1
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Sakurabayashi S, Yamada T, Nakatani K. The heterodimer of 2-amino-1,8-naphthyridine and 3-aminoisoquinoline binds to the CTG/CTG triad via hydrogen bonding. Bioorg Med Chem Lett 2024:129985. [PMID: 39393501 DOI: 10.1016/j.bmcl.2024.129985] [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: 08/05/2024] [Revised: 09/25/2024] [Accepted: 10/06/2024] [Indexed: 10/13/2024]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by the aberrant expansion of CTG repeats within the DMPK gene. This study investigated the potential binding of "X-linker-Y" type molecules to the CTG/CTG motif present in CTG repeats, using heterocyclic units X and Y capable of forming complementary hydrogen bonds with nucleobases. Among the tested molecules, the heterodimer of 2-amino-1,8-naphthyridine (X) and 3-aminoisoquinoline (Y) showed significant binding to the CTG/CTG motif. NMR analysis suggested hydrogen-bonded interactions between 3-aminoisoquinoline and thymine.
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Affiliation(s)
- Shuhei Sakurabayashi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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2
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Yamada T, Furuita K, Sakurabayashi S, Nomura M, Kojima C, Nakatani K. NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA. Nucleic Acids Res 2022; 50:9621-9631. [PMID: 36095126 PMCID: PMC9508812 DOI: 10.1093/nar/gkac740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
Trinucleotide repeat (TNR) diseases are caused by the aberrant expansion of CXG (X = C, A, G and T) sequences in genomes. We have reported two small molecules binding to TNR, NCD, and NA, which strongly bind to CGG repeat (responsible sequence of fragile X syndrome) and CAG repeat (Huntington's disease). The NMR structure of NA binding to the CAG/CAG triad has been clarified, but the structure of NCD bound to the CGG/CGG triad remained to be addressed. We here report the structural determination of the NCD-CGG/CGG complex by NMR spectroscopy and the comparison with the NA-CAG/CAG complex. While the NCD-CGG/CGG structure shares the binding characteristics with that of the NA-CAG/CAG complex, a significant difference was found in the overall structure caused by the structural fluctuation at the ligand-bound site. The NCD-CGG/CGG complex was suggested in the equilibrium between stacked and kinked structures, although NA-CAG/CAG complex has only the stacked structures. The dynamic fluctuation of the NCD-CGG/CGG structure at the NCD-binding site suggested room for optimization in the linker structure of NCD to gain improved affinity to the CGG/CGG triad.
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Affiliation(s)
- Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuhei Sakurabayashi
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Makoto Nomura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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3
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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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4
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CAG repeat-binding small molecule improves motor coordination impairment in a mouse model of Dentatorubral-pallidoluysian atrophy. Neurobiol Dis 2021; 163:105604. [PMID: 34968706 DOI: 10.1016/j.nbd.2021.105604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/06/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022] Open
Abstract
Dentatorubral-pallidoluysian atrophy (DRPLA) is a devastating genetic disease presenting myoclonus, epilepsy, ataxia, and dementia. DRPLA is caused by the expansion of a CAG repeat in the ATN1 gene. Aggregation of the polyglutamine-expanded ATN1 protein causes neuro-degeneration of the dentatorubral and pallidoluysian systems. The expanded CAG repeats are unstable, and ongoing repeat expansions contribute to disease onset, progression, and severity. Inducing contractions of expanded repeats can be a means to treat DRPLA, for which no disease-modifying or curative therapies exist at present. Previously, we characterized a small molecule, naphthyridine-azaquinolone (NA), which binds to CAG slip-out structures and induces repeat contraction in Huntington's disease mice. Here, we demonstrate that long-term intracerebroventricular infusion of NA leads to repeat contraction, reductions in mutant ATN1 aggregation, and improved motor phenotype in a murine model of DRPLA. Furthermore, NA-induced contraction resulted in the modification of repeat-length-dependent dysregulation of gene expression profiles in DRPLA mice. Our study reveals the therapeutic potential of repeat contracting small molecules for repeat expansion disorders, such as DRPLA.
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5
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Dohno C, Hagihara M, Binti Mohd Zaifuddin N, Nihei M, Saito K, Nakatani K. Small molecule-induced trinucleotide repeat contractions during in vitro DNA synthesis. Chem Commun (Camb) 2021; 57:3235-3238. [PMID: 33646236 DOI: 10.1039/d1cc00349f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrated that a synthetic ligand NA, which selectively binds to a 5'-CAG-3'/5'-CAG-3' triad, induced repeat contractions during DNA polymerase-mediated primer extension through the CAG repeat template. A thorough capillary electrophoresis and sequencing analysis revealed that the d(CAG)20 template gave shortened nascent strands mainly containing 3-6 CTG units in the presence of NA.
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Affiliation(s)
- Chikara Dohno
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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6
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Theoretical study of lumichrome, 1-methyl-lumichrome and lumiflavin binding ability with thymine. ACTA CHIMICA SLOVACA 2021. [DOI: 10.2478/acs-2021-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Gas-phase geometry and electronic structure of lumichrome, 1-methyl-lumichrome and lumiflavin in the electronic ground state and their excited states were investigated using the Density Functional Theory. Their binding ability with thymine was estimated for model van der Waals dimers with two intermolecular hydrogen bonds. The influence of hydrogen bonds on their photophysical properties was analyzed. Obtained theoretical data were compared with available experimental absorption and fluorescence spectra.
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7
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Mukherjee S, Błaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatani K, Kiliszek A. Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats. Nucleic Acids Res 2019; 47:10906-10913. [PMID: 31566242 PMCID: PMC6847237 DOI: 10.1093/nar/gkz832] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/07/2019] [Accepted: 09/26/2019] [Indexed: 12/17/2022] Open
Abstract
The trinucleotide repeat expansion disorders (TREDs) constitute of a group of >40 hereditary neurodegenerative human diseases associated with abnormal expansion of repeated sequences, such as CAG repeats. The pathogenic factor is a transcribed RNA or protein whose function in the cell is compromised. The disorders are progressive and incurable. Consequently, many ongoing studies are oriented at developing therapies. We have analyzed crystal structures of RNA containing CAG repeats in complex with synthetic cyclic mismatch-binding ligands (CMBLs). The models show well-defined interactions between the molecules in which the CMBLs mimic nucleobases as they form pseudo-canonical base pairs with adenosine residues and engage in extensive stacking interactions with neighboring nucleotides. The binding of ligands is associated with major structural changes of the CAG repeats, which is consistent with results of biochemical studies. The results constitute an early characterization of the first lead compounds in the search for therapy against TREDs. The crystallographic data indicate how the compounds could be further refined in future biomedical studies.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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8
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Lahiri H, Banerjee S, Mukhopadhyay R. Free-Energy-Based Gene Mutation Detection Using LNA Probes. ACS Sens 2019; 4:2688-2696. [PMID: 31549503 DOI: 10.1021/acssensors.9b01115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We have developed a label-free approach for direct detection of gene mutations using free-energy values that are derived from single-molecule force spectroscopy (SMFS)-based nucleic acid unbinding experiments. From the duplex unbinding force values acquired by SMFS, the force-loading-rate-independent Gibbs free-energy values were derived using Jarzinsky's equality treatment. Because it provides molecule-by-molecule information, this approach is a major shift compared to the earlier reports on label-free detection of DNA sequences, which are mostly based on ensemble level data. We tested our approach in the disease model framework of multiple drug-resistant tuberculosis using the nuclease-resistant and conformationally rigid locked nucleic acid probes that are a robust and efficient alternative to the DNA probes. All of the major mutations in Mycobacterium tuberculosis (MTB), as relevant to MTB's resistance to the first-line anti-TB drugs rifampicin and isoniazid, could be identified, and the wild type could be discriminated from the most prevalent mutation and the most prevalent mutation from the less occurring ones. Our approach could also identify DNA sequences (45 mer), having overhang stretches at different positions with respect to the complementary stretch. Probably for the first time, the findings show that free-energy-based detection of gene mutations is possible at molecular resolution.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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9
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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10
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Yagi Y, Aikawa H, Yamada T, Nakatani K. Expanding chemical space of DNA-binding molecules with three base-binding units. Bioorg Med Chem Lett 2018; 28:2894-2898. [PMID: 30025901 DOI: 10.1016/j.bmcl.2018.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
A new molecule NC3-3 designed to expand chemical space of parent molecule NCD by adding the third base-binding unit was reported. NC3-3 bound to the G-G mismatch in the 5'-CGG-3'/5'-CGG-3' motif but not to that in 5'-GGC-3'/5'-GGC-3'. This binding selectivity is similar to that reported for NCD. Fluorimetric screening of NCD and NC3-3 to dsDNA library containing yGw/xGz motifs showed that NC3-3 still kept the sequence selectivity as we observed for NCD-binding. The third naphthyridine heterocycle in NC3-3 affected the mode of the binding, but a little effect on the sequence selectivity.
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Affiliation(s)
- Yuki Yagi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Haruo Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kazuhiko 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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11
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Patent Highlights February-March 2018. Pharm Pat Anal 2018; 7:147-154. [PMID: 29882729 DOI: 10.4155/ppa-2018-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research development.
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12
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Ohshiro T, Verma RK, Yokota K, Tsutsui M, Mukherjee S, Kawai T, Nakatani K, Taniguchi M. Electrical Nucleotide Sensor Based on Synthetic Guanine-Receptor-Modified Electrodes. ChemistrySelect 2018. [DOI: 10.1002/slct.201702341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Takahito Ohshiro
- Bio-nanotechnology Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Rajiv Kumar Verma
- Regulatory Bioorganic Chemistry Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Kazumichi Yokota
- Bio-nanotechnology Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Makusu Tsutsui
- Bio-nanotechnology Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Sanjukta Mukherjee
- Regulatory Bioorganic Chemistry Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Tomoji Kawai
- Bio-nanotechnology Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Kazuhiko Nakatani
- Regulatory Bioorganic Chemistry Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Masateru Taniguchi
- Bio-nanotechnology Laboratory, The Institute of Scientific and Industrial Research (ISIR); Osaka University; 8-1, Mihogaoka, Ibaraki Osaka 567-0047 Japan
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13
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Huang CJ, Lin ZE, Yang YS, Chan HWH, Chen WY. Neutralized chimeric DNA probe for detection of single nucleotide polymorphism on surface plasmon resonance biosensor. Biosens Bioelectron 2017; 99:170-175. [PMID: 28755610 DOI: 10.1016/j.bios.2017.07.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/27/2022]
Abstract
An implementation of neutralized chimeric DNA oligomer as a probe for sensitive detection of single nucleotide polymorphisms (SNPs) on a surface plasmon resonance imaging sensor is investigated. The chimeric DNA oligomer was synthesized in a conventional DNA synthesizer, containing neutral nucleotides with a methylated phosphate group. The secondary structures and melting points of the chimeric DNA fragment and its complexes with perfect-matched and single-mismatched complementary DNA molecules were examined by using circular dichroism and UV-vis spectroscopy in comparison with the native probe DNA counterpart. The results indicate that the chimeric DNA complexes can form a B-form structure and exhibit high thermostability. Moreover, the hybridization and discrimination efficiency of the chimeric probe DNA for the SNP genotyping were verified by using the SPRi sensor under different experimental conditions. The data reveal the effects of the ionic strength and operation temperature on the selectivity of the chimeric probe DNA for the SNP detection. The hybridization condition with a low ionic strength and high temperature allows the chimeric probe DNA distinguishing perfect-matched and single-mismatched target DNA molecules to the best extent, likely due to the reduced electrostatic repulsive force and presence of the additional methyl group on the backbone. Consequently, the direct and label-free detection with the SPR technique and neutralized chimeric probe DNA can be realized for the SNP genotyping by optimizing the operation condition and sequence design.
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Affiliation(s)
- Chun-Jen Huang
- Department of Biomedical Sciences and Engineering, National Central University, Jhong-Li 320, Taiwan; Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan
| | - Zhong-En Lin
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan
| | - Yuh-Shyong Yang
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | | | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li 320, Taiwan.
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14
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Murata A, Otabe T, Zhang J, Nakatani K. BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer. ACS Chem Biol 2016; 11:2790-2796. [PMID: 27536863 DOI: 10.1021/acschembio.6b00214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We here report the synthesis of novel molecule BzDANP having a three-ring benzo[c][1,8]naphthyridine system, the evaluation of its binding properties to a single nucleotide bulge in RNA duplexes, and BzDANP-induced suppression of pre-miR-29a processing by Dicer. BzDANP showed much increased affinity to the bulged RNAs as compared with the parent molecule DANP, which possesses the same hydrogen-bonding surface as BzDANP but in a two-ring [1,8]naphthyridine system. Melting temperature analysis of bulged RNAs showed that BzDANP most effectively stabilized the C-bulged RNA. Dicer-mediated processing of pre-miR-29a was suppressed by BzDANP in a concentration dependent manner. The presence of the C-bulge at the Dicer cleavage site was effective for the suppression of pre-miR-29a processing by BzDANP. These results demonstrated that the small molecule binding to the bulged site in the vicinity of the Dicer cleavage site could be a potential modulator for the maturation of pre-miRNA.
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Affiliation(s)
- Asako Murata
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takahiro Otabe
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Jinhua Zhang
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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15
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Mukherjee S, Dohno C, Asano K, Nakatani K. Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base. Nucleic Acids Res 2016; 44:7090-9. [PMID: 27466390 PMCID: PMC5009760 DOI: 10.1093/nar/gkw672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022] Open
Abstract
A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaori Asano
- Comprehensive Analysis Center, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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16
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Li J, Sakata A, He H, Bai LP, Murata A, Dohno C, Nakatani K. Naphthyridine-Benzoazaquinolone: Evaluation of a Tricyclic System for the Binding to (CAG)nRepeat DNA and RNA. Chem Asian J 2016; 11:1971-81. [DOI: 10.1002/asia.201600527] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jinxing Li
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Akihiro Sakata
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Hanping He
- Chemistry and Chemical Engineering College; Hubei University; Road Youyi 368, Wuchang, Wuhan Hubei 430062 China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, and Macau Institute for Applied Research in Medicine and Health; Macau University of Science and Technology; Avenida Wai Long, Taipa Macau China
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Kazuhiko 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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Zhu X, Li J, He H, Huang M, Zhang X, Wang S. Application of nanomaterials in the bioanalytical detection of disease-related genes. Biosens Bioelectron 2015; 74:113-33. [PMID: 26134290 DOI: 10.1016/j.bios.2015.04.069] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/09/2015] [Accepted: 04/21/2015] [Indexed: 12/15/2022]
Abstract
In the diagnosis of genetic diseases and disorders, nanomaterials-based gene detection systems have significant advantages over conventional diagnostic systems in terms of simplicity, sensitivity, specificity, and portability. In this review, we describe the application of nanomaterials for disease-related genes detection in different methods excluding PCR-related method, such as colorimetry, fluorescence-based methods, electrochemistry, microarray methods, surface-enhanced Raman spectroscopy (SERS), quartz crystal microbalance (QCM) methods, and dynamic light scattering (DLS). The most commonly used nanomaterials are gold, silver, carbon and semiconducting nanoparticles. Various nanomaterials-based gene detection methods are introduced, their respective advantages are discussed, and selected examples are provided to illustrate the properties of these nanomaterials and their emerging applications for the detection of specific nucleic acid sequences.
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Affiliation(s)
- Xiaoqian Zhu
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Jiao Li
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China.
| | - Min Huang
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
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Li J, Matsumoto J, Otabe T, Dohno C, Nakatani K. 2-Aminophenanthroline dimer stabilized the C–C mismatched duplex DNA. Bioorg Med Chem 2015; 23:753-8. [DOI: 10.1016/j.bmc.2014.12.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 10/24/2022]
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Artigas G, Marchán V. Synthesis and tau RNA binding evaluation of ametantrone-containing ligands. J Org Chem 2015; 80:2155-64. [PMID: 25602935 DOI: 10.1021/jo502661j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We describe the synthesis and characterization of ametantrone-containing RNA ligands based on the derivatization of this intercalator with two neamine moieties (Amt-Nea,Nea) or with one azaquinolone heterocycle and one neamine (Amt-Nea,Azq) as well as its combination with guanidinoneamine (Amt-NeaG4). Biophysical studies revealed that guanidinylation of the parent ligand (Amt-Nea) had a positive effect on the binding of the resulting compound for Tau pre-mRNA target as well as on the stabilization upon complexation of some of the mutated RNA sequences associated with the development of tauopathies. Further studies by NMR revealed the existence of a preferred binding site in the stem-loop structure, in which ametantrone intercalates in the characteristic bulged region. Regarding doubly-functionalized ligands, binding affinity and stabilizing ability of Amt-Nea,Nea were similar to those of the guanidinylated ligand, but the two aminoglycoside fragments seem to interfere with its accommodation in a single binding site. However, Amt-Nea,Azq binds at the bulged region in a similar way than Amt-NeaG4. Overall, these results provide new insights on fine-tuning RNA binding properties of ametantrone by single or double derivatization with other RNA recognition motifs, which could help in the future design of new ligands with improved selectivity for disease-causing RNA molecules.
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Affiliation(s)
- Gerard Artigas
- Departament de Química Orgànica and IBUB, Universitat de Barcelona , Martí i Franquès 1-11, E-08028 Barcelona, Spain
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20
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Okumura S, Kuroda R, Inouye K. Single Nucleotide Polymorphism Typing with a Surface Plasmon Resonance-Based Sensor Using Hybridization Enhancement Blockers. Appl Biochem Biotechnol 2014; 174:494-505. [DOI: 10.1007/s12010-014-1072-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
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21
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Kume H, Hino K, Galipon J, Ui-Tei K. A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency. Nucleic Acids Res 2014; 42:10050-60. [PMID: 25056317 PMCID: PMC4150774 DOI: 10.1093/nar/gku662] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Hydrolytic deamination of adenosine to inosine (A-to-I) by adenosine deaminases acting on RNA (ADARs) is a post-transcriptional modification which results in a discrepancy between genomic DNA and the transcribed RNA sequence, thus contributing to the diversity of the transcriptome. Inosine preferentially base pairs with cytidine, meaning that A-to-I modifications in the mRNA sequences may be observed as A-to-G substitutions by the protein-coding machinery. Genome-wide studies have revealed that the majority of editing events occur in non-coding RNA sequences, but little is known about their functional meaning. MiRNAs are small non-coding RNAs that regulate the expression of target mRNAs with complementarities to their seed region. Here, we confirm that A-to-I editing in the miRNA seed duplex globally reassigns their target mRNAs in vivo, and reveal that miRNA containing inosine in the seed region exhibits a different degree of silencing efficiency compared to the corresponding miRNA with guanosine at the same position. The difference in base-pairing stability, deduced by melting temperature measurements, between seed-target duplexes containing either C:G or I:C pairs may account for the observed silencing efficiency. These findings unequivocally show that C:G and I:C pairs are biologically different in terms of gene expression regulation by miRNAs.
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Affiliation(s)
- Hideaki Kume
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kimihiro Hino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Josephine Galipon
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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22
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Hong C, Otabe T, Matsumoto S, Dohno C, Murata A, Hagihara M, Nakatani K. Formation of a Ligand-Assisted Complex of Two RNA Hairpin Loops. Chemistry 2014; 20:5282-7. [DOI: 10.1002/chem.201304683] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 01/16/2023]
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23
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Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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24
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Bag SS, Kundu R, Jana S. Sensing of biomolecules and label-free discrimination of DNA containing a triple T–C/T–G mismatch pair with a fluorescence light-up probe, triazolylpyrene (TNDMBPy). Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Selective recognition of G–G mismatch using the double functional probe with electrochemical activeferrocenyl. Biosens Bioelectron 2013. [DOI: 10.1016/j.bios.2012.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Detection of mismatched caspase-3 DNA oligonucleotides with an SPR biosensor following amplification by Taq polymerase. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0799-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Jourdan M, Granzhan A, Guillot R, Dumy P, Teulade-Fichou MP. Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch. Nucleic Acids Res 2012; 40:5115-28. [PMID: 22362757 PMCID: PMC3367172 DOI: 10.1093/nar/gks067] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The macrocyclic bis-naphthalene macrocycle (2,7-BisNP), belonging to the cyclobisintercalator family of DNA ligands, recognizes T–T mismatch sites in duplex DNA with high affinity and selectivity, as evidenced by thermal denaturation experiments and NMR titrations. The binding of this macrocycle to an 11-mer DNA oligonucleotide containing a T–T mismatch was studied using NMR spectroscopy and NMR-restrained molecular modeling. The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex. The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking. The polyammonium linking chains of the macrocycle are located in the minor and the major grooves of the oligonucleotide and participate in the stabilization of the complex by formation of hydrogen bonds with the encapsulated thymine base and the mismatched thymine remaining inside the helix. The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.
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Affiliation(s)
- Muriel Jourdan
- CNRS UMR5250, ICMG FR2607, Département de Chimie Moléculaire, Université Joseph Fourier, 570 rue de la Chimie, 38041 Grenoble Cedex 9, France.
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29
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Hu L, Wang Y, Wang W, Gao Q, Qi H, Zhang C. Recognition of a C-C mismatch in a DNA duplex using a fluorescent small molecule with application for "off-on" discrimination of C/G mutation. APPLIED SPECTROSCOPY 2012; 66:170-174. [PMID: 22449280 DOI: 10.1366/11-06410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The fluorescent small molecule 2-amino-7-methyl-1,8-naphthyridine (AMND) can selectively bind to a cytosine (C) at a C-C mismatch in double-stranded DNA (dsDNA). The interactions between AMND and C-C mismatch-containing dsDNA were investigated by measuring ultraviolet (UV) absorption as a function of temperature to obtain melting curves as well as circular dichroism and fluorescence spectra. Results show that AMND strongly stabilizes C-C mismatch-containing dsDNA, whereas fully matched duplexes are not stabilized under the same conditions. The fluorescence of AMND was efficiently quenched when it was bound to a C-C mismatch in dsDNA. Binding constants (K(11)), obtained by fluorescence titration, were 1.2 × 10(5) M(-1). Although sensing functions depend on the sequences flanking the mismatch site, the change in AMND fluorescence intensity can be utilized to detect the C-C mismatch-containing dsDNA. Accordingly, discrimination of the C/G mutation in the model sequence (PGR gene rs1255998) was achieved by visualizing fluorescence of AMND. A probe DNA molecule was designed to contain a C opposite the C/G base in the target DNA, and this probe was used to hybridize the target DNA. The fluorescence of AMND was "on" for a C-G match, while the fluorescence was "off" for a C-C mismatch. This assay is simple and does not require DNA labeling.
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Affiliation(s)
- Liangliang Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an 710062, China
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30
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Sato Y, Zhang Y, Seino T, Sugimoto T, Nishizawa S, Teramae N. Highly selective binding of naphthyridine with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes. Org Biomol Chem 2012; 10:4003-6. [DOI: 10.1039/c2ob25513h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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31
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Atsumi H, Maekawa K, Nakazawa S, Shiomi D, Sato K, Kitagawa M, Takui T, Nakatani K. Tandem Arrays of TEMPO and Nitronyl Nitroxide Radicals with Designed Arrangements on DNA. Chemistry 2011; 18:178-83. [DOI: 10.1002/chem.201102693] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/24/2022]
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32
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Miura S, Nishizawa S, Suzuki A, Fujimoto Y, Ono K, Gao Q, Teramae N. DNA-Binding Small-Ligand-Immobilized Surface Plasmon Resonance Biosensor for Detecting Thymine-Related Single-Nucleotide Polymorphisms. Chemistry 2011; 17:14104-10. [DOI: 10.1002/chem.201101290] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Indexed: 01/28/2023]
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33
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Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011; 50:4390-3. [DOI: 10.1002/anie.201100075] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/11/2022]
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35
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López-Senín P, Gómez-Pinto I, Grandas A, Marchán V. Identification of ligands for the Tau exon 10 splicing regulatory element RNA by using dynamic combinatorial chemistry. Chemistry 2011; 17:1946-53. [PMID: 21274946 DOI: 10.1002/chem.201002065] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Indexed: 01/25/2023]
Abstract
We describe the use of dynamic combinatorial chemistry (DCC) to identify ligands for the stem-loop structure located at the exon 10-5'-intron junction of Tau pre-mRNA, which is involved in the onset of several tauopathies including frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). A series of ligands that combine the small aminoglycoside neamine and heteroaromatic moieties (azaquinolone and two acridines) have been identified by using DCC. These compounds effectively bind the stem-loop RNA target (the concentration required for 50% RNA response (EC(50)): 2-58 μM), as determined by fluorescence titration experiments. Importantly, most of them are able to stabilize both the wild-type and the +3 and +14 mutated sequences associated with the development of FTDP-17 without producing a significant change in the overall structure of the RNA (as analyzed by circular dichroism (CD) spectroscopy), which is a key factor for recognition by the splicing regulatory machinery. A good correlation has been found between the affinity of the ligands for the target and their ability to stabilize the RNA secondary structure.
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Affiliation(s)
- Paula López-Senín
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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36
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Milkani E, Khaing AM, Morais S, Lambert CR, McGimpsey WG. SPR-based single nucleotide mismatch biosensor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:122-132. [PMID: 32938121 DOI: 10.1039/c0ay00492h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and characterization of the hybridization event of 21-base, unlabeled DNA oligonucleotides with a monolayer of complementary DNA immobilized on a gold surface, by electrochemical impedance spectroscopy and surface plasmon resonance (SPR) is presented. A thiol modification on the probe DNA strand allowed for its attachment to the surface via self-assembly. For the hybridization of full match target DNA a detection limit of 20 pM was determined. RNA hybridization was also detectable with the same sensor, with a similar detection limit. The SPR signal generated upon hybridization of the full match was always distinguishable from the single mismatch target DNA oligonucleotides when the mismatch was in the middle or at the proximal end of the target DNA sequence. However, the response of the sensor was identical for the hybridization of the full match and the distal end mismatch. The SPR sensor described is reusable over at least 20 hybridization/regeneration cycles and is insensitive to flow rate (20-800 µL min-1) or temperature (20-60 °C). Based on the SPR response, the surface density of the probe was estimated to be at least 4.3 × 1012 molecules per cm2.
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Affiliation(s)
- Eftim Milkani
- Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Bioengineering Institute, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA.
| | - Aung M Khaing
- Bioengineering Institute, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA.
- Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Sergi Morais
- Instituto de Química Molecular Aplicada, Universidad Politécnica de Valencia, Camino de Vera s/n, 46071, Valencia, Spain
| | - Christopher R Lambert
- Bioengineering Institute, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA.
| | - W Grant McGimpsey
- Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Bioengineering Institute, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA.
- Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
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37
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Granzhan A, Largy E, Saettel N, Teulade-Fichou MP. Macrocyclic DNA-mismatch-binding ligands: structural determinants of selectivity. Chemistry 2010; 16:878-89. [PMID: 19938008 DOI: 10.1002/chem.200901989] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A collection of 15 homodimeric and 5 heterodimeric macrocyclic bisintercalators was prepared by one- or two-step condensation of aromatic dialdehydes with aliphatic diamines; notably, the heterodimeric scaffolds were synthesized for the first time. The binding of these macrocycles to DNA duplexes containing a mispaired thymine residue (TX), as well as to the fully paired control (TA), was investigated by thermal denaturation and fluorescent-intercalator-displacement experiments. The bisnaphthalene derivatives, in particular, the 2,7-disubstituted ones, have the highest selectivity for the TX mismatches, as these macrocycles show no apparent binding to the fully paired DNA. By contrast, other macrocyclic ligands, as well as seven conventional DNA binders, show lesser or no selectivity for the mismatch sites. The study demonstrates that the topology of the ligands plays a crucial role in determining the mismatch-binding affinity and selectivity of the macrocyclic bisintercalators.
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Affiliation(s)
- Anton Granzhan
- UMR176 CNRS, Institut Curie, Centre de Recherche, Centre Universitaire, 91405 Orsay, France
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38
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Rajendar B, Rajendran A, Ye Z, Kanai E, Sato Y, Nishizawa S, Sikorski M, Teramae N. Effect of substituents of alloxazine derivatives on the selectivity and affinity for adenine in AP-site-containing DNA duplexes. Org Biomol Chem 2010; 8:4949-59. [DOI: 10.1039/c0ob00057d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Thiagarajan V, Rajendran A, Satake H, Nishizawa S, Teramae N. NBD-Based Green Fluorescent Ligands for Typing of Thymine-Related SNPs by Using an Abasic Site-Containing Probe DNA. Chembiochem 2009; 11:94-100. [DOI: 10.1002/cbic.200900530] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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He H, Hagihara M, Nakatani K. A Small Molecule Affecting the Replication of Trinucleotide Repeat d(GAA)n. Chemistry 2009; 15:10641-8. [DOI: 10.1002/chem.200901088] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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41
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903251] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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42
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009; 48:7362-5. [DOI: 10.1002/anie.200903251] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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43
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Nakatani K. Recognition of Mismatched Base Pairs in DNA. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1055] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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44
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Dohno C, Yamamoto T, Nakatani K. Photoswitchable Unsymmetrical Ligand for DNA Hetero-Mismatches. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900323] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Atsumi H, Yoshimoto K, Saito S, Ohkuma M, Maeda M, Nagasaki Y. Luminescence-based colorimetric discrimination of single-nucleotide transversions by the combined use of the derivatives of DOTA-conjugated naphthyridine and its terbium complex. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.02.152] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Granzhan A, Teulade-Fichou MP. A Fluorescent Bisanthracene Macrocycle Discriminates between Matched and Mismatch-Containing DNA. Chemistry 2009; 15:1314-8. [DOI: 10.1002/chem.200802421] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Sankaran NB, Sato Y, Sato F, Rajendar B, Morita K, Seino T, Nishizawa S, Teramae N. Small-Molecule Binding at an Abasic Site of DNA: Strong Binding of Lumiflavin for Improved Recognition of Thymine-Related Single Nucleotide Polymorphisms. J Phys Chem B 2009; 113:1522-9. [DOI: 10.1021/jp808576t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. B. Sankaran
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Fuyuki Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Burki Rajendar
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Kotaro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Takehiro Seino
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
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48
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Sato Y, Nishizawa S, Yoshimoto K, Seino T, Ichihashi T, Morita K, Teramae N. Influence of substituent modifications on the binding of 2-amino-1,8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization. Nucleic Acids Res 2009; 37:1411-22. [PMID: 19136458 PMCID: PMC2655693 DOI: 10.1093/nar/gkn1079] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Here, we report on a significant effect of substitutions on the binding affinity of a series of 2-amino-1,8-naphthyridines, i.e., 2-amino-1,8-naphthyridine (AND), 2-amino-7-methyl-1,8-naphthyridine (AMND), 2-amino-5,7-dimethyl-1,8-naphthyridine (ADMND) and 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), all of which can bind to cytosine opposite an AP site in DNA duplexes. Fluorescence titration experiments show that the binding affinity for cytosine is effectively enhanced by the introduction of methyl groups to the naphthyridine ring, and the 1:1 binding constant (106 M−1) follows in the order of AND (0.30) < AMND (2.7) < ADMND (6.1) < ATMND (19) in solutions containing 110 mM Na+ (pH 7.0, at 20°C). The thermodynamic parameters obtained by isothermal titration calorimetry experiments indicate that the introduction of methyl groups effectively reduces the loss of binding entropy, which is indeed responsible for the increase in the binding affinity. The heat capacity change (ΔCp), as determined from temperature dependence of the binding enthalpy, is found to be significantly different between AND (−161 cal/mol K) and ATMND (−217 cal/mol K). The hydrophobic contribution appears to be a key force to explain the observed effect of substitutions on the binding affinity when the observed binding free energy (ΔGobs) is dissected into its component terms.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, CREST, Japan Science and Technology Agency, Aoba-ku, Sendai 980-8578, Japan
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Jung YK, Kim TW, Jung C, Cho DY, Park HG. A polydiacetylene microchip based on a biotin-streptavidin interaction for the diagnosis of pathogen infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:1778-1784. [PMID: 18819132 DOI: 10.1002/smll.200800947] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A micropatterned polydiacetylene (PDA) chip, utilizing the unique fluorogenic property of PDA and a specific biotin-streptavidin (STA) interaction, is constructed to detect pathogen infections. To construct the PDA chip, biotin-modified diacetylene liposomes are immobilized on aldehyde glass and conjugated with STA, followed by UV irradiation to polymerize the STA-functionalized diacetylene liposomes. Genomic DNA of a model pathogen, Chlamydia trachomatis, is isolated from human samples and biotin-labeled target DNA is obtained through PCR amplification using biotin-11-dUTP. Owing to the stimulus caused by the biotin-STA interaction, the biotinylated DNA induces an intense fluorescence signal on the immobilized PDA. By using this strategy, it is possible to diagnose Chlamydia infections by applying DNA samples from several nonhealthy humans to a single PDA chip. The results of this study serve as the basis for a new strategy for fluorogenic PDA microarray-based diagnosis of pathogen infections.
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Affiliation(s)
- Yun Kyung Jung
- Department of Chemical and Biomolecular Engineering (BK 21 Program), KAIST, Daejeon 305-701, Korea
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50
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Peng T, He H, Hagihara M, Nakatani K. DNA Labeling by Ligand Inducible Secondary Structure. Chembiochem 2008; 9:1893-7. [DOI: 10.1002/cbic.200800254] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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