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Flores-Contreras EA, González-González E, Trujillo-Rodríguez GDJ, Rodríguez-Sánchez IP, Ancer-Rodríguez J, Pérez-Maya AA, Alvarez-Cuevas S, Martinez-Fierro ML, Marino-Martínez IA, Garza-Veloz I. Isothermal Technologies for HPV Detection: Current Trends and Future Perspectives. Pathogens 2024; 13:653. [PMID: 39204253 PMCID: PMC11357395 DOI: 10.3390/pathogens13080653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
The human papillomavirus (HPV) is a non-enveloped DNA virus transmitted through skin-to-skin contact that infects epithelial and mucosal tissue. It has over 200 known genotypes, classified by their pathogenicity as high-risk and low-risk categories. High-risk HPV genotypes are associated with the development of different types of cancers, including cervical cancer, which is a leading cause of mortality in women. In clinical practice and the market, the principal tests used to detect HPV are based on cytology, hybrid detection, and qPCR. However, these methodologies may not be ideal for the required timely diagnosis. Tests have been developed based on isothermal nucleic acid amplification tests (INAATs) as alternatives. These tests offer multiple advantages over the qPCR, such as not requiring specialized laboratories, highly trained personnel, or expensive equipment like thermocyclers. This review analyzes the different INAATs applied for the detection of HPV, considering the specific characteristics of each test, including the HPV genotypes, gene target, the limit of detection (LOD), detection methods, and detection time. Additionally, we discuss the tests available on the market that are approved by the Food and Drug Administration (FDA). Finally, we address the challenges and potential solutions for the large-scale implementation of INAATs, particularly in rural or underserved areas.
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Affiliation(s)
- Elda A. Flores-Contreras
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Everardo González-González
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Gerardo de Jesús Trujillo-Rodríguez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iram P. Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - Jesús Ancer-Rodríguez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Antonio Alí Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico;
| | - Salomon Alvarez-Cuevas
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iván A. Marino-Martínez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
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Yu L, Tang Z, Sun Y, Yi H, Tang Y, Zhong Y, Dian D, Cong Y, Wang H, Xie Z, He S, Chen Z. A polyethylene glycol enhanced ligation-triggered self-priming isothermal amplification for the detection of SARS-CoV-2 D614G mutation. Talanta 2023; 262:124711. [PMID: 37244245 DOI: 10.1016/j.talanta.2023.124711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
We presented a polyethylene glycol (PEG) enhanced ligation-triggered self-priming isothermal amplification (PEG-LSPA) for the detection D614G mutation in S-glycoprotein of SARS-CoV-2. PEG was employed to improve the ligation efficiency of this assay by constructing a molecular crowding environment. Two hairpin probes (H1 and H2) were designed to contain 18 nt and 20 nt target binding site at their 3' end and 5' end, respectively. In presence of target sequence, it complemented with H1 and H2 to trigger ligation by ligase under molecular crowding condition to form ligated H1-H2 duplex. Then 3' terminus of the H2 would be extended by DNA polymerase under isothermal conditions to form a longer extended hairpin (EHP1). 5' terminus of EHP1 with phosphorothioate (PS) modification could form hairpin structure due to the lower Tm value. The resulting 3' end overhang would also fold back as a new primer to initiate the next round of polymerization, resulting in the formation of a longer extended hairpin (EHP2) containing two target sequence domains. In the circle of LSPA, long extended hairpin (EHPx) containing numerous target sequence domains was produced. The resulting DNA products can be monitored in real-time fluorescence signaling. Our proposed assay owns an excellent linear range from 10 fM to 10 nM with a detection limit down to 4 fM. Thus, this work provides a potential isothermal amplification method for monitoring mutations in SARS-CoV-2 variants.
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Affiliation(s)
- Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zibin Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuanzhong Sun
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Hai Yi
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuebiao Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yangqing Zhong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Dongchun Dian
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Yanguang Cong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Houqi Wang
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zhaoyang Xie
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Suhui He
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Zhangquan Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
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Electrochemical biosensor based on efficient target-trigger T-structure recycling with dual strand displacement amplification for sensing miRNA-155. Anal Chim Acta 2022; 1238:340609. [DOI: 10.1016/j.aca.2022.340609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
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4
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Xiao X, Lin Z, Huang X, Lu J, Zhou Y, Zheng L, Lou Y. Rapid and Sensitive Detection of Vibrio vulnificus Using CRISPR/Cas12a Combined With a Recombinase-Aided Amplification Assay. Front Microbiol 2021; 12:767315. [PMID: 34745075 PMCID: PMC8566878 DOI: 10.3389/fmicb.2021.767315] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/04/2021] [Indexed: 12/19/2022] Open
Abstract
Vibrio vulnificus is an important zoonotic and aquatic pathogen and can cause vibriosis in humans and aquatic animals (especially farmed fish and shrimp species). Rapid and sensitive detection methods for V. vulnificus are still required to diagnose human vibriosis early and reduce aquaculture losses. Herein, we developed a rapid and sensitive diagnostic method comprising a recombinase-aided amplification (RAA) assay and the CRISPR/Cas12a system (named RAA-CRISPR/Cas12a) to detect V. vulnificus. The RAA-CRISPR/Cas12a method allows rapid and sensitive detection of V. vulnificus in 40 min without a sophisticated instrument, and the limit of detection is two copies of V. vulnificus genomic DNA per reaction. Meanwhile, the method shows satisfactory specificity toward non-target bacteria and high accuracy in the spiked blood, stool, and shrimp samples. Therefore, our proposed rapid and sensitive V. vulnificus detection method, RAA-CRISPR/Cas12a, has great potential for early diagnosis of human vibriosis and on-site V. vulnificus detection in aquaculture and food safety control.
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Affiliation(s)
- Xingxing Xiao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ziqin Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xianhui Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Jinfang Lu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yan Zhou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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Chen J, Zhu D, Huang T, Yang Z, Liu B, Sun M, Chen JX, Dai Z, Zou X. Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins. Anal Chem 2021; 93:12707-12713. [PMID: 34491714 DOI: 10.1021/acs.analchem.1c02588] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2n. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.
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Affiliation(s)
- Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Daozhong Zhu
- Guangzhou Customs Technology Center, Guangzhou 510623, P. R. China
| | - Ting Huang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zizhong Yang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Birong Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Mengxu Sun
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Jin-Xiang Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zong Dai
- Key Laboratory of Sensing Techno logy and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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6
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Lee S, Jang H, Kim HY, Park HG. Three-way junction-induced isothermal amplification for nucleic acid detection. Biosens Bioelectron 2019; 147:111762. [PMID: 31654822 DOI: 10.1016/j.bios.2019.111762] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 02/04/2023]
Abstract
We, herein, describe a three-way junction (3WJ)-induced isothermal amplification (ThIsAmp) reaction for target nucleic acid detection. In this strategy, target nucleic acid induces the formation of 3WJ structure by associating a specially designed ThIsAmp template and ThIsAmp primer. Upon the formation of 3WJ structure, ThIsAmp primer is subjected to continuously repeated extension and nicking reaction by the combined activities of DNA polymerase and nicking endonuclease, consequently producing a large number of trigger strands. The trigger strands then initiate two separate but interconnected pathways by binding to either 3' overhang of ThIsAmp template within the 3WJ structure or free ThIsAmp template. As a consequence, a large number of final double-stranded DNA products are produced under an isothermal condition, which can be monitored in real-time by detecting the fluorescence intensity resulting from SYBR Green I staining. Based on this principle, we successfully detected target DNA down to 78.1 aM with excellent specificity. The sophisticated design principle employed in this work would provide great insight for the development of self-operative isothermal amplifying system enabling target nucleic acid detection.
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Affiliation(s)
- Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyowon Jang
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea.
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7
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Espinosa JR, Galván M, Quiñones AS, Ayala JL, Durón SM. DNA Biosensor Based on Double-Layer Discharge for the Detection of HPV Type 16. SENSORS 2019; 19:s19183956. [PMID: 31540232 PMCID: PMC6767228 DOI: 10.3390/s19183956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
DNA electrochemical biosensors represent a feasible alternative for the diagnosis of different pathologies. In this work, the development of an electrochemical method for Human Papillomavirus-16 (HPV-16) sensing is reported based on potential relaxation measurements related to the discharge of a complex double layer of a DNA-modified gold electrode. The method used allows us to propose an equivalent circuit (EC) for a DNA/Au electrode, which was corroborated by electrochemical impedance spectroscopy (EIS) measurement. This model differs from the Randles circuit that is commonly used in double-layer simulations. The change in the potential relaxation and associated charge transfer resistance were used for sensing the DNA hybridization by using the redox pair Fe(CN)64-/Fe(CN)63+ as an electrochemical indicator. In order to determinate only the potential relaxation of the composed double layer, the faradic and double-layer current contributions were separated using a rectifier diode arrangement. A detection limit of 0.38 nM was obtained for the target HPV-16 DNA sequences. The biosensor showed a qualitative discrimination between a single-base mismatched sequence and the fully complementary HPV-16 DNA target. The results indicate that the discharge of the double-layer detection method can be used to develop an HPV DNA biosensor.
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Affiliation(s)
- José R. Espinosa
- Electrical Engineering Department, Autonomous University of Zacatecas, Col. Centro, Av. Ramón López Velarde 801. Zacatecas, Zacatecas C.P. 98000, Mexico;
| | - Marisol Galván
- Chemistry Department, Autonomous University of Zacatecas, Campus Siglo XXI, Edif. 6, Km 6 carr. Zacatecas-Guadalajara, Zacatecas C.P. 98160, Mexico; (M.G.); (A.S.Q.); (J.L.A.)
| | - Arturo S. Quiñones
- Chemistry Department, Autonomous University of Zacatecas, Campus Siglo XXI, Edif. 6, Km 6 carr. Zacatecas-Guadalajara, Zacatecas C.P. 98160, Mexico; (M.G.); (A.S.Q.); (J.L.A.)
| | - Jorge L. Ayala
- Chemistry Department, Autonomous University of Zacatecas, Campus Siglo XXI, Edif. 6, Km 6 carr. Zacatecas-Guadalajara, Zacatecas C.P. 98160, Mexico; (M.G.); (A.S.Q.); (J.L.A.)
| | - Sergio M. Durón
- Chemistry Department, Autonomous University of Zacatecas, Campus Siglo XXI, Edif. 6, Km 6 carr. Zacatecas-Guadalajara, Zacatecas C.P. 98160, Mexico; (M.G.); (A.S.Q.); (J.L.A.)
- Correspondence: ; Tel.: +52-49-2925-6690 (ext. 4655)
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8
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A thin film polyethylene terephthalate (PET) electrochemical sensor for detection of glucose in sweat. Talanta 2019; 198:86-92. [DOI: 10.1016/j.talanta.2019.01.104] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/24/2019] [Accepted: 01/29/2019] [Indexed: 12/21/2022]
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9
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He P, Lou X, Woody SM, He L. Amplification-by-Polymerization in Biosensing for Human Genomic DNA Detection. ACS Sens 2019; 4:992-1000. [PMID: 30942069 DOI: 10.1021/acssensors.9b00133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A polymerization reaction was employed as a signal amplification method to realize direct visualization of gender-specific DNA extracted from human blood in a polymerase chain reaction (PCR)-free fashion. Clear distinction between X and Y chromosomes was observed by naked eyes for detector-free sensing purposes. The grown polymer films atop X and Y chromosomes were quantitatively measured by ellipsometry for thickness readings. Detection assays have been optimized for genomic DNA recognition to a maximum extent by varying the selection of the proper blocking reagents, the annealing temperature, and the annealing time. Traditional PCR and gel electrophoresis for amplicon identification were conducted in parallel for performance comparison. In the blind test for blood samples examined by the new approach, 25 out of 26 were correct and one was false negative, which was comparable to, if not better than, the PCR results. This is the first time our amplification-by-polymerization technique is being used for chromosome DNA analysis. The potential of adopting the described sensing technique without PCR was demonstrated, which could further promote the development of a portable, PCR-free DNA sensing device for point-of-need applications.
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Affiliation(s)
- Peng He
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, North Carolina 27411, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xinhui Lou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Susan M. Woody
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Lin He
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
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Jang H, Lee CY, Lee S, Park KS, Park HG. Flap endonuclease-initiated enzymatic repairing amplification for ultrasensitive detection of target nucleic acids. NANOSCALE 2019; 11:3633-3638. [PMID: 30741288 DOI: 10.1039/c8nr06699j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A new isothermal nucleic acid amplification method termed FERA (Flap endonuclease-initiated Enzymatic Repairing Amplification) is developed for the ultrasensitive detection of target nucleic acids. In the FERA method, flap endonuclease (FEN) catalyzes the hydrolytic cleavage at the junction of single- and double-stranded DNAs which is formed only in the presence of target nucleic acids, and releases short oligonucleotides to promote the cyclic enzymatic repairing amplification (ERA) combined with FEN-based amplification. As a result, a large amount of single- and double-stranded DNAs are generated under the isothermal conditions, leading to the high fluorescence intensity from the SYBR I green dye. Relying on the powerful amplification method, we successfully determined the target nucleic acids with a limit of detection as low as 15.16 aM, which corresponds to approximately 180 molecules in 20 μL reaction volume, and verified the practical applicability by detecting long target nucleic acids derived from Chlamydia trachomatis.
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Affiliation(s)
- Hyowon Jang
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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11
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Tabata M, Miyahara Y. Liquid biopsy in combination with solid-state electrochemical sensors and nucleic acid amplification. J Mater Chem B 2019; 7:6655-6669. [DOI: 10.1039/c9tb00718k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Solid-state electrochemical sensors are developing as a new platform for liquid biopsy, combining detection and analysis of nucleic acids with isothermal nucleic acid amplification reactions.
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Affiliation(s)
- Miyuki Tabata
- Institute of Biomaterials and Bioengineering
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
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12
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Abrosimova LA, Migur AY, Kubareva EA, Zatsepin TS, Gavshina AV, Yunusova AK, Perevyazova TA, Pingoud A, Oretskaya TS. A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides. PLoS One 2018; 13:e0207302. [PMID: 30475809 PMCID: PMC6261011 DOI: 10.1371/journal.pone.0207302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anzhela Yu. Migur
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Timofei S. Zatsepin
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia
| | - Aleksandra V. Gavshina
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alfiya K. Yunusova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Tatiana S. Oretskaya
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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13
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Liu Q, Li L, Zhao Y, Chen Z. Colorimetric detection of DNA at the nanomolar level based on enzyme-induced gold nanoparticle de-aggregation. Mikrochim Acta 2018; 185:301. [DOI: 10.1007/s00604-018-2833-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
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14
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Zingg JM, Daunert S. Trinucleotide Rolling Circle Amplification: A Novel Method for the Detection of RNA and DNA. Methods Protoc 2018. [PMCID: PMC6526412 DOI: 10.3390/mps1020015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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15
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Huang M, Zhou X, Wang H, Xing D. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection. Anal Chem 2018; 90:2193-2200. [PMID: 29260561 DOI: 10.1021/acs.analchem.7b04542] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.
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Affiliation(s)
- Mengqi Huang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, PR China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, PR China
| | - Huiying Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, PR China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University , Guangzhou 510631, PR China
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16
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Zhang C, Zhang C, Huang J, Wu Z, Mei X, Shi W. Prevalence and genotype distribution of human papillomavirus among females in the suburb of Shanghai, China. J Med Virol 2017; 90:157-164. [PMID: 28700089 DOI: 10.1002/jmv.24899] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/04/2017] [Indexed: 12/11/2022]
Abstract
To describe the prevalence of human papillomavirus (HPV) and its genotype distribution among females in the suburb of Shanghai. A total of 33 562 participants were enrolled in this study from January to December 2016. HPV GenoArray test kit was used to perform HPV genotyping and was also used in DNA amplification and HybriBio's proprietary flow-through hybridization technique. The overall prevalence of HPV was 18.98% and the top ten genotypes of HPV infection were HPV 16 (3.36%), HPV 58 (2.65%), HPV 52 (2.48%), HPV 51 (1.58%), HPV 54 (1.40%), HPV 68 (1.32%), HPV 18 (1.23%), HPV 6 (1.15%), HPV 56 (1.10%), and HPV 33 (1.07%). Single infection (4749, 14.15%) was the most common types among all the infected cases. Significant differences were found among age groups and month groups in terms of simple and multiple infection (P < 0.05), pure HR, LR and mixed HPV infection (P < 0.05). The prevalence of HR and LR HPV infection among females in the suburb of Shanghai is high, prevalence of single and multiple infection, pure HR, LR and mixed infection is correlated with the age and month.
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Affiliation(s)
- Chengzhong Zhang
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chao Zhang
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Dermatology, Shanghai Songjiang Jiuting Hospital, Shanghai, China
| | - Jie Huang
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhouwei Wu
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xingyu Mei
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weimin Shi
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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17
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Chen W, Fang X, Li H, Cao H, Kong J. DNA-mediated inhibition of peroxidase-like activities on platinum nanoparticles for simple and rapid colorimetric detection of nucleic acids. Biosens Bioelectron 2017; 94:169-175. [PMID: 28284076 DOI: 10.1016/j.bios.2017.02.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 01/20/2023]
Abstract
In this research, we found that the peroxidase-like activities of noncovalent DNA-Pt hybrid nanoparticles could be obviously blocked, when Pt nanoparticles (PtNPs) were synthesized in situ using DNA as a template. Moreover, this self-assembled synthetic process was very convenient and rapid (within few mintues), and the inhibition mediated by DNA was also very effective. First, by the paper-based analytical device (PAD) we found the catalytic activities of DNA-Pt hybrid nanoparticles exhibited a linear response to the concentration of DNA in the range from 0.0075 to 0.25µM. Then, with the magnetic bead isolated system and target DNA-induced hybridization chain reaction (HCR), we realized the specific target DNA analysis with a low detection of 0.228nM, and demonstrated its effectivity in distinguishing the target DNA from other interferences. To our knowledge, this is the first report that used the nanoassembly between DNA and PtNPs for colorimetric detection of nucleic acids, which was based on DNA-mediated inhibition of catalytic activities of platinum nanoparticles. The results may be useful for understanding the interactions between DNA and metal nanoparticles, and for development of other convenient and effective analytical strategies.
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Affiliation(s)
- Weiwei Chen
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China.
| | - Hua Li
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
| | - Hongmei Cao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China.
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