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Faikhruea K, Supabowornsathit K, Angsujinda K, Aonbangkhen C, Chaikeeratisak V, Palaga T, Assavalapsakul W, Wagenknecht HA, Vilaivan T. Nucleic Acid-Templated Synthesis of Cationic Styryl Dyes in Vitro and in Living Cells. Chemistry 2024; 30:e202400913. [PMID: 38563862 DOI: 10.1002/chem.202400913] [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: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A novel method for synthesizing cationic styryl dyes through a nucleic acid-templated reaction has been developed. This approach overcomes issues associated with traditional synthesis methods, such as harsh conditions, low throughput, and wasteful chemicals. The presence of a nucleic acid template accelerated the styryl dye formation from quaternized heteroaromatic and cationic aldehyde substrates. These styryl dyes show remarkable optical properties change when bound to nucleic acids, hence the success of the synthesis could be readily monitored in situ by UV-Vis and fluorescence spectroscopy and the optical properties data were also observable at the same time. This method provides the desired products from a broad range of coupling partners. By employing different substrates and templates, it is possible to identify new dyes that can bind to a specific type of nucleic acid such as a G-quadruplex. The templated dye synthesis is also successfully demonstrated in live HeLa cells. This approach is a powerful tool for the rapid synthesis and screening of dyes specific for diverse types of nucleic acids or cellular organelles, facilitating new biological discoveries.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Kitipong Angsujinda
- Aquatic Resources Research Institute, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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Tepper O, Appella DH, Zheng H, Dzikowski R, Yavin E. A Biotinylated cpFIT-PNA Platform for the Facile Detection of Drug Resistance to Artemisinin in Plasmodium falciparum. ACS Sens 2024; 9:1458-1464. [PMID: 38446423 PMCID: PMC10964236 DOI: 10.1021/acssensors.3c02553] [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: 11/28/2023] [Revised: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
The evolution of drug resistance to many antimalarial drugs in the lethal strain of malaria (Plasmodium falciparum) has been a great concern over the past 50 years. Among these drugs, artemisinin has become less effective for treating malaria. Indeed, several P. falciparum variants have become resistant to this drug, as elucidated by specific mutations in the pfK13 gene. This study presents the development of a diagnostic kit for the detection of a common point mutation in the pfK13 gene of P. falciparum, namely, the C580Y point mutation. FIT-PNAs (forced-intercalation peptide nucleic acid) are DNA mimics that serve as RNA sensors that fluoresce upon hybridization to their complementary RNA. Herein, FIT-PNAs were designed to sense the C580Y single nucleotide polymorphism (SNP) and were conjugated to biotin in order to bind these molecules to streptavidin-coated plates. Initial studies with synthetic RNA were conducted to optimize the sensing system. In addition, cyclopentane-modified PNA monomers (cpPNAs) were introduced to improve FIT-PNA sensing. Lastly, total RNA was isolated from red blood cells infected with P. falciparum (WT strain - NF54-WT or mutant strain - NF54-C580Y). Streptavidin plates loaded with either FIT-PNA or cpFIT-PNA were incubated with the total RNA. A significant difference in fluorescence for mutant vs WT total RNA was found only for the cpFIT-PNA probe. In summary, this study paves the way for a simple diagnostic kit for monitoring artemisinin drug resistance that may be easily adapted to malaria endemic regions.
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Affiliation(s)
- Odelia Tepper
- The
Institute for Drug Research, The School of Pharmacy, The Faculty of
Medicine, The Hebrew University of Jerusalem,
Hadassah Ein-Kerem, Jerusalem 9112102, Israel
| | - Daniel H. Appella
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC),
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Hongchao Zheng
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC),
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Ron Dzikowski
- Department
of Microbiology and Molecular Genetics, The institute for Medical
Research Israel - Canada, The Kuvin Center for the Study of Infectious
and Tropical Diseases, The Hebrew University-Hadassah
Medical School, Jerusalem 9112102, Israel
| | - Eylon Yavin
- The
Institute for Drug Research, The School of Pharmacy, The Faculty of
Medicine, The Hebrew University of Jerusalem,
Hadassah Ein-Kerem, Jerusalem 9112102, Israel
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3
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Efimova AS, Ustimova MA, Chmelyuk NS, Abakumov MA, Fedorov YV, Fedorova OA. Specific Fluorescent Probes for Imaging DNA in Cell-Free Solution and in Mitochondria in Living Cells. BIOSENSORS 2023; 13:734. [PMID: 37504132 PMCID: PMC10377282 DOI: 10.3390/bios13070734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
New styryl dyes consisting of N-methylpyridine or N-methylquinoline scaffolds were synthesized, and their binding affinities for DNA in cell-free solution were studied. The replacement of heterocyclic residue from the pyridine to quinoline group as well as variation in the phenyl part strongly influenced their binding modes, binding affinities, and spectroscopic responses. Biological experiments showed the low toxicity of the obtained dyes and their applicability as selective dyes for mitochondria in living cells.
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Affiliation(s)
- Anna S Efimova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova Str. 28, 119334 Moscow, Russia
- Department of Technology of Fine Organic Synthesis and Chemistry of Dyes, Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya Sqr. 9, 125047 Moscow, Russia
| | - Mariya A Ustimova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova Str. 28, 119334 Moscow, Russia
| | - Nelly S Chmelyuk
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, 117997 Moscow, Russia
| | - Maxim A Abakumov
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, 117997 Moscow, Russia
| | - Yury V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova Str. 28, 119334 Moscow, Russia
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova Str. 28, 119334 Moscow, Russia
- Department of Technology of Fine Organic Synthesis and Chemistry of Dyes, Dmitry Mendeleev University of Chemical Technology of Russia, Miusskaya Sqr. 9, 125047 Moscow, Russia
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Filho MS, Moraes ES, da Luz LC, da Silveira Santos F, Martin AR, Benhida R, Duarte LGTA, Rodembusch FS. Synthesis, photophysics, and theoretical calculations of styryl-based fluorophores harboring substituted benzothiazole acceptors. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Ustimova MA, Fedorov YV, Chmelyuk NS, Abakumov MA, Fedorova OA. Fluorescence turn-on probes for intracellular DNA/RNA distribution based on asymmetric bis(styryl) dyes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121446. [PMID: 35667137 DOI: 10.1016/j.saa.2022.121446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Two bis(styryl) dyes, varying in type of spacer between two mono(styryl) units, were tested for interactions with ct-DNA or cl-RNA. Both compounds showed strong affinity toward ds-DNA/ss-RNA, the binding mode of the interaction is shifting between DNA groove binding to RNA intercalation. Consequently, interaction with DNA shows a stronger flare-up of fluorescence (151 times for dye 1 and 118 times for dye 2) than when binding with RNA (23 times and 36 times correspondingly). The presence of energy transfer in the bis(styryl) system increases the Stokes shift of the dye, so when irradiating the system in the region of 370-380 nm, fluorescence is detected at 610-620 nm. The biological experiments showed that the efficient intracellular fluorescence quench was observed in the DNase digest test suggested that dyes can be applied by recognition of DNA in the presence of RNA molecules.
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Affiliation(s)
- Maria A Ustimova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia.
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia
| | - Nelly S Chmelyuk
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Maxim A Abakumov
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia.
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6
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Supabowornsathit K, Faikhruea K, Ditmangklo B, Jaroenchuensiri T, Wongsuwan S, Junpra-Ob S, Choopara I, Palaga T, Aonbangkhen C, Somboonna N, Taechalertpaisarn J, Vilaivan T. Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids. Sci Rep 2022; 12:14250. [PMID: 35995925 PMCID: PMC9395382 DOI: 10.1038/s41598-022-18460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.
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Affiliation(s)
- Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Theeranuch Jaroenchuensiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sutthida Wongsuwan
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sirikarn Junpra-Ob
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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7
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Zhang T, Ding F, Yang Y, Zhao G, Zhang C, Wang R, Huang X. Research Progress and Future Trends of Microfluidic Paper-Based Analytical Devices in In-Vitro Diagnosis. BIOSENSORS 2022; 12:bios12070485. [PMID: 35884289 PMCID: PMC9313202 DOI: 10.3390/bios12070485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
In vitro diagnosis (IVD) has become a hot topic in laboratory research and achievement transformation. However, due to the high cost, and time-consuming and complex operation of traditional technologies, some new technologies are being introduced into IVD, to solve the existing problems. As a result, IVD has begun to develop toward point-of-care testing (POCT), a subdivision field of IVD. The pandemic has made governments and health institutions realize the urgency of accelerating the development of POCT. Microfluidic paper-based analytical devices (μPADs), a low-cost, high-efficiency, and easy-to-operate detection platform, have played a significant role in advancing the development of IVD. μPADs are composed of paper as the core material, certain unique substances as reagents for processing the paper, and sensing devices, as auxiliary equipment. The published reviews on the same topic lack a comprehensive and systematic introduction to μPAD classification and research progress in IVD segmentation. In this paper, we first briefly introduce the origin of μPADs and their role in promoting IVD, in the introduction section. Then, processing and detection methods for μPADs are summarized, and the innovative achievements of μPADs in IVD are reviewed. Finally, we discuss and prospect the upgrade and improvement directions of μPADs, in terms of portability, sensitivity, and automation, to help researchers clarify the progress and overcome the difficulties in subsequent μPAD research.
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8
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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9
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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10
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Ditmangklo B, Muangkaew P, Supabowornsathit K, Vilaivan T. Synthesis of Pyrrolidinyl PNA and Its Site-Specific Labeling at Internal Positions by Click Chemistry. Methods Mol Biol 2021; 2105:35-60. [PMID: 32088863 DOI: 10.1007/978-1-0716-0243-0_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pyrrolidinyl PNA with an α-/β-dipeptide backbone consisting of alternating nucleobase-modified D-proline and (1S,2S)-2-aminocyclopentanecarboxylic acid (also known as acpcPNA) is a class of conformationally constrained PNA that shows exceptional DNA hybridization properties including very high specificity and the inability to form self-pairing hybrids. In this chapter, details of the syntheses of acpcPNA as well as its monomers and a protocol for site-specific labeling with a fluorescent dye via click chemistry are reported.
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Affiliation(s)
- Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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11
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Das A, Pradhan B. Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology. Chem Biol Drug Des 2020; 97:865-892. [PMID: 33314595 DOI: 10.1111/cbdd.13815] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/17/2020] [Accepted: 12/05/2020] [Indexed: 01/23/2023]
Abstract
Peptide nucleic acids (PNAs) are getting prodigious interest currently in the biomedical and diagnostic field as an extremely powerful tool because of their potentiality to hybridize with natural nucleic acids. Although PNA has strong affinity and sequence specificity to DNA/RNA, there is a considerable ongoing effort to further enhance their special chemical and biological properties for potential application in numerous fields, notably in the field of therapeutics. The toolbox for backbone modified PNAs synthesis has been extended substantially in recent decades, providing a more efficient synthesis of peptides with numerous scaffolds and modifications. This paper reviews the various strategies that have been developed so far for the modification of the PNA backbone, challenging the search for new PNA systems with improved chemical and physical properties lacking in the original aegPNA backbone. The various practical issues and limitations of different PNA systems are also summarized. The focus of this review is on the evolution of PNA by its backbone modification to improve the cellular uptake, sequence specificity, and compatibility of PNA to bind to DNA/RNA. Finally, an insight was also gained into major applications of backbone modified PNAs for the development of biosensors.
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Affiliation(s)
- Anuradha Das
- National Institute of Science Education and Research Bhubaneswar (HBNI), Bhubaneswar, India
| | - Biswaranjan Pradhan
- S. K. Dash Center of Excellence of Biosciences and Engineering & Technology, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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12
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Zhao J, Huang L, Yan M, Qu Y, Feng H, Sun Y. A lysosome specific ratiometric fluorescent probe for detection of bisulfite ion based on hybrid coumarin-benzimidazolium compounds. PHOSPHORUS SULFUR 2020. [DOI: 10.1080/10426507.2020.1835904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jiangdong Zhao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Liliang Huang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Meiling Yan
- Chinese Academy of Sciences, Shanghai Institute of Applied Physics, Shanghai, China
- Laboratory of Physical Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Qu
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Huangdi Feng
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Yanhong Sun
- Chinese Academy of Sciences, Shanghai Institute of Applied Physics, Shanghai, China
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13
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Muangkaew P, Vilaivan T. Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency. Chembiochem 2020; 22:241-252. [PMID: 32889765 DOI: 10.1002/cbic.202000589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/03/2020] [Indexed: 12/27/2022]
Abstract
In this study, we describe a furan-modified acpcPNA as a probe that can form an interstrand crosslink (ICL) with its DNA target upon activation with N-bromosuccinimide (NBS). To overcome the problem of furan instability under acidic conditions, a simple and versatile post-synthetic methodology for the attachment of the furan group to the PNA probe was developed. Unlike in other designs, the furan was placed at the end of the PNA molecule or tethered to the PNA backbone with all the base pairs in the PNA ⋅ DNA duplexes fully preserved. Hence, the true reactivity of each nucleobase towards the crosslinking could be compared. We show that all DNA bases except T could participate in the crosslinking reaction when the furan was placed at the end of the PNA strand. The crosslinking process was sensitive to mispairing, and lower crosslinking efficiency was observed in the presence of a base-mismatch in the PNA ⋅ DNA duplex. In contrast, when the furan was placed at internal positions of the acpcPNA ⋅ DNA duplex, no ICL was observed; this was explained by the inability of a hydrogen-bonded nucleobase to participate in the crosslinking reaction. The crosslinking efficiency was considerably improved, despite lower duplex stability, when an unpaired base (in the form of C-insertion) was present in the complementary DNA strand close to the furan modification site.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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Srimongkol G, Ditmangklo B, Choopara I, Thaniyavarn J, Dean D, Kokpol S, Vilaivan T, Somboonna N. Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products. Sci Rep 2020; 10:7768. [PMID: 32385390 PMCID: PMC7211006 DOI: 10.1038/s41598-020-64710-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus strains carrying enterotoxin A gene (sea) causes food poisoning and cannot be distinguished from non-pathogenic strains by the culture method. Here, we developed a rapid, specific and sensitive visual detection of sea using loop-mediated isothermal amplification (LAMP) combined with nanogold probe (AuNP) or styryl dye (STR). LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2 sea copies, respectively, which were lower than PCR (97 fg or 32 sea copies). The excellent performance of these new assays was demonstrated in food samples using crude DNA lysates. While the culture method detected 104 CFU/g in ground pork and 10 CFU/mL in milk in 5-7 days, LAMP-AuNP could detect down to 10 CFU/g for both samples in 27 minutes. Analyzing 80 pork and milk samples revealed that the LAMP-AuNP showed 100% sensitivity, 97-100% specificity and 97.5-100% accuracy, which were superior to the culture method, and comparable to PCR but without requirement of a thermal cycler. Furthermore, our LAMP-AuNP detect sea at a range below the food safety control (<100 CFU/g). The LAMP-STR quantitated sea in 10-1,000 CFU (7.2-720 copies). Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facilitate appropriate control strategies.
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Affiliation(s)
- Grittaya Srimongkol
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiraporn Thaniyavarn
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens. Molecules 2020; 25:molecules25040769. [PMID: 32053960 PMCID: PMC7070780 DOI: 10.3390/molecules25040769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
During the treatment of viral or bacterial infections, it is important to evaluate any resistance to the therapeutic agents used. An amino acid substitution arising from a single base mutation in a particular gene often causes drug resistance in pathogens. Therefore, molecular tools that discriminate a single base mismatch in the target sequence are required for achieving therapeutic success. Here, we synthesized peptide nucleic acids (PNAs) derivatized with tolane via an amide linkage at the N-terminus and succeeded in improving the sequence specificity, even with a mismatched base pair located near the terminal region of the duplex. We assessed the sequence specificities of the tolane-PNAs for single-strand DNA and RNA by UV-melting temperature analysis, thermodynamic analysis, an in silico conformational search, and a gel mobility shift assay. As a result, all of the PNA-tolane derivatives stabilized duplex formation to the matched target sequence without inducing mismatch target binding. Among the different PNA-tolane derivatives, PNA that was modified with a naphthyl-type tolane could efficiently discriminate a mismatched base pair and be utilized for the detection of resistance to neuraminidase inhibitors of the influenza A/H1N1 virus. Therefore, our molecular tool can be used to discriminate single nucleotide polymorphisms that are related to drug resistance in pathogens.
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Charoenpakdee C, Vilaivan T. Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing. Org Biomol Chem 2020; 18:5951-5962. [DOI: 10.1039/d0ob01299h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oligodeoxyguanosine effectively quenches the fluorescence of PNA probes via electrostatic interaction, and the signal is restored by the addition of complementary DNA targets.
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Affiliation(s)
- Chayan Charoenpakdee
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
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