1
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Kim BK, Lee SA, Park M, Jeon EJ, Kim MJ, Kim JM, Kim H, Jung S, Kim SK. Ultrafast Real-Time PCR in Photothermal Microparticles. ACS NANO 2022; 16:20533-20544. [PMID: 36475304 PMCID: PMC9799066 DOI: 10.1021/acsnano.2c07017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/07/2022] [Indexed: 05/20/2023]
Abstract
As the turnaround time of diagnosis becomes important, there is an increasing demand for rapid, point-of-care testing (POCT) based on polymerase chain reaction (PCR), the most reliable diagnostic tool. Although optical components in real-time PCR (qPCR) have quickly become compact and economical, conventional PCR instruments still require bulky thermal systems, making it difficult to meet emerging needs. Photonic PCR, which utilizes photothermal nanomaterials as heating elements, is a promising platform for POCT as it reduces power consumption and process time. Here, we develop a photonic qPCR platform using hydrogel microparticles. Microparticles consisting of hydrogel matrixes containing photothermal nanomaterials and primers are dubbed photothermal primer-immobilized networks (pPINs). Reduced graphene oxide is selected as the most suitable photothermal nanomaterial to generate heat in pPIN due to its superior light-to-heat conversion efficiency. The photothermal reaction volume of 100 nL (predefined by the pPIN dimensions) provides fast heating and cooling rates of 22.0 ± 3.0 and 23.5 ± 2.6 °C s-1, respectively, enabling ultrafast qPCR within 5 min only with optical components. The microparticle-based photonic qPCR facilitates multiplex assays by loading multiple encoded pPIN microparticles in a single reaction. As a proof of concept, four-plex pPIN qPCR for bacterial discrimination are successfully demonstrated.
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Affiliation(s)
- Bong Kyun Kim
- Division
of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- BioActs
Co., Ltd., Incheon 21666, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Sang-A Lee
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Minju Park
- Soft
Hybrid Materials Research Center, KIST, Seoul 02792, Korea
| | - Eui Ju Jeon
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Mi Jung Kim
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Jung Min Kim
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Heesuk Kim
- Soft
Hybrid Materials Research Center, KIST, Seoul 02792, Korea
- Division
of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Korea
| | - Seungwon Jung
- Center
for Advanced Biomolecular Recognition, KIST, Seoul 02792, Korea
- Department
of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Sang Kyung Kim
- Center
for Advanced Biomolecular Recognition, KIST, Seoul 02792, Korea
- KHU-KIST
Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
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2
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Kifaro EG, Kim MJ, Jung S, Noh JY, Song CS, Misinzo G, Kim SK. Direct Reverse Transcription Real-Time PCR of Viral RNA from Saliva Samples Using Hydrogel Microparticles. BIOCHIP JOURNAL 2022; 16:409-421. [PMID: 35968254 PMCID: PMC9358062 DOI: 10.1007/s13206-022-00065-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022]
Abstract
In recent decades "saliva" has emerged as an important non-invasive biofluid for diagnostic purposes in both human and animal health sectors. However, with the rapid evolution of molecular detection technologies, the limitation has been the lack of an efficient method for the facile amplification of target RNA from such a complex matrix. Herein, we demonstrate the novel application of hydrogel microparticles of primer-immobilized networks (PIN) for direct quantitative reverse transcription PCR (dirRT-qPCR) of viral RNA from saliva samples without prior RNA purification. Each of these highly porous PIN particles operates as an independent reactor. They filter in micro-volumes of the analyte solution. Viral RNA is captured and converted to complementary DNA (cDNA) through the RT step using covalently incorporated RT primers. The PIN with cDNA of the viral target will be ready for subsequent highly specific qPCR. Preceded by heat-treatment for viral lysis, we were able to conduct PIN dirRT-qPCR with 95% efficiency of the matrix (M) gene for influenza A virus (IAV) and 5' untranslated region (5' UTR) for chicken coronavirus spiked into saliva samples. The addition of reverse transcriptase enzyme (RTase) and 10% dilution of the matrix improved the assay sensitivity considerably. PIN particles' compatibility with microfluidic PCR chip technology has significantly reduced total sample processing time to 50 min, instead of an average of 120 min that are normally used by other assays. We anticipate this technology will be useful for other viral RNA targets by changing the incorporated RT primer sequences and can be adapted for onsite diagnostics. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00065-0.
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Affiliation(s)
- Emmanuel George Kifaro
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea ,grid.11887.370000 0000 9428 8105Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), PO Box 3019, Morogoro, Tanzania ,grid.502906.80000 0004 7707 5959Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), PO Box 3297, Morogoro, Tanzania
| | - Mi Jung Kim
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | - Seungwon Jung
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | | | - Chang-Seon Song
- KCAV Co., Ltd., Seoul, Republic of Korea ,grid.258676.80000 0004 0532 8339Avian Diseases Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, 05029 Republic of Korea
| | - Gerald Misinzo
- grid.11887.370000 0000 9428 8105Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), PO Box 3019, Morogoro, Tanzania ,grid.502906.80000 0004 7707 5959Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), PO Box 3297, Morogoro, Tanzania
| | - Sang Kyung Kim
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea ,grid.289247.20000 0001 2171 7818KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, 02447 Republic of Korea
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3
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Kim JM, Jung S, Jeon EJ, Kim BK, No JY, Kim MJ, Kim H, Song CS, Kim SK. Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:30295-30305. [PMID: 34165969 DOI: 10.1021/acsami.1c03434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.
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Affiliation(s)
- Jung Min Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eui Ju Jeon
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bong Kyun Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin Yong No
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Myung Jong Kim
- Functional Composite Materials Research Center, KIST, Jeonbuk 55324, Republic of Korea
| | - Heesuk Kim
- Photo-Electronic Hybrids Research Center, KIST, Seoul 02792, Republic of Korea
- Division of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Republic of Korea
| | - Chang Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
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4
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Kim MY, Jung S, Kim J, Lee HJ, Jeong S, Sim SJ, Kim SK. Highly sensitive and multiplexed one-step RT-qPCR for profiling genes involved in the circadian rhythm using microparticles. Sci Rep 2021; 11:6463. [PMID: 33742035 PMCID: PMC7979730 DOI: 10.1038/s41598-021-85728-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022] Open
Abstract
Given the growing interest in molecular diagnosis, highly extensive and selective detection of genetic targets from a very limited amount of samples is in high demand. We demonstrated the highly sensitive and multiplexed one-step RT-qPCR platform for RNA analysis using microparticles as individual reactors. Those particles are equipped with a controlled release system of thermo-responsive materials, and are able to capture RNA targets inside. The particle-based assay can successfully quantify multiple target RNAs from only 200 pg of total RNA. The assay can also quantify target RNAs from a single cell with the aid of a pre-concentration process. We carried out 8-plex one-step RT-qPCR using tens of microparticles, which allowed extensive mRNA profiling. The circadian cycles were shown by the multiplex one-step RT-qPCR in human cell and human hair follicles. Reliable 24-plex one-step RT-qPCR was developed using a single operation in a PCR chip without any loss of performance (i.e., selectivity and sensitivity), even from a single hair. Many other disease-related transcripts can be monitored using this versatile platform. It can also be used non–invasively for samples obtained in clinics.
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Affiliation(s)
- Mi Yeon Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.,Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Seungwon Jung
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea
| | - Junsun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.,Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Heon Jeong Lee
- Department of Psychiatry and Chronobiology Institute, Korea University College of Medicine, Seoul, KS013, Korea
| | - Seunghwa Jeong
- Department of Psychiatry and Chronobiology Institute, Korea University College of Medicine, Seoul, KS013, Korea
| | - Sang Jun Sim
- Department of Chemical Biological Engineering, Korea University, Seoul, KS013, Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology(KIST), Seoul, KS013, Korea.
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5
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Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021; 50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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6
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Song Y, Xu Z, Wang F. Genetically Encoded Reporter Genes for MicroRNA Imaging in Living Cells and Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:555-567. [PMID: 32721876 PMCID: PMC7390858 DOI: 10.1016/j.omtn.2020.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/12/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base paring with the complementary sequences of the target mRNAs, and then exert their function through degrading mRNA or inhibiting protein translation. They play a significant role as a regulatory factor in biological processes of organism development, cell proliferation, differentiation, and cell death. Some of the traditional methods for studying miRNAs, such as northern blot, real-time PCR, or microarray, have been extensively used to investigate the biological properties and expression patterns of miRNAs. However, these methods often require considerable time, cell samples, and the design of effective primers or specific probes. Therefore, in order to gain a deeper understanding of the role of miRNAs in biological processes and accelerate the clinical application of miRNAs in the field of disease treatment, non-invasive, sensitive, and efficient imaging methods are needed to visualize the dynamic expression of miRNAs in living cells and animals. In this study, we reviewed the recent progress in the genetically encoded reporter genes for miRNA imaging.
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Affiliation(s)
- Yingzhuang Song
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zhijing Xu
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Fu Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710071, China.
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7
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Hydrogels for Efficient Multiplex PCR. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0134-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Jung S, Kim WJ, Kim BK, Kim J, Kim MJ, Kim KP, Kim SK. In-particle stem-loop RT-qPCR for specific and multiplex microRNA profiling. Biosens Bioelectron 2020; 163:112301. [PMID: 32568699 DOI: 10.1016/j.bios.2020.112301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/23/2020] [Accepted: 05/13/2020] [Indexed: 01/15/2023]
Abstract
Here we report a novel method of microRNA (miRNA) profiling with particle-based multiplex quantitative reverse transcription polymerase chain reaction (RT-qPCR). To achieve target-specific reaction in a particle, the stem-loop RT primer and forward primer for each target miRNA were chemically immobilized to the particle. Target-specific cDNA synthesis proceeds with the stem-loop RT primer and then qPCR subsequently proceeds with the forward primer to rapidly achieve a quantitative result. High-fidelity multiplex assay was also accomplished in a single PCR process by loading multiple particles for each specific miRNA. The method for primer supply in the particles, involving confinement of the target-specific RT and PCR primers in the matrix of particles, led to the reduction of nonspecific reactions and improved the selectivity of the miRNA assay while minimizing labor in a multiple target assay. Specifically, this particle-based assay enabled the differentiation of mature miRNA from precursor with selectivity of 270:1 in terms of amplification speed. This advanced method also showed good discrimination among highly homologous let-7 family members, with cross-reaction rates of less than 5%. We demonstrated a very simple process of five-plex miRNA profiling in total RNA, and the measured changes in expression level were consistent with those from a conventional singleplex method.
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Affiliation(s)
- Seungwon Jung
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Won Jin Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bong Kyun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Biomedical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Junsun Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Mi Jung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kwang Pyo Kim
- Applied Chemistry, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition Research, Materials and Life Science Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Biomedical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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9
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Kim J, Jung S, Kim MY, Kim BK, Kwon SH, Kim SK. Thermo-Responsive Polymer Capsules in Real-Time One-Step RT-PCR for Highly Multiplex RNA Analysis. Adv Healthc Mater 2020; 9:e1900790. [PMID: 32134572 DOI: 10.1002/adhm.201900790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/13/2019] [Indexed: 11/09/2022]
Abstract
Rapid and simple detection of RNA targets is in high demand due to the growing threat of pandemic viruses. One-step real-time, reverse transcription-polymerase chain reaction (One-step RT-qPCR) using a controlled release system of thermo-responsive materials is developed in this paper to enable high-fidelity RNA analysis as suppressing by-products. The nanocapsules, consisting of upper critical solution temperature (UCST) material and PCR primers, carry or release the primers depending upon the temperature. The UCST nanocapsules are introduced into hydrogel microparticles incorporated with RT primers and then the target RNA is selectively amplified in the microparticle through one-step RT-qPCR. Severe side products are sharply subdued by separating the PCR primers from the RT process by means of the microparticles with nanocapsules. Because the one-step assay is now implemented in a single microparticle, multiple target RNAs can be analyzed in a simple RT-qPCR of multiple particles. Reliable 18-plex one-step RT-qPCR is successfully conducted within 30 min using single-color fluorescent optics. This work also explains the facile fabrication processes used for the thermo-responsive nanocapsules and hydrogel microparticles by the blending polymerization method. Extensible multiplex analysis of influenza virus demonstrates the versatile uses of this one-step RT-qPCR platform.
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Affiliation(s)
- Junsun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Seungwon Jung
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Applied ChemistryKyung Hee University Yongin 17104 Republic of Korea
| | - Mi Yeon Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Bong Kyun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
| | - Soon Hwan Kwon
- Armed Forces Medical Research Institute Daejeon 34059 Republic of Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
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10
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Kim JM, Kim WJ, Kim MY, Kim KP, Sim SJ, Kim SK. Development of Hydrogel Microparticle based RT-qPCR for Advanced Detection of BCR-ABL1 Transcripts. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-018-3209-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Novel electrochemical nanoswitch biosensor based on self-assembled pH-sensitive continuous circular DNA. Biosens Bioelectron 2019; 131:274-279. [DOI: 10.1016/j.bios.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023]
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12
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Multiplex real-time PCR using temperature sensitive primer-supplying hydrogel particles and its application for malaria species identification. PLoS One 2018; 13:e0190451. [PMID: 29293604 PMCID: PMC5749795 DOI: 10.1371/journal.pone.0190451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
Real-time PCR, also called quantitative PCR (qPCR), has been powerful analytical tool for detection of nucleic acids since it developed. Not only for biological research but also for diagnostic needs, qPCR technique requires capacity to detect multiple genes in recent years. Solid phase PCR (SP-PCR) where one or two directional primers are immobilized on solid substrates could analyze multiplex genetic targets. However, conventional SP-PCR was subjected to restriction of application for lack of PCR efficiency and quantitative resolution. Here we introduce an advanced qPCR with primer-incorporated network (PIN). One directional primers are immobilized in the porous hydrogel particle by covalent bond and the other direction of primers are temporarily immobilized at so-called 'Supplimers'. Supplimers released the primers to aqueous phase in the hydrogel at the thermal cycling of PCR. It induced the high PCR efficiency over 92% with high reliability. It reduced the formation of primer dimers and improved the selectivity of qPCR thanks to the strategy of 'right primers supplied to right place only'. By conducting a six-plex qPCR of 30 minutes, we analyzed DNA samples originated from malaria patients and successfully identified malaria species in a single reaction.
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Xu Z, Liao L, Chai Y, Wang H, Yuan R. Ultrasensitive Electrochemiluminescence Biosensor for MicroRNA Detection by 3D DNA Walking Machine Based Target Conversion and Distance-Controllable Signal Quenching and Enhancing. Anal Chem 2017; 89:8282-8287. [DOI: 10.1021/acs.analchem.7b01409] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ziqi Xu
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Linli Liao
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Haijun Wang
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescence
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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14
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Chen T, Romesberg FE. Polymerase Chain Transcription: Exponential Synthesis of RNA and Modified RNA. J Am Chem Soc 2017; 139:9949-9954. [DOI: 10.1021/jacs.7b03981] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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15
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Ha JH, Kim TH, Lee JM, Ahrberg CD, Chung BG. Analysis of 3D multi-layer microfluidic gradient generator. Electrophoresis 2016; 38:270-277. [DOI: 10.1002/elps.201600443] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Jang Ho Ha
- Department of Mechanical Engineering; Sogang University; Seoul Korea
| | - Tae Hyeon Kim
- Department of Mechanical Engineering; Sogang University; Seoul Korea
| | - Jong Min Lee
- Department of Mechanical Engineering; Sogang University; Seoul Korea
| | | | - Bong Geun Chung
- Department of Mechanical Engineering; Sogang University; Seoul Korea
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16
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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17
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Oh EH, Jung S, Kim WJ, Kim KP, Kim SK. Microparticle-based RT-qPCR for highly selective rare mutation detection. Biosens Bioelectron 2016; 87:229-235. [PMID: 27566396 DOI: 10.1016/j.bios.2016.08.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Accepted: 08/17/2016] [Indexed: 01/08/2023]
Abstract
The quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become one of the most widely used methods in the detection of disease-specific RNAs. The RT-qPCR involves two separate steps, RT and qPCR. In this study, we suggest a new RT-qPCR protocol with the particles of primer-immobilized networks (PINs), performing capture, RT and amplification of a target RNA in one particle. The production of undesired cDNAs was dramatically suppressed by the specific capture of the target RNA within the particle. Afterward, RT and amplification processes are performed without loss of cDNAs as exchanging the reaction solution. The biomarker gene of chronic myeloid leukemia, Bcr-Abl fusion transcript, is detected in the sensitivity of single mutant leukemic cell mixed in 104 normal cell using this protocol with the excellent restraint of non-specific signal. This protocol that whole processes are performed in the particle in a row is preferred for the highly specific detection of target RNAs in complex sample.
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Affiliation(s)
- Eun Hae Oh
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Won Jin Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Sang Kyung Kim
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biomedical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
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