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Tachibana A, Fujimura N, Takeuchi M, Watanabe K, Teruuchi Y, Uchiki T. Cationic copolymers that enhance wild-type-specific suppression in BNA-clamp PCR and preferentially increase the Tm of fully matched complementary DNA and BNA strands. BIOLOGY METHODS AND PROTOCOLS 2022; 7:bpac009. [PMID: 35664806 PMCID: PMC9154250 DOI: 10.1093/biomethods/bpac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mutation detection is of major interest in molecular diagnostics, especially in the field of oncology. However, detection can be challenging as mutant alleles often coexists with excess copies of wild-type alleles. Bridged nucleic acid (BNA)-clamp PCR circumvents this challenge by preferentially suppressing the amplification of wild-type alleles and enriching rare mutant alleles. In this study, we screened cationic copolymers containing nonionic and anionic repeat units for their ability to 1) increase the Tm of double-stranded DNA, 2) avoid PCR inhibition, and 3) enhance the suppression of wild-type amplification in BNA-clamp PCR to detect the KRAS G13D mutation. The selected copolymers that met these criteria consisted of four types of amines and anionic and/or nonionic units. In BNA-clamp PCR, these copolymers increased the threshold cycle (Ct) of the wild-type allele only and enabled mutation detection from templates with a 0.01% mutant-to-wild-type ratio. Melting curve analysis with 11-mer DNA-DNA or BNA-DNA complementary strands showed that these copolymers preferentially increased the Tm of perfectly matched strands over strands containing 1-bp mismatches. These results suggested that these copolymers preferentially stabilize perfectly matched DNA and BNA strands and thereby enhance rare mutant detection in BNA-clamp PCR.
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Affiliation(s)
- Ami Tachibana
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
| | | | | | - Koji Watanabe
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Yoko Teruuchi
- Nittobo Medical Co. Ltd., Koriyama, Fukushima, 963-8061, Japan
| | - Tomoaki Uchiki
- Nitto Boseki Co. Ltd., Kawasaki, Kanagawa, 210-0821, Japan
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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Saito K, Shimada N, Maruyama A. Cooperative enhancement of deoxyribozyme activity by chemical modification and added cationic copolymer. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2016; 17:437-442. [PMID: 27877894 PMCID: PMC5102035 DOI: 10.1080/14686996.2016.1208627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 05/27/2023]
Abstract
Deoxyribozymes (DNAzymes) having RNA-cleaving activity have widely been explored as tools for therapeutic and diagnostic purposes. Both the chemical cleaving step and the turnover step should be improved for enhancing overall activity of DNAzymes. We have shown that cationic copolymer enhanced DNAzyme activity by increasing turnover efficacy. In this paper, effects of the copolymer on DNAzymes modified with locked nucleic acids (LNA) or 2'-O-methylated (2'-OMe) nucleic acids were studied. The copolymer increased activity of these chemically modified DNAzymes. More than 30-fold enhancement in multiple-turnover catalytic activity was observed with 2'-OMe-modified DNAzyme in the presence of the copolymer. DNAzyme catalytic activity was successfully enhanced by cooperation of the added copolymer and chemical modification of DNAzyme.
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Affiliation(s)
- Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Gao J, Luo X, Li Y, Gao R, Chen H, Ji D. Synthesis and biological evaluation of 2-oxo-pyrazine-3-carboxamide-yl nucleoside analogues and their epimers as inhibitors of influenza A viruses. Chem Biol Drug Des 2014; 85:245-52. [PMID: 24954298 DOI: 10.1111/cbdd.12382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/22/2014] [Accepted: 06/12/2014] [Indexed: 12/24/2022]
Abstract
Novel 2-oxo-pyrazine-3-carboxamide-yl nucleoside analogues and their epimers were designed, synthesized and evaluated for their activities against influenza A viruses H1N1 and H3N2 in Madin-Darby canine kidney cells. All the compounds showed low cytotoxicities in these anti-influenza tests. One of the epimers, 4-[(1S, 3R, 4R, 7R)-7-hydroxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-3-yl]-3-oxo-3,4-dihydropyrazine-2-carboxamide 8a, with high antiviral activities (IC50 = 7.41, 5.63 μm for H3N2 and H1N1, respectively) and remarkable low cytotoxicity (TC50 > 200 μm), has great potential for further development as a novel anti-influenza A agent. Molecular docking of compound 8a with RNA-dependent RNA polymerase was performed to understand the binding mode between these inhibitors and the active site of RdRp and to rationalize some SARs.
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Affiliation(s)
- Jingjing Gao
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai, 200240, China
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Torigoe H, Sato N, Nagasawa N. 2'-O,4'-C-ethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability under physiological condition. J Biochem 2012; 152:17-26. [PMID: 22563101 DOI: 10.1093/jb/mvs049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Since pyrimidine motif triplex DNA is unstable at physiological neutral pH, triplex stabilization at physiological neutral pH is important for improvement of its potential to be applied to various methods in vivo, such as repression of gene expression, mapping of genomic DNA and gene-targeted mutagenesis. For this purpose, we studied the thermodynamic and kinetic effects of a chemical modification, 2'-O,4'-C-ethylene bridged nucleic acid (ENA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological neutral pH. Thermodynamic investigations indicated that the modification achieved more than 10-fold increase in the binding constant of the triplex formation. The increased number of the modification in TFO enhanced the increased magnitude of the binding constant. On the basis of the obtained thermodynamic parameters, we suggested that the remarkably increased binding constant by the modification may result from the increased stiffness of TFO in the unbound state. Kinetic studies showed that the considerably decreased dissociation rate constant resulted in the observed increased binding constant by the modification. We conclude that ENA modification of TFO could be a useful chemical modification to promote the triplex formation under physiological neutral condition, and may advance various triplex formation-based methods in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Tokyo 162-8601, Japan.
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Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH. Biochimie 2012; 94:1032-40. [PMID: 22245184 DOI: 10.1016/j.biochi.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 01/04/2012] [Indexed: 11/21/2022]
Abstract
Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in wide variety of potential applications, such as artificial regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis in vivo. Stabilization of pyrimidine motif triplex at physiological pH is, therefore, crucial for improving its potential in various triplex-formation-based strategies in vivo. To this end, we investigated the effect of 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification of triplex-forming oligonucleotide (TFO), in which 2'-O and 4'-C of the sugar moiety were bridged with the methylene chain and 3'-O was replaced by 3'-NH, on pyrimidine motif triplex formation at physiological pH. The modification not only significantly increased the thermal stability of the triplex but also increased the binding constant of triplex formation about 15-fold. The increased magnitude of the binding constant was not significantly changed when the number and position of the modification in TFO changed. The consideration of the observed thermodynamic parameters suggested that the increased rigidity of the modified TFO in the free state resulting from the bridging of different positions of the sugar moiety with an alkyl chain and the increased hydration of the modified TFO in the free state caused by the introduction of polar nitrogen atoms may significantly increase the binding constant at physiological pH. The study on the TFO viability in human serum showed that the modification significantly increased the resistance of TFO against nuclease degradation. This study presents an effective approach for designing novel chemically modified TFOs with higher binding affinity of triplex formation at physiological pH and higher nuclease resistance under physiological condition, which may eventually lead to progress in various triplex-formation-based strategies in vivo.
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Moriyama R, Shimada N, Kano A, Maruyama A. The role of cationic comb-type copolymers in chaperoning DNA annealing. Biomaterials 2011; 32:7671-6. [DOI: 10.1016/j.biomaterials.2011.06.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/23/2011] [Indexed: 02/05/2023]
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Singh SK, Sharma VK, Bohra K, Olsen CE, Prasad AK. Biocatalytic Deacylation Studies on Tetra-O-acyl-β-d-xylofuranosyl Nucleosides: Synthesis of xylo-LNA Monomers. J Org Chem 2011; 76:7556-62. [DOI: 10.1021/jo201060t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunil K. Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Vivek K. Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Kapil Bohra
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Carl E. Olsen
- Faculty of Life Sciences, Department of Natural Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ashok K. Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India
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Torigoe H, Rahman SMA, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K. Interrupted 2'-o,4'-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:63-81. [PMID: 21259164 DOI: 10.1080/15257770.2010.543118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Due to instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex formation-based strategies in vivo, such as regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis. To this end, we investigated the effect of our previously reported chemical modification, 2'-O,4'-C-aminomethylene bridged nucleic acid (2',4'- BNA(NC)) modification, introduced into interrupted and continuous positions of triplex-forming oligonucleotide (TFO) on pyrimidine motif triplex formation at physiological pH. The interrupted 2',4'-BNA(NC) modifications of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold, and significantly increased the nuclease resistance of TFO. On the other hand, the continuous 2',4'-BNA(NC) modification of TFO showed lower ability to promote the triplex formation at physiological pH than the interrupted 2',4'-BNA(NC) modifications of TFO, and did not significantly change the nuclease resistance of TFO. Selection of the interruptedly 2',4'-BNA(NC)-modified positions in TFO was more favorable for achieving the higher binding affinity of the pyrimidine motif triplex formation at physiological pH and the higher nuclease resistance of TFO than that of the continuously 2',4'-BNA(NC)-modified positions in TFO. We conclude that the interrupted 2',4'-BNA(NC) modification of TFO could be a key chemical modification to enhance pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition, and may eventually lead to progress in various triplex formation-based strategies in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
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Torigoe H, Rahman SMA, Takuma H, Sato N, Imanishi T, Obika S, Sasaki K. 2'-O,4'-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH. Chemistry 2011; 17:2742-51. [PMID: 21264967 DOI: 10.1002/chem.201002745] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 11/28/2010] [Indexed: 11/08/2022]
Abstract
Due to the instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex-formation-based strategies in vivo, such as gene expression regulation, genomic DNA mapping, and gene-targeted mutagenesis. To this end, we investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA(NC)) modification of triplex-forming oligonucleotide (TFO), on triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA(NC) modification of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold. The number and position of the 2',4'-BNA(NC) modification in TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity and the increased degree of hydration of the 2',4'-BNA(NC)-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant. Kinetic data demonstrated that the observed increase in the binding constant by the 2',4'-BNA(NC) modification resulted mainly from the considerable decrease in the dissociation rate constant. The TFO stability in human serum showed that the 2',4'-BNA(NC) modification significantly increased the nuclease resistance of TFO. Our results support the idea that the 2',4'-BNA(NC) modification of TFO could be a key chemical modification to achieve higher binding affinity and higher nuclease resistance in the triplex formation under physiological conditions, and may lead to progress in various triplex-formation-based strategies in vivo.
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Affiliation(s)
- Hidetaka Torigoe
- Departmentof Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
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Moriyama R, Shimada N, Kano A, Maruyama A. DNA assembly and re-assembly activated by cationic comb-type copolymer. Biomaterials 2010; 32:2351-8. [PMID: 21186054 DOI: 10.1016/j.biomaterials.2010.11.064] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 11/26/2010] [Indexed: 11/16/2022]
Abstract
Guanine-rich oligonucleotides, such as TG(4)T and TG(5)T, assemble into a tetramolecular quadruplexes with layers of G-quartets stabilized by coordination to monovalent cations. Association rates of the quadruplexes are extremely slow, likely owing to electrostatic repulsion among the four strands. We have shown that comb-type copolymers with a polycation backbone and abundant hydrophilic graft chains form water-soluble polyelectrolyte complexes with DNA and promote DNA hybridization. Here, we report the effect of cationic comb-type copolymers on the kinetics of tetramolecular quadruplex formation. The copolymer significantly increased the association rate of tetramolecular quadruplexes without altering kinetic effects of metal cations in quadruplex formation. Dissociation rates of the quadruplexes were also accelerated by the copolymer suggesting that the copolymer has chaperone-like activity that reduces the energy barriers associated with dissociation and re-assembly of base pairs. This hypothesis was further supported by the observation that the copolymer activated the strand exchange reaction between the quadruplex and a constituting single-stranded.
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Affiliation(s)
- Rui Moriyama
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 CE11 Motooka, Nishi, Fukuoka 819-0395, Japan
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Obika S, Imanishi T, Kawada Y, Baba T, Fujisaka A. Bridged Nucleic Acids: Development, Synthesis and Properties. HETEROCYCLES 2010. [DOI: 10.3987/rev-10-667] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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