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Chen SJ, Rai CI, Wang SC, Chen YC. Point-of-Care Testing for Infectious Diseases Based on Class 2 CRISPR/Cas Technology. Diagnostics (Basel) 2023; 13:2255. [PMID: 37443646 PMCID: PMC10340307 DOI: 10.3390/diagnostics13132255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The early detection of infectious diseases and microorganisms is critical for effective disease treatment, control, and prevention. Currently, nucleic acid testing and antigen-antibody serum reaction are the two methods most commonly used for the detection of infectious diseases. The former is highly accurate, specific, and sensitive, but it is time-consuming, expensive, and has special technician and instrument requirements. The latter is rapid and economical, but it may not be accurate and sensitive enough. Therefore, it is necessary to develop a quick and on-site diagnostic test for point-of-care testing (POCT) to enable the clinical detection of infectious diseases that is accurate, sensitive, convenient, cheap, and portable. Here, CRISPR/Cas-based detection methods are detailed and discussed in depth. The powerful capacity of these methods will facilitate the development of diagnostic tools for POCT, though they still have some limitations. This review explores and highlights POCT based on the class 2 CRISPR/Cas assay, such as Cas12 and Cas13 proteins, for the detection of infectious diseases. We also provide an outlook on perspectives, multi-application scenarios, clinical applications, and limitations for POCT based on class 2 CRISPR/Cas technology.
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Affiliation(s)
- Shiu-Jau Chen
- Department of Neurosurgery, Mackay Memorial Hospital, Taipei 10449, Taiwan;
- Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Chung-I Rai
- Health Care Business Group, Foxconn Technology Co., Ltd., New Taipei City 23680, Taiwan;
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei City 106335, Taiwan
| | - Shao-Cheng Wang
- Department of Psychiatric, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 33004, Taiwan
- Department of Nurse-Midwifery and Women Health, National Taipei University of Nursing and Health Sciences, Taipei 112303, Taiwan
| | - Yuan-Chuan Chen
- Department of Nursing, Jenteh Junior College of Medicine, Nursing and Management, Miaoli County 35664, Taiwan
- Department of Medical Technology, Jenteh Junior College of Medicine, Nursing and Management, Miaoli County 35664, Taiwan
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
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2
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High allele discrimination in the typing of single nucleotide polymorphisms of miRNA. Bioorg Med Chem 2021; 46:116363. [PMID: 34419822 DOI: 10.1016/j.bmc.2021.116363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) belonging to the same family have similar sequences and are difficult to identify. Herein, we report the reverse transcription-hairpin-probe-polymerase chain reaction (RT-Hpro-PCR) technique, which utilises a reverse transcription (RT) primer containing a 5'-end deoxyribonucleic acid (DNA) tag, to detect miRNAs with similar sequences. This strategy follows a two-step RT-PCR method using 6-7-mer RT-primers with a ~ 10-mer tag sequence at the 5'-end and a probe with a hairpin structure (Hpro), including two C-bulges, attached. The findings demonstrate that the specificity of RT could be increased by shortening the complementary part of the RT primer containing a different base, wherein the PCR could successfully progress with the use of 5'-end DNA tag because of an increase in the length of the hybridised tagged primer. This study shows the potential of RT-Hpro-PCR to precisely detect miRNAs with similar sequences, which could help explore the roles of miRNAs in several biological processes.
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3
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Takei F, Akiyama M, Murata A, Sugai A, Nakatani K, Yamashita I. RT-Hpro-PCR: A MicroRNA Detection System Using a Primer with a DNA Tag. Chembiochem 2019; 21:477-480. [PMID: 31397042 DOI: 10.1002/cbic.201900382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) are short RNAs that regulate the expression of complementary messenger RNAs and are involved in numerous human diseases. However, current detection techniques lack the sensitivity to detect miRNAs of low abundance. Moreover, at a length of 20-25 bases, miRNAs are too short for the reverse transcription (RT) polymerase chain reaction (PCR). Here we have developed a new, rapid, and simple miRNA detection system utilizing an RT primer containing a DNA tag at the 5'-end to increase the length of the cDNA. This strategy increases the length of the hybridized tagged primer and the complementary template DNA, as well as the melting temperature of the primer⋅template DNA duplex. PCR efficiency is thus increased, thereby enhancing miRNA detection sensitivity.
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Affiliation(s)
- Fumie Takei
- National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Misaki Akiyama
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Asako Murata
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Ayako Sugai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Ichiro Yamashita
- Graduate School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
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Takei F, Akiyama M, Nobusawa K, Sabani NB, Han H, Nakatani K, Yamashita I. PCR under Low Ionic Concentration Buffer Conditions. ChemistrySelect 2018. [DOI: 10.1002/slct.201702542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Fumie Takei
- Department of MedicineNational Defense Medical College 3-2 Namiki, Tokorozawa Saitama 359–8513 Japan
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Misaki Akiyama
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Kazuyuki Nobusawa
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Norhayati Binti Sabani
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Huanwen Han
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Ichiro Yamashita
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
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5
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Aikawa H, Yano A, Nakatani K. A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH. Org Biomol Chem 2017; 15:1313-1316. [PMID: 27847943 DOI: 10.1039/c6ob02273a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of 2,7-diamino-1,4,8-triazanaphthalene (azaDANP) are described. AzaDANP is protonated only at a weakly acidic pH to bind to the cytosine bulge DNA duplex selectively. Upon binding of azaDANP to the cytosine bulge DNA, a new absorption band at 407 nm appears, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped pH-absorption profile.
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Affiliation(s)
- H Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - A Yano
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - K Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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Abstract
A new fluorescence turn-on type of PCR monitoring system (Hpro-PCR) using a hairpin probe and a primer having a tag sequence at the 5′ end with the fluorescent molecule 2,7-diamino-1,8-naphthyridine derivative (DANP) has been developed.
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Affiliation(s)
- F. Takei
- National Defense Medical College, 3-2 Namiki
- Tokorozawa
- Japan
| | - K. Nakatani
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki
- Japan
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7
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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Takei F, Chen X, Yu G, Shibata T, Dohno C, Nakatani K. Cytosine-bulge-dependent fluorescence quenching for the real-time hairpin primer PCR. Chem Commun (Camb) 2015; 50:15195-8. [PMID: 25338232 DOI: 10.1039/c4cc06780k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The progress of a polymerase chain reaction (PCR) was sensitively monitored based on the increase in fluorescence of N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine, which was covalently anchored on the cytosine bulge directly neighbouring the 5'-T_G-3'/5'-CCA-3' sequence in the hairpin tag at the 5' end of the PCR primer.
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Affiliation(s)
- F Takei
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047 Japan.
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