arabia
| | - Mona S AlTami
- Biology Department, College of Science, Qassim University, Burydah 52571, Saudi Arabia
| | - Muhammad Zubair Yousaf
- KAM School of Life Sciences, Forman Christian College University, Ferozpur Road, Lahore 54600, Pakistan
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Kim J, Kim C, Park JS, Lee NE, Lee S, Cho SY, Park C, Yoon DS, Yoo YK, Lee JH. Affordable on-site COVID-19 test using non-powered preconcentrator. Biosens Bioelectron 2023; 222:114965. [PMID: 36493723 PMCID: PMC9715458 DOI: 10.1016/j.bios.2022.114965] [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: 09/02/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022]
Abstract
A simple, affordable point of care test (POCT) is necessary for on-site detection of coronavirus disease 2019 (COVID-19). The lateral flow assay (LFA) has great potential for use in POCT mainly because of factors such as low time consumption, low cost, and ease of use. However, it lacks sensitivity and limits of detection (LOD), which are essential for early diagnostics. In this study, we proposed a non-powered preconcentrator (NPP) based on nanoelectrokinetics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Antigen (Ag) lateral flow assay. The non-powered preconcentrator is composed of glass fiber-based composite paper and ion permselective material, and it can be simply operated by force balancing gravitational, capillary, and depletion-induced forces. The proposed approach helps enrich the SARS-CoV-2 viral nucleocapsid (N) proteins based on a 10-min operation, and it improved the LOD by up to 10-fold. The corresponding virus enrichment, which was evaluated using the reverse-transcriptase polymerase chain reaction (RT-PCR), revealed an improvement in ΔCt values > 3. We successfully demonstrated the enhancement of the NPP-assisted LFA, we extended to applying it to clinical samples. Further, we demonstrated an affordable, easy-to-implement form of LFA by simply designing NPP directly on the LFA buffer tube.
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Affiliation(s)
- Jinhwan Kim
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Cheonjung Kim
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea; Department of Electronic Engineering, Catholic Kwandong University, Gangneung-si, Gangwon-do, 25601, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Na Eun Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea; Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea; School of Biomedical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary's Hospital, Catholic Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul, 02841, Republic of Korea.
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, Gangneung-si, Gangwon-do, 25601, Republic of Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea.
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Li B, Wang Q, Sohail M, Zhang X, He H, Lin L. Facilitating the determination of microcystin toxins with bio-inspired sensors. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Tu T, Huan S, Ke G, Zhang X. Functional Xeno Nucleic Acids for Biomedical Application. Chem Res Chin Univ 2022:1-7. [PMID: 35814030 PMCID: PMC9253239 DOI: 10.1007/s40242-022-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022]
Abstract
Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.
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Affiliation(s)
- Tingting Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Shuangyan Huan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaobing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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Zhang T, Ding F, Yang Y, Zhao G, Zhang C, Wang R, Huang X. Research Progress and Future Trends of Microfluidic Paper-Based Analytical Devices in In-Vitro Diagnosis. BIOSENSORS 2022; 12:bios12070485. [PMID: 35884289 PMCID: PMC9313202 DOI: 10.3390/bios12070485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
In vitro diagnosis (IVD) has become a hot topic in laboratory research and achievement transformation. However, due to the high cost, and time-consuming and complex operation of traditional technologies, some new technologies are being introduced into IVD, to solve the existing problems. As a result, IVD has begun to develop toward point-of-care testing (POCT), a subdivision field of IVD. The pandemic has made governments and health institutions realize the urgency of accelerating the development of POCT. Microfluidic paper-based analytical devices (μPADs), a low-cost, high-efficiency, and easy-to-operate detection platform, have played a significant role in advancing the development of IVD. μPADs are composed of paper as the core material, certain unique substances as reagents for processing the paper, and sensing devices, as auxiliary equipment. The published reviews on the same topic lack a comprehensive and systematic introduction to μPAD classification and research progress in IVD segmentation. In this paper, we first briefly introduce the origin of μPADs and their role in promoting IVD, in the introduction section. Then, processing and detection methods for μPADs are summarized, and the innovative achievements of μPADs in IVD are reviewed. Finally, we discuss and prospect the upgrade and improvement directions of μPADs, in terms of portability, sensitivity, and automation, to help researchers clarify the progress and overcome the difficulties in subsequent μPAD research.
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Wang X, Hong XZ, Li YW, Li Y, Wang J, Chen P, Liu BF. Microfluidics-based strategies for molecular diagnostics of infectious diseases. Mil Med Res 2022; 9:11. [PMID: 35300739 PMCID: PMC8930194 DOI: 10.1186/s40779-022-00374-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/10/2022] [Indexed: 02/08/2023] Open
Abstract
Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging microfluidics, a highly miniaturized, automatic, and integrated technology, are a potential substitute for traditional methods in performing rapid, low-cost, accurate, and on-site diagnoses. Molecular diagnostics are widely used in microfluidic devices as the most effective approaches for pathogen detection. This review summarizes the latest advances in microfluidics-based molecular diagnostics for infectious diseases from academic perspectives and industrial outlooks. First, we introduce the typical on-chip nucleic acid processes, including sample preprocessing, amplification, and signal read-out. Then, four categories of microfluidic platforms are compared with respect to features, merits, and demerits. We further discuss application of the digital assay in absolute nucleic acid quantification. Both the classic and recent microfluidics-based commercial molecular diagnostic devices are summarized as proof of the current market status. Finally, we propose future directions for microfluidics-based infectious disease diagnosis.
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Affiliation(s)
- Xin Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xian-Zhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yi-Wei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
| | - Jie Wang
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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Faikhruea K, Choopara I, Somboonna N, Assavalapsakul W, Kim BH, Vilaivan T. Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects. ACS APPLIED BIO MATERIALS 2022; 5:789-800. [PMID: 35119822 DOI: 10.1021/acsabm.1c01177] [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] [Indexed: 12/25/2022]
Abstract
Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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Chen H, Lin S, Wang Y, Fu S, Ma Y, Xia Q, Lin Y. Paper-based detection of Epstein-Barr virus using asymmetric polymerase chain reaction and gold silicon particles. Anal Chim Acta 2022; 1197:339514. [DOI: 10.1016/j.aca.2022.339514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/27/2022]
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Song P, Zhang R, He C, Chen T. Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases. Curr Protoc 2021; 1:e188. [PMID: 34232574 DOI: 10.1002/cpz1.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Although enzymatic synthesis provides an attractive alternative that also allows the replication and artificial evolution of these molecules, it is crucially dependent on the availability of polymerases capable of synthesizing these backbone-modified nucleotides. Previously, a series of thermostable polymerases that can efficiently synthesize or even amplify backbone-modified DNA or RNA have been evolved through a polymerase evolution method based on phage display. Herein we summarize protocols to use these evolved polymerase mutants to transcribe, reverse transcribe, and PCR amplify backbone-modified nucleic acids. We also outline the polymerase chain transcription method, developed later for the rapid production of RNA or backbone-modified RNA with one of these evolved polymerases, SFM4-3. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transcription/synthesis of modified DNA/RNA from DNA templates with evolved polymerases SFM4-3 or SFM4-6 Basic Protocol 2: Reverse transcription of modified DNA/RNA with evolved polymerase SFM4-9 Basic Protocol 3: PCR amplification of modified DNA with evolved polymerase SFM4-3 Basic Protocol 4: Polymerase chain transcription for the production of RNA/modified RNA oligonucleotides with evolved polymerase SFM4-3.
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Affiliation(s)
- Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Rujie Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Chuanping He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
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Watson EE, Angerani S, Sabale PM, Winssinger N. Biosupramolecular Systems: Integrating Cues into Responses. J Am Chem Soc 2021; 143:4467-4482. [DOI: 10.1021/jacs.0c12970] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Emma E. Watson
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Simona Angerani
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M. Sabale
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chem Biol, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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Kelwick RJR, Webb AJ, Freemont PS. Biological Materials: The Next Frontier for Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:399. [PMID: 32478045 PMCID: PMC7235315 DOI: 10.3389/fbioe.2020.00399] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Alexander J. Webb
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation & Innovation Hub, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, United Kingdom
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