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Kim H, Lee S, Ju Y, Kim H, Jang H, Park Y, Lee SM, Yong D, Kang T, Park HG. Multifunctional self-priming hairpin probe-based isothermal nucleic acid amplification and its applications for COVID-19 diagnosis. Biosens Bioelectron 2024; 253:116147. [PMID: 38452568 DOI: 10.1016/j.bios.2024.116147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024]
Abstract
We herein present a multifunctional self-priming hairpin probe-based isothermal amplification, termed MSH, enabling one-pot detection of target nucleic acids. The sophisticatedly designed multifunctional self-priming hairpin (MSH) probe recognizes the target and rearranges to prime itself, triggering the amplification reaction powered by the continuously repeated extension, nicking, and target recycling. As a consequence, a large number of double-stranded DNA (dsDNA) amplicons are produced that could be monitored in real-time using a dsDNA-intercalating dye. Based on this unique design approach, the nucleocapsid (N) and the open reading frame 1 ab (ORF1ab) genes of SARS-CoV-2 were successfully detected down to 1.664 fM and 0.770 fM, respectively. The practical applicability of our method was validated by accurately diagnosing 60 clinical samples with 93.33% sensitivity and 96.67% specificity. This isothermal one-pot MSH technique holds great promise as a point-of-care testing protocol for the reliable detection of a wide spectrum of pathogens, particularly in resource-limited settings.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyoyong Kim
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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2
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Kim HJ, Park JG, Moon KS, Jung SB, Kwon YM, Kang NS, Kim JH, Nam SJ, Choi G, Baek YB, Park SI. Identification and characterization of a marine bacterium extract from Mameliella sp. M20D2D8 with antiviral effects against influenza A and B viruses. Arch Virol 2024; 169:41. [PMID: 38326489 PMCID: PMC10850258 DOI: 10.1007/s00705-024-05979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/24/2023] [Indexed: 02/09/2024]
Abstract
Despite significant improvements in vaccines and chemotherapeutic drugs, pathogenic RNA viruses continue to have a profound impact on the global economy and pose a serious threat to animal and human health through emerging and re-emerging outbreaks of diseases. To overcome the challenge of viral adaptation and evolution, increased vigilance is required. Particularly, antiviral drugs derived from new, natural sources provide an attractive strategy for controlling problematic viral diseases. In this antiviral study, we discovered a previously unknown bacterium, Mameliella sp. M20D2D8, by conducting an antiviral screening of marine microorganisms. An extract from M20D2D8 exhibited antiviral activity with low cytotoxicity and was found to be effective in vitro against multiple influenza virus strains: A/PR8 (IC50 = 2.93 µg/mL, SI = 294.85), A/Phil82 (IC50 = 1.42 µg/mL, SI = 608.38), and B/Yamagata (IC50 = 1.59 µg/mL, SI = 543.33). The antiviral action was found to occur in the post-entry stages of viral replication and to suppress viral replication by inducing apoptosis in infected cells. Moreover, it efficiently suppressed viral genome replication, protein synthesis, and infectivity in MDCK and A549 cells. Our findings highlight the antiviral capabilities of a novel marine bacterium, which could potentially be useful in the development of drugs for controlling viral diseases.
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Affiliation(s)
- Hyo-Jin Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jun-Gyu Park
- Laboratory of Veterinary Zoonotic Diseases, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kyeong-Seo Moon
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Bin Jung
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea
| | - Yong Min Kwon
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Nam Seon Kang
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Jeong-Hyeon Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Grace Choi
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea.
| | - Yeong-Bin Baek
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Sang-Ik Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea.
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea.
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Jung J, Sung JS, Bong JH, Kim TH, Kwon S, Bae HE, Kang MJ, Jose J, Lee M, Shin HJ, Pyun JC. One-step immunoassay of SARS-CoV-2 using screened Fv-antibodies and switching peptides. Biosens Bioelectron 2024; 245:115834. [PMID: 37995624 DOI: 10.1016/j.bios.2023.115834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/21/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The Fv-antibodies were correponded to VH region of immunoglobulin G, which were composed of three complementarity determining regions (CDRs) for the specific binding of antigens. In this work, the Fv-antibodies against SARS-CoV-2 spike protein (SP) were screened from an autodisplayed Fv-antibody library which was expressed on E. coli outer membrane, and the receptor binding domain (RBD) of SP was used as a screening probe. The screened target clones were analyzed to have quantitative binding properties to the RBD, and the Fv-antibodies from the screened target clones were expressed as soluble proteins. The binding affinity (KD) of expressed Fv-antibodies to the RBD was estimated to be 70-85 nM using SPR biosensor. The specific binding properties of Fv-antibodies were analyzed for pseudo-virus particles with SARS-CoV-2 SP on the Lenti-virus envelope, such as wild type (Wuhan-1) and variants (Delta, Omicron BA.2, Omicron BA.4/5) using a SPR biosensor. The detection of real SARS-CoV-2 (Wild type, Wuhan-1) based on a SPR biosensor was also presented using the Fv-antibodies with the binding constant (KD) of cycle threshold value (Ct) = 33.8-32.9 (2.19-4.08 copies/μL) and LOD of 0.67-0.83 copies/μL (Ct = 35.5-35.2). Finally, one-step immunoassay based on switching peptide was demonstrated for the detection of the real SARS-CoV-2 (Wuhan-1) without any washing step. The binding constant (KD) was estimated to be Ct = 35.2-33.9 (0.83-2.04 copies/μL), and LOD was estimated to be 0.14-0.47 copies/μL (Ct = 37.8-36.0). Considering the LOD of the conventional RT-PCR (Ct = 35), the LOD of the one-step immunoassay based on the switching peptide was determined to be feasible for the medical diagnosis of COVID-19.
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Affiliation(s)
- Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jeong Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Soonil Kwon
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Hyung Eun Bae
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), Seoul, 02456, South Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medical Chemistry, Westphalian Wilhelms-University Münster, Münster 48149, Germany
| | - Misu Lee
- Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon, 22012, South Korea
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, South Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
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Lee SM, Nai YH, Doeven EH, Balakrishnan HK, Yuan D, Guijt RM. Abridged solid-phase extraction with alkaline Poly(ethylene) glycol lysis (ASAP) for direct DNA amplification. Talanta 2024; 266:125006. [PMID: 37572478 DOI: 10.1016/j.talanta.2023.125006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Complexity of sample preparation decelerate the development of sample-in-answer-out devices for point-of-need nucleic acid amplification testing. Here, we present the consolidation of alkaline poly(ethylene) glycol-based lysis and solid-phase extraction for rapid and simple sample preparation compatible with direct on-bead amplification. Simultaneous cell lysis and binding of DNA were achieved using an optimised reagent comprising 15% PEG8000, 0.5 M NaCl, and 3.5 mM KOH. This was combined with direct, on-bead amplification using 1.5 μg beads per 20 μL PCR reaction mix. The novel single reagent, 5-min method improved the detection limit by 10 and 100-fold compared with commercial DNA extraction kits and the original alkaline PEG lysis method, respectively. The sensitivity can be further enhanced by one amplification cycle with an ethanol wash or by extending the incubation to 10 min before collecting the magnetic particles. Both methods successfully detected a single copy of Escherichia coli DNA. In biological fluids (saliva, sweat, and urine), the 5-min method was delayed by about one cycle compared to the 15-min method. The proposed methods are attractive for incorporation in the workflow for point-of-need testing of biological samples by providing a practical and chemical method for simple alternative DNA sample preparation.
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Affiliation(s)
- Soo Min Lee
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia
| | - Yi H Nai
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia
| | - Egan H Doeven
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; Deakin University, School of Life and Environmental Sciences, Waurn Ponds, VIC 3216, Australia
| | - Hari Kalathil Balakrishnan
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; Department of Chemical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Dan Yuan
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Rosanne M Guijt
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia.
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Kim SA, Lee Y, Park K, Park J, An S, Oh J, Kang M, Lee Y, Jo Y, Cho SW, Seo J. 3D printing of mechanically tough and self-healing hydrogels with carbon nanotube fillers. Int J Bioprint 2023; 9:765. [PMID: 37555082 PMCID: PMC10406165 DOI: 10.18063/ijb.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/06/2023] [Indexed: 08/10/2023] Open
Abstract
Hydrogels have the potential to play a crucial role in bioelectronics, as they share many properties with human tissues. However, to effectively bridge the gap between electronics and biological systems, hydrogels must possess multiple functionalities, including toughness, stretchability, self-healing ability, three-dimensional (3D) printability, and electrical conductivity. Fabricating such tough and self-healing materials has been reported, but it still remains a challenge to fulfill all of those features, and in particular, 3D printing of hydrogel is in the early stage of the research. In this paper, we present a 3D printable, tough, and self-healing multi-functional hydrogel in one platform made from a blend of poly(vinyl alcohol) (PVA), tannic acid (TA), and poly(acrylic acid) (PAA) hydrogel ink (PVA/TA/PAA hydrogel ink). Based on a reversible hydrogen-bond (H-bond)-based double network, the developed 3D printable hydrogel ink showed excellent printability via shear-thinning behavior, allowing high printing resolution (~100 μm) and successful fabrication of 3D-printed structure by layer-by-layer printing. Moreover, the PVA/TA/PAA hydrogel ink exhibited high toughness (tensile loading of up to ~45.6 kPa), stretchability (elongation of approximately 650%), tissue-like Young's modulus (~15 kPa), and self-healing ability within 5 min. Furthermore, carbon nanotube (CNT) fillers were successfully added to enhance the electrical conductivity of the hydrogel. We confirmed the practicality of the hydrogel inks for bioelectronics by demonstrating biocompatibility, tissue adhesiveness, and strain sensing ability through PVA/TA/PAA/CNT hydrogel ink.
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Affiliation(s)
- Soo A Kim
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Yeontaek Lee
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Kijun Park
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Jae Park
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
- LYNK Solutec Inc., Seoul 03722, Republic of Korea
| | - Soohwan An
- Department of Biotechnology, Yonsei University, Seoul
03722, Republic of Korea
| | - Jinseok Oh
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Minkyong Kang
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Yurim Lee
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Yejin Jo
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul
03722, Republic of Korea
| | - Jungmok Seo
- School of Electrical and Electronic Engineering, Yonsei
University, Seoul 03722, Republic of Korea
- LYNK Solutec Inc., Seoul 03722, Republic of Korea
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Antitumor Effect of Cycloastragenol in Colon Cancer Cells via p53 Activation. Int J Mol Sci 2022; 23:ijms232315213. [PMID: 36499536 PMCID: PMC9737126 DOI: 10.3390/ijms232315213] [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: 09/26/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer cell (CRC) is the fourth most common cancer in the world. There are several chemotherapy drugs available for its treatment, though they have side effects. Cycloastragenol (CY) is a compound from Astragalus membranaceus (Fisch.) Bge known to be effective in aging, anti-inflammatory, anticancer, and anti-heart failure treatments. Although many studies have demonstrated the functions of CY in cancer cells, no studies have shown the effects of p53 in colon cancer cells. In this study, we found that CY reduces the viability of colon cancer cells in p53 wild-type cells compared to p53 null cells and HT29. Furthermore, CY induces apoptosis by p53 activation in a dose- and time-dependent manner. And it was confirmed that it affects the L5 gene related to p53. Additionally, CY enhanced p53 expression compared to when either doxorubicin or 5-FU was used alone. Altogether, our findings suggest that CY induces apoptosis via p53 activation and inhibits the proliferation of colon cancer cells. In addition, apoptosis occurs in colon cancer cells due to other factors. Moreover, CY is expected to have a combined effect when used together with existing treatments for colon cancer in the future.
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