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NAKATANI K. Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:30-48. [PMID: 35013029 PMCID: PMC8795530 DOI: 10.2183/pjab.98.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.
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Affiliation(s)
- Kazuhiko NAKATANI
- SANKEN, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
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High allele discrimination in the typing of single nucleotide polymorphisms of miRNA. Bioorg Med Chem 2021; 46:116363. [PMID: 34419822 DOI: 10.1016/j.bmc.2021.116363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) belonging to the same family have similar sequences and are difficult to identify. Herein, we report the reverse transcription-hairpin-probe-polymerase chain reaction (RT-Hpro-PCR) technique, which utilises a reverse transcription (RT) primer containing a 5'-end deoxyribonucleic acid (DNA) tag, to detect miRNAs with similar sequences. This strategy follows a two-step RT-PCR method using 6-7-mer RT-primers with a ~ 10-mer tag sequence at the 5'-end and a probe with a hairpin structure (Hpro), including two C-bulges, attached. The findings demonstrate that the specificity of RT could be increased by shortening the complementary part of the RT primer containing a different base, wherein the PCR could successfully progress with the use of 5'-end DNA tag because of an increase in the length of the hybridised tagged primer. This study shows the potential of RT-Hpro-PCR to precisely detect miRNAs with similar sequences, which could help explore the roles of miRNAs in several biological processes.
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Takei F, Akiyama M, Murata A, Sugai A, Nakatani K, Yamashita I. RT-Hpro-PCR: A MicroRNA Detection System Using a Primer with a DNA Tag. Chembiochem 2019; 21:477-480. [PMID: 31397042 DOI: 10.1002/cbic.201900382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) are short RNAs that regulate the expression of complementary messenger RNAs and are involved in numerous human diseases. However, current detection techniques lack the sensitivity to detect miRNAs of low abundance. Moreover, at a length of 20-25 bases, miRNAs are too short for the reverse transcription (RT) polymerase chain reaction (PCR). Here we have developed a new, rapid, and simple miRNA detection system utilizing an RT primer containing a DNA tag at the 5'-end to increase the length of the cDNA. This strategy increases the length of the hybridized tagged primer and the complementary template DNA, as well as the melting temperature of the primer⋅template DNA duplex. PCR efficiency is thus increased, thereby enhancing miRNA detection sensitivity.
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Affiliation(s)
- Fumie Takei
- National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Misaki Akiyama
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Asako Murata
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Ayako Sugai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Ichiro Yamashita
- Graduate School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
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Takei F, Akiyama M, Nobusawa K, Sabani NB, Han H, Nakatani K, Yamashita I. PCR under Low Ionic Concentration Buffer Conditions. ChemistrySelect 2018. [DOI: 10.1002/slct.201702542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Fumie Takei
- Department of MedicineNational Defense Medical College 3-2 Namiki, Tokorozawa Saitama 359–8513 Japan
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Misaki Akiyama
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Kazuyuki Nobusawa
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Norhayati Binti Sabani
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Huanwen Han
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
| | - Ichiro Yamashita
- Graduate School of EngineeringOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567–0047 Japan
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Aikawa H, Yano A, Nakatani K. A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH. Org Biomol Chem 2017; 15:1313-1316. [PMID: 27847943 DOI: 10.1039/c6ob02273a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of 2,7-diamino-1,4,8-triazanaphthalene (azaDANP) are described. AzaDANP is protonated only at a weakly acidic pH to bind to the cytosine bulge DNA duplex selectively. Upon binding of azaDANP to the cytosine bulge DNA, a new absorption band at 407 nm appears, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped pH-absorption profile.
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Affiliation(s)
- H Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - A Yano
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - K Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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Abstract
A new fluorescence turn-on type of PCR monitoring system (Hpro-PCR) using a hairpin probe and a primer having a tag sequence at the 5′ end with the fluorescent molecule 2,7-diamino-1,8-naphthyridine derivative (DANP) has been developed.
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Affiliation(s)
- F. Takei
- National Defense Medical College, 3-2 Namiki
- Tokorozawa
- Japan
| | - K. Nakatani
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki
- Japan
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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Takei F, Chen X, Yu G, Shibata T, Dohno C, Nakatani K. Cytosine-bulge-dependent fluorescence quenching for the real-time hairpin primer PCR. Chem Commun (Camb) 2015; 50:15195-8. [PMID: 25338232 DOI: 10.1039/c4cc06780k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The progress of a polymerase chain reaction (PCR) was sensitively monitored based on the increase in fluorescence of N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine, which was covalently anchored on the cytosine bulge directly neighbouring the 5'-T_G-3'/5'-CCA-3' sequence in the hairpin tag at the 5' end of the PCR primer.
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Affiliation(s)
- F Takei
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047 Japan.
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Takei F, Nakatani K. The Chemistry of Polymerase Chain Reaction^|^mdash;Development of the PCR Method Using New Modified Primers^|^mdash;. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Takei F, Tani H, Matsuura Y, Nakatani K. Detection of hepatitis C virus by single-step hairpin primer RT-PCR. Bioorg Med Chem Lett 2014; 24:394-6. [DOI: 10.1016/j.bmcl.2013.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
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A novel DANP-coupled hairpin RT-PCR for rapid detection of Chikungunya virus. J Mol Diagn 2013; 15:227-33. [PMID: 23313361 DOI: 10.1016/j.jmoldx.2012.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/10/2012] [Accepted: 10/31/2012] [Indexed: 11/21/2022] Open
Abstract
Chikungunya has re-emerged as an important arboviral infection of global health significance. Because of lack of a vaccine and effective treatment, rapid diagnosis plays an important role in early clinical management of patients. In this study, we have developed a novel molecular diagnostic platform that ensures a rapid and cost-effective one-step RT-PCR assay, with high sensitivity and specificity, for the early detection of the Chikungunya virus (CHIKV). It uses 2,7-diamino-1,8-naphthyridine derivative (DANP)-labeled cytosine-bulge hairpin primers to amplify the nsP2 region of the CHIKV genome, followed by measurement of the fluorescence emitted from DANP-primer complexes after PCRs. The detection limit of our assay was 0.01 plaque-forming units per reaction of CHIKV. Furthermore, the HP-nsP2 primers were highly specific in detecting CHIKV, without any cross-reactivity with the panel of RNA viruses validated in this study. The feasibility of the DANP-coupled hairpin RT-PCR for clinical diagnosis was evaluated using clinical serum samples from CHIKV-infected patients, and the specificity and sensitivity were 100% (95% CI, 80.0% to 100%) and 95.5% (95% CI, 75.1% to 99.8%), respectively. These findings confirmed its potential as a point-of-care clinical molecular diagnostic assay for CHIKV in acute-phase patient serum samples.
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