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Kaisti M, Kerko A, Aarikka E, Saviranta P, Boeva Z, Soukka T, Lehmusvuori A. Real-time wash-free detection of unlabeled PNA-DNA hybridization using discrete FET sensor. Sci Rep 2017; 7:15734. [PMID: 29147003 PMCID: PMC5691077 DOI: 10.1038/s41598-017-16028-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/06/2017] [Indexed: 11/25/2022] Open
Abstract
We demonstrate an electrochemical sensor for detection of unlabeled single-stranded DNA using peptide nucleic acid (PNA) probes coupled to the field-effect transistor (FET) gate. The label-free detection relies on the intrinsic charge of the DNA backbone. Similar detection schemes have mainly concentrated on sensitivity improvement with an emphasis on new sensor structures. Our approach focuses on using an extended-gate that separates the FET and the sensing electrode yielding a simple and mass fabricable device. We used PNA probes for efficient hybridization in low salt conditions that is required to avoid the counter ion screening. As a result, significant part of the target DNA lies within the screening length of the sensor. With this, we achieved a wash-free detection where typical gate potential shifts are more than 70 mV with 1 µM target DNA. We routinely obtained a real-time, label- and wash-free specific detection of target DNA in nanomolar concentration with low-cost electronics and the responses were achieved within minutes after introducing targets to the solution. Furthermore, the results suggest that the sensor performance is limited by specificity rather than by sensitivity and using low-cost electronics does not limit the sensor performance in the presented sensor configuration.
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Affiliation(s)
- Matti Kaisti
- University of Turku, Department of Future Technologies, 20500, Turku, Finland.
| | - Anssi Kerko
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Eero Aarikka
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Petri Saviranta
- Medical Biotechnology Centre, VTT Technical Research Centre of Finland, Espoo FI-02044, VTT, Finland
| | - Zhanna Boeva
- Åbo Akademi University, Department of Science and Engineering, 20500, Turku, Finland
| | - Tero Soukka
- University of Turku, Department of Biotechnology, 20520, Turku, Finland
| | - Ari Lehmusvuori
- University of Turku, Department of Biotechnology, 20520, Turku, Finland.
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Wang Y, Wang Y, Zhang L, Li M, Luo L, Liu D, Li H, Cao X, Hu S, Jin D, Xu J, Ye C. Endonuclease Restriction-Mediated Real-Time Polymerase Chain Reaction: A Novel Technique for Rapid, Sensitive and Quantitative Detection of Nucleic-Acid Sequence. Front Microbiol 2016; 7:1104. [PMID: 27468284 PMCID: PMC4942466 DOI: 10.3389/fmicb.2016.01104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/01/2016] [Indexed: 11/17/2022] Open
Abstract
The article reported a novel methodology for real-time PCR analysis of nucleic acids, termed endonuclease restriction-mediated real-time polymerase chain reaction (ET-PCR). Just like PCR, ET-PCR only required one pair of primers. A short sequence, which was recognized by restriction enzyme BstUI, was attached to the 5′ end of the forward (F) or reverse (R) PCR primer, and the new F or R primer was named EF or ER. EF/ER was labeled at the 5′ end with a reporter dye and in the middle with a quenching dye. BstUI cleaves the newly synthesized double-stranded terminal sequences (5′ end recognition sequences and their complementary sequences) during the extension phase, which separates the reporter molecule from the quenching dye, leading to a gain of fluorescence signal. This process is repeated in each amplification cycle and unaffected the exponential synthesis of the PCR amplification. ET-PCR allowed real-time analysis of single or multiple targets in a single vessel, and provided the reproducible quantitation of nucleic acids. The analytical sensitivity and specificity of ET-PCR were successfully evaluated, detecting down to 250 fg of genomic DNA per tube of target pathogen DNA examined, and the positive results were generated in a relatively short period. Moreover, the practical application of ET-PCR for simultaneous detection of multiple target pathogens was also demonstrated in artificially contaminated blood samples. In conclusion, due to the technique’s simplicity of design, reproducible data and low contamination risk, ET-PCR assay is an appealing alternative to conventional approaches currently used for real-time nucleic acid analysis.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Yan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Lu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Machao Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Lijuan Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Dongxin Liu
- Pathogenic Biology Institute, University of South China Hengyang, China
| | - Hua Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Xiaolong Cao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing, China; Department of Microbiology, Guiyang Medical UniversityGuiyang, China
| | - Shoukui Hu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention Beijing, China
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Lehmusvuori A, Soikkeli M, Tuunainen E, Seppä T, Spangar A, Rantakokko-Jalava K, von Lode P, Karhunen U, Soukka T, Wittfooth S. Ready to use dry-reagent PCR assays for the four common bacterial pathogens using switchable lanthanide luminescence probe system. J Microbiol Methods 2015; 118:64-9. [DOI: 10.1016/j.mimet.2015.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/23/2022]
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