1
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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2
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Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
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Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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3
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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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4
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Duprey JLHA, Bassani DM, Hyde EI, Jonusauskas G, Ludwig C, Rodger A, Spencer N, Vyle JS, Wilkie J, Zhao ZY, Tucker JHR. Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes. Org Biomol Chem 2018; 16:6576-6585. [DOI: 10.1039/c8ob01710g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
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Affiliation(s)
| | - Dario M. Bassani
- Institut des Sciences Moléculaires, CNRS UMR 5255
- Université Bordeaux
- Talence 33405
- France
| | - Eva I. Hyde
- School of Biosciences
- The University of Birmingham
- Edgbaston
- UK
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine
- UMR CNRS 5798
- Université Bordeaux
- Talence 33405
- France
| | - Christian Ludwig
- Henry Wellcome Building for Biomolecular NMR Spectroscopy
- Institute of Cancer & Genomic Sciences
- College of Medical & Dental Sciences
- University of Birmingham
- Edgbaston
| | - Alison Rodger
- Department of Molecular Sciences
- Faculty of Science and Engineering
- Macquarie University
- North Ryde
- Australia
| | - Neil Spencer
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - John Wilkie
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
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5
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Takada T, Umakoshi Y, Nakamura M, Yamana K. A Luminescent Perylenediimide as a Binding Ligand for Pyrimidine/Pyrimidine Mismatches Within a DNA Duplex. ChemistrySelect 2017. [DOI: 10.1002/slct.201701310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yu Umakoshi
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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6
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Matsumoto S, Iida K, Murata A, Denawa M, Hagiwara M, Nakatani K. Synthetic ligand promotes gene expression by affecting GC sequence in promoter. Bioorg Med Chem Lett 2017; 27:3391-3394. [PMID: 28610980 DOI: 10.1016/j.bmcl.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/18/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.
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Affiliation(s)
- Saki Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Masatoshi Hagiwara
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan; Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan.
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7
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Obliosca JM, Cheng SY, Chen YA, Llanos MF, Liu YL, Imphean DM, Bell DR, Petty JT, Ren P, Yeh HC. LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature. J Am Chem Soc 2017; 139:7110-7116. [PMID: 28463488 DOI: 10.1021/jacs.7b03395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-resolution melting (HRM) analysis of DNA is a closed-tube single-nucleotide polymorphism (SNP) detection method that has shown many advantages in point-of-care diagnostics and personalized medicine. While recently developed melting probes have demonstrated significantly improved discrimination of mismatched (mutant) alleles from matched (wild-type) alleles, no effort has been made to design a simple melting probe that can reliably distinguish all four SNP alleles in a single experiment. Such a new probe could facilitate the discovery of rare genetic mutations at lower cost. Here we demonstrate that a melting probe embedded with a single locked thymidine monomer (tL) can reliably differentiate the four SNP alleles by four distinct melting temperatures (termed the "4Tm probe"). This enhanced discriminatory power comes from the decreased melting temperature of the tL·C mismatched hybrid as compared to that of the t·C mismatched hybrid, while the melting temperatures of the tL-A, tL·G and tL·T hybrids are increased or remain unchanged as compared to those of their canonical counterparts. This phenomenon is observed not only in the HRM experiments but also in the molecular dynamics simulations.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Sara Y Cheng
- Department of Physics, College of Natural Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mariana F Llanos
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Darren M Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - David R Bell
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jeffrey T Petty
- Department of Chemistry, Department of Chemistry, Furman University , Greenville, South Carolina 29613, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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8
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Ogawa A, Tabuchi J, Doi Y, Takamatsu M. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract. Bioorg Med Chem Lett 2016; 26:3658-61. [PMID: 27289318 DOI: 10.1016/j.bmcl.2016.05.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Takamatsu
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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9
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Heo HY, Chung S, Kim YT, Kim DH, Seo TS. A valveless rotary microfluidic device for multiplex point mutation identification based on ligation-rolling circle amplification. Biosens Bioelectron 2016; 78:140-146. [DOI: 10.1016/j.bios.2015.11.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
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10
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Verga D, Welter M, Steck AL, Marx A. DNA polymerase-catalyzed incorporation of nucleotides modified with a G-quadruplex-derived DNAzyme. Chem Commun (Camb) 2016; 51:7379-81. [PMID: 25825211 DOI: 10.1039/c5cc01387a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We show that nucleotides which are modified with a G-quadruplex-derived DNAzyme are substrates for DNA polymerases. Based on this finding we developed a naked-eye detection system that allows the detection of single nucleotide variations in DNA.
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Affiliation(s)
- D Verga
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
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11
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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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12
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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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13
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Wu Y, Zhang DY, Yin P, Vollmer F. Ultraspecific and highly sensitive nucleic acid detection by integrating a DNA catalytic network with a label-free microcavity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2067-76. [PMID: 24585636 PMCID: PMC4096343 DOI: 10.1002/smll.201303558] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/15/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid detection with label-free biosensors circumvents costly fluorophore functionalization steps associated with conventional assays by utilizing transducers of impressive ultimate detection limits. Despite this technological prowess, molecular recognition at a surface limits the biosensors' sensitivity, specificity, and reusability. It is therefore imperative to integrate novel molecular approaches with existing label-free transducers to overcome those limitations. Here, we demonstrate this concept by integrating a DNA strand displacement circuit with a micron-scale whispering gallery mode (WGM) microsphere biosensor. The integrated biosensor exhibits at least 25-fold improved nucleic acid sensitivity, and sets a new record for label-free microcavity biosensors by detecting 80 pM (32 fmol) of a 22nt oligomer; this improvement results from the catalytic behavior of the circuit. Furthermore, the integrated sensor exhibits extremely high specificity; single nucleotide variants yield 40- to 100-fold lower signal. Finally, the same physical sensor was demonstrated to alternatingly detect 2 different nucleic acid sequences through 5 cycles of detection, showcasing both its reusability and its versatility.
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Affiliation(s)
- Yuqiang Wu
- Laboratory of Nanophotonics and Biosensing, Max Planck Insitute for the Science of Light, Erlangen 91058, Germany
| | - David Yu Zhang
- Department of Bioengineering Rice, University Houston, USA
| | - Peng Yin
- The Wyss Institute for Biologically Inspired Engineering and Department of Systems Biology, Harvard Medical School, Boston, USA
| | - Frank Vollmer
- Laboratory of Nanophotonics and Biosensing, Max Planck Insitute for the Science of Light, Erlangen 91058, Germany. Division of Biomedical Engineering, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
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14
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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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15
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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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16
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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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17
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Kholodar SA, Novopashina DS, Meschaninova MI, Venyaminova AG. Multipyrene tandem probes for point mutations detection in DNA. J Nucleic Acids 2013; 2013:860457. [PMID: 24455205 PMCID: PMC3886547 DOI: 10.1155/2013/860457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/11/2013] [Indexed: 01/26/2023] Open
Abstract
Here we report design, synthesis and characterization of highly sensitive, specific and stable in biological systems fluorescent probes for point mutation detection in DNA. The tandems of 3'- and 5'-mono- and bis-pyrene conjugated oligo(2'-O-methylribonucleotides), protected by 3'-"inverted" thymidine, were constructed and their potential as new instruments for genetic diagnostics was studied. Novel probes have been shown to exhibit an ability to form stable duplexes with DNA target due to the stabilizing effect of multiple pyrene units at the junction. The relationship between fluorescent properties of developed probes, the number of pyrene residues at the tandem junction, and the location of point mutation has been studied. On the basis of the data obtained, we have chosen the probes possessing the highest fluorescence intensity along with the best mismatch discrimination and deletion and insertion detection ability. Application of developed probes for detection of polymorphism C677T in MTHFR gene has been demonstrated on model systems.
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Affiliation(s)
- Svetlana A. Kholodar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
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18
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Abstract
Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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19
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20
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Weinberger M, Berndt F, Mahrwald R, Ernsting NP, Wagenknecht HA. Synthesis of 4-Aminophthalimide and 2,4-Diaminopyrimidine C-Nucleosides as Isosteric Fluorescent DNA Base Substitutes. J Org Chem 2013; 78:2589-99. [DOI: 10.1021/jo302768f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Weinberger
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Nikolaus P. Ernsting
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Hans-Achim Wagenknecht
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
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21
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Doi K, Toyokita Y, Akamatsu S, Kawano S. Reaction-diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces. Comput Methods Biomech Biomed Engin 2012; 17:661-77. [PMID: 23013145 DOI: 10.1080/10255842.2012.723701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Deoxyribonucleic acid (DNA) is a vital molecule for life since it contains genetic information. However, DNA has recently been reported to have unique properties that make it suitable for bionanoelectronic applications, such as the possibility of electrical conductivity and self-organisation. Self-assembled DNA network structures have been observed on several substrates, but the detailed self-assembly mechanism has yet to be determined. The present study investigates self-assembled structures of DNA both theoretically and experimentally. We developed a reaction-diffusion model and used it to investigate pattern formations observed by atomic force microscopy. The computational results qualitatively replicate the network patterns of DNA molecules based on a quantitative agreement with the surface size and timescale. The model can account for the effect of the DNA concentration on pattern formation. Furthermore, peculiar geometric patterns are simulated for mica and highly oriented pyrolytic graphite surfaces.
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Affiliation(s)
- Kentaro Doi
- a Department of Mechanical Science and Bioengineering , Graduate School of Engineering Science, Osaka University , Toyonaka , Osaka 560-8531 , Japan
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22
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Hövelmann F, Bethge L, Seitz O. Single labeled DNA FIT probes for avoiding false-positive signaling in the detection of DNA/RNA in qPCR or cell media. Chembiochem 2012; 13:2072-81. [PMID: 22936610 DOI: 10.1002/cbic.201200397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 12/13/2022]
Abstract
Oligonucleotide hybridization probes that fluoresce upon binding to complementary nucleic acid targets allow the real-time detection of DNA or RNA in homogeneous solution. The most commonly used probes rely on the distance-dependent interaction between a fluorophore and another label. Such dual-labeled oligonucleotides signal the change of the global conformation that accompanies duplex formation. However, undesired nonspecific binding events and/or probe degradation also lead to changes in the label-label distance and, thus, to ambiguities in fluorescence signaling. Herein, we introduce singly labeled DNA probes, "DNA FIT probes", that are designed to avoid false-positive signals. A thiazole orange (TO) intercalator dye serves as an artificial base in the DNA probe. The probes show little background because the attachment mode hinders 1) interactions of the "TO base" in cis with the disordered nucleobases of the single strand, and 2) intercalation of the "TO nucleotide" with double strands in trans. However, formation of the probe-target duplex enforces stacking and increases the fluorescence of the TO base. We explored open-chain and carbocyclic nucleotides. We show that the incorporation of the TO nucleotides has no effect on the thermal stability of the probe-target complexes. DNA and RNA targets provided up to 12-fold enhancements of the TO emission upon hybridization of DNA FIT probes. Experiments in cell media demonstrated that false-positive signaling was prevented when DNA FIT probes were used. Of note, DNA FIT probes tolerate a wide range of hybridization temperature; this enabled their application in quantitative polymerase chain reactions.
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Affiliation(s)
- Felix Hövelmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany
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23
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Takei F, Igarashi M, Oka Y, Koga Y, Nakatani K. Competitive allele-specific hairpin primer PCR for extremely high allele discrimination in typing of single nucleotide polymorphisms. Chembiochem 2012; 13:1409-12. [PMID: 22689446 DOI: 10.1002/cbic.201200266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Fumie Takei
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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24
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Jia X, Li J, Han L, Ren J, Yang X, Wang E. DNA-hosted copper nanoclusters for fluorescent identification of single nucleotide polymorphisms. ACS NANO 2012; 6:3311-7. [PMID: 22417109 DOI: 10.1021/nn3002455] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metal nanoclusters have received considerable interest due to their unique properties and potential applications in numerous fields. Particularly, newly emerging Cu nanoclusters offer excellent potential as functional biological probes. In this work, we for the first time report that the fluorescence of DNA-hosted Cu nanoclusters is very sensitive to base type located in the major groove. This intriguing finding provides a sensitive fluorimetric diagnostic of the mismatch type in a specific DNA sequence, which is difficult to achieve by traditional methods. Furthermore, the research results have shed some light on the luminescent mechanism of Cu nanoclusters. Owing to its high specificity and easy operation without rigorously controlled temperature and arduous probe DNA design, it is expected that the proposed procedure can provide a tool for early diagnosis and risk assessment of malignancy.
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Affiliation(s)
- Xiaofang Jia
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
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25
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Logvina NA, Yakubovskaya MG, Dolinnaya NG. Rapid photometric detection of thymine residues partially flipped out of double helix as a method for direct scanning of point mutations and apurinic DNA sites. BIOCHEMISTRY (MOSCOW) 2011; 76:245-52. [PMID: 21568858 DOI: 10.1134/s0006297911020118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A spectroscopic assay for detection of extrahelical thymine residues in DNA heteroduplexes under their modification by potassium permanganate has been developed. The assay is based on increase in absorbance at 420 nm due to accumulation of thymidine oxidation intermediates and soluble manganese dioxide. The analysis was carried out using a set of 19-bp DNA duplexes containing unpaired thymidines opposite tetrahydrofuranyl derivatives mimicking a widespread DNA damage (apurinic (AP) sites) and a library of 50-bp DNA duplexes containing all types of base mismatches in different surroundings. The relation between the selectivity of unpaired T oxidation and the thermal stability of DNA double helix was investigated. The method described here was shown to discriminate between DNA duplexes with one or two AP sites and to reveal thymine-containing mismatches and all noncanonical base pairs in AT-surroundings. Comparative results of CCM analysis and the rapid photometric assay for mismatch detection are demonstrated for the first time in the same model system. The chemical reactivity of target thymines was shown to correlate with local disturbance of double helix at the mismatch site. As the spectroscopic assay does not require the DNA cleavage reaction and gel electrophoresis, it can be easily automated and used for primary screening of somatic mutations.
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Affiliation(s)
- N A Logvina
- Chemical Faculty, Lomonosov Moscow State University, Russia
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26
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Gardarsson H, Kale AS, Sigurdsson ST. Structure-function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy. Chembiochem 2011; 12:567-75. [PMID: 21322103 DOI: 10.1002/cbic.201000478] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Indexed: 12/13/2022]
Abstract
The effects of the flanking sequence on the mismatch-detection capabilities of the fluorescent nucleoside phenoxazine (tC(O)) were examined in a systematic fashion, and compared to the previously reported fluorescent, phenoxazine-based nucleoside Ç(f) . We see some similarities for the two fluorescent nucleosides, for example, the emission intensity of the C-mismatched duplex is always the highest, and a three-peak pattern in the spectrum emerges when the fluorosides are base-paired with A. However, phenoxazine was only able to distinguish a mismatch from the fully base-paired duplex in 11 out of 16 flanking sequences, and was able to identify each of the mismatches in six of those sequences. Therefore, tC(O) shows poorer discrimination of mismatches than was previously reported for Ç(f) , which could be used to identify all base-pairing partners in all immediately flanking sequences, albeit in some cases by using mercuric ions to selectively quench the emission of the T-mismatched duplex. The mercuric titration might resolve the overlap of fluorescence curves of tC(O) in some flanking sequences, but not for 5'-d(CtC(O) G) and 5'-d(TtC(O) A) due to overlap of A-mismatch and G-match fluorescence curves. A pH titration was performed on Ç(f) , tC(O) and a N5-methylated derivative of tC(O) , which showed that the emergence of the three-peak pattern is associated with the de-protonation of N5 in the fluorosides. We also show that neither the α- nor β-anomer of the phenothiazine nucleoside (tC) was able to detect a mismatch in any of the flanking sequences examined.
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27
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Xie Y, Maxson T, Tor Y. Fluorescent nucleoside analogue displays enhanced emission upon pairing with guanine. Org Biomol Chem 2010; 8:5053-5. [PMID: 20862439 PMCID: PMC3032630 DOI: 10.1039/c0ob00413h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorescent nucleobase analogue, 7-aminoquinazoline-2,4-(1H,3H)-dione, is incorporated into a DNA oligonucleotide and senses mismatched pairing by displaying G-specific fluorescence enhancement.
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Affiliation(s)
- Yun Xie
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Tucker Maxson
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
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28
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Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments. J Mol Model 2010; 17:1457-65. [PMID: 20853125 DOI: 10.1007/s00894-010-0840-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 08/30/2010] [Indexed: 11/27/2022]
Abstract
DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-dCGTATATATA-3'. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.
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29
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Chien MP, Thompson MP, Gianneschi NC. DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes. Chem Commun (Camb) 2010; 47:167-9. [PMID: 20830351 DOI: 10.1039/c0cc02291h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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30
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Gardarsson H, Sigurdsson ST. Large flanking sequence effects in single nucleotide mismatch detection using fluorescent nucleoside C(f). Bioorg Med Chem 2010; 18:6121-6. [PMID: 20638291 DOI: 10.1016/j.bmc.2010.06.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/11/2010] [Accepted: 06/16/2010] [Indexed: 01/28/2023]
Abstract
The first systematic study of flanking sequence effects on mismatch detection by a fluorescent nucleotide is described, using fluoroside C(f). Although a high degree of variance was observed in fluorescence intensity of mismatched duplexes between different flanking sequences, C(f) was able to distinguish a mismatch from the fully base-paired duplex in 13 out of 16 sequences, and even identify each mismatch in 10 of those flanking sequences. For the flanking sequences where fluoroside C(f) did not unambiguously determine its base-pairing partner, the experimental conditions were varied in an attempt to facilitate mismatch identification. No beneficial effect on the relative fluorescence intensities was achieved by changing the temperature, adding organic co-solvents or potassium iodide. In contrast, mercuric ions selectively quenched the fluorescence intensity of the C(f).T mismatch, effectively resolving the overlap of all emission spectra and thereby facilitating identification of all base-pairing partners in any flanking sequence by C(f). This is the first time mercuric ions have been used to selectively quench the fluorescence of a single mismatch. A noticeable characteristic of C(f) is that, unlike most fluorosides, the fluorescence intensity of C(f) was not quenched to a discernable degree by a flanking G-C pair.
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31
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Bethge L, Singh I, Seitz O. Designed thiazole orange nucleotides for the synthesis of single labelled oligonucleotides that fluoresce upon matched hybridization. Org Biomol Chem 2010; 8:2439-48. [PMID: 20448904 DOI: 10.1039/c000697a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probe molecules that enable the detection of specific DNA sequences are used in diagnostic and basic research. Most methods rely on the specificity of hybridization reactions, which complicates the detection of single base mutations at low temperature. Significant efforts have been devoted to the development of oligonucleotides that allow discrimination of single base mutations at temperatures where both the match and the mismatch probe-target complexes coexist. Oligonucleotides that contain environmentally sensitive fluorescence dyes such as thiazole orange (TO) provide single nucleotide specific fluorescence. However, most previously reported dye-DNA conjugates showed only little if any difference between the fluorescence of the single and the double stranded state. Here, we introduce a TO-containing acyclic nucleotide, which is coupled during automated oligonucleotide synthesis and provides for the desired fluorescence-up properties. The study reveals the conjugation mode as the most important issue. We show a design that leads to low fluorescence of the unbound probe (background) yet permits TO to adopt fluorescent binding modes after the probe-target complex has formed. In these probes, TO replaces a canonical nucleobase. Of note, the fluorescence of the "TO-base" remains low when a base mismatch is positioned in immediate vicinity.
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Affiliation(s)
- Lucas Bethge
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, Berlin, D-12489, Germany
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32
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Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis. Biochimie 2010; 92:762-71. [PMID: 20171258 DOI: 10.1016/j.biochi.2010.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
Abstract
Systematic study of chemical reactivity of non-Watson-Crick base pairs depending on their type and microenvironment was performed on a model system that represents two sets of synthetic DNA duplexes with all types of mismatched and unmatched bases flanked by T.A or G.C pairs. Using comparative cleavage pattern analysis, we identified the main and additional target bases and performed quantitative study of the time course and efficacy of DNA modification caused by potassium permanganate or hydroxylamine. Potassium permanganate in combination with tetraethylammonium chloride was shown to induce DNA cleavage at all mismatched or bulged T residues, as well as at thymines of neighboring canonical pairs. Other mispaired (bulged) bases and thymine residues located on the second position from the mismatch site were not the targets for KMnO(4) attack. In contrast, hydroxylamine cleaved only heteroduplexes containing mismatched or unmatched C residues, and did not modify adjacent cytosines. However when G.C pairs flank bulged C residue, neighboring cytosines are also attacked by hydroxylamine due to defect migration. Chemical reactivity of target bases was shown to correlate strongly with the local disturbance of DNA double helix at mismatch or bulge site. With our model system, we were able to prove the absence of false-negative and false-positive results. Portion of heteroduplex reliably revealed in a mixture with corresponding homoduplex consists of 5% for bulge bases and "open" non-canonical pairs, and 10% for wobble base pairs giving minimal violations in DNA structure. This study provides a complete understanding of the principles of mutation detection methodology based on chemical cleavage of mismatches and clarifies the advantages and limitations of this approach in various biological and conformational studies of DNA.
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Affiliation(s)
- Marianna G Yakubovskaya
- Institute of Carcinogenesis, Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow 115478, Russia.
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34
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Jeng ES, Nelson JD, Prather KLJ, Strano MS. Detection of a single nucleotide polymorphism using single-walled carbon-nanotube near-infrared fluorescence. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:40-43. [PMID: 19911391 DOI: 10.1002/smll.200900944] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Esther S Jeng
- 77 Massachusetts Avenue, Building 66-566, Cambridge, MA 02139-4307, USA
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35
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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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36
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Cekan P, Sigurdsson ST. Identification of Single-Base Mismatches in Duplex DNA by EPR Spectroscopy. J Am Chem Soc 2009; 131:18054-6. [DOI: 10.1021/ja905623k] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pavol Cekan
- University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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37
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Takei F, Igarashi M, Hagihara M, Oka Y, Soya Y, Nakatani K. Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR. Angew Chem Int Ed Engl 2009; 48:7822-4. [DOI: 10.1002/anie.200902449] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Takei F, Igarashi M, Hagihara M, Oka Y, Soya Y, Nakatani K. Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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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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40
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Yoshimura Y, Ohtake T, Okada H, Ami T, Tsukaguchi T, Fujimoto K. SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2009; 10:034603. [PMID: 27877298 PMCID: PMC5090425 DOI: 10.1088/1468-6996/10/3/034603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 07/14/2009] [Accepted: 04/01/2009] [Indexed: 06/06/2023]
Abstract
We describe a simple and inexpensive single-nucleotide polymorphism (SNP) typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Tomoko Ohtake
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Hajime Okada
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takehiro Ami
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Tadashi Tsukaguchi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
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41
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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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42
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Berndl S, Wagenknecht HA. Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base. Angew Chem Int Ed Engl 2009; 48:2418-21. [PMID: 19229903 DOI: 10.1002/anie.200805981] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).
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Affiliation(s)
- Sina Berndl
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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43
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Takahashi T, Sakurai T, Hirata K, Hoshino H. Separation of oligonucleotides with single-base mutation by capillary electrophoresis using specific interaction of metal ion with nucleotide. Analyst 2009; 134:1299-301. [PMID: 19562193 DOI: 10.1039/b903440d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A unique tactic for the separation of single-base sequential isomers of oligomeric single-stranded DNA by a CE separation system employing the specific interaction of metal ion with nucleotide was demonstrated, enabling the separation of the mixture of a 12-mer oligonucleotide and its single-base mutants, as well as their positional isomers.
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Affiliation(s)
- Toru Takahashi
- Division of Environmentally Benign Systems, Graduate School of Environmental Studies, Tohoku University, 20 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
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44
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Fluoreszenz-Farbwechsel bei der DNA-Hybridisierung mit Thiazolorange als artifizieller DNA-Base. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805981] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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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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46
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Ong HC, Arambula JF, Rao Ramisetty S, Baranger AM, Zimmerman SC. Molecular recognition of a thymine bulge by a high affinity, deazaguanine-based hydrogen-bonding ligand. Chem Commun (Camb) 2009:668-70. [DOI: 10.1039/b817733n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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47
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Socher E, Bethge L, Knoll A, Jungnick N, Herrmann A, Seitz O. Low-noise stemless PNA beacons for sensitive DNA and RNA detection. Angew Chem Int Ed Engl 2008; 47:9555-9. [PMID: 18949813 DOI: 10.1002/anie.200803549] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elke Socher
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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48
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Seo YJ, Lee IJ, Kim BH. Homoadenine signalling system for SNP typing. MOLECULAR BIOSYSTEMS 2008; 5:235-7. [PMID: 19225612 DOI: 10.1039/b821543j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a homoadenine-based fluorescent probing system containing two pyrene-modified deoxyadenosine units for SNP typing in homoadenine and homothymine.
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Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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49
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Socher E, Bethge L, Knoll A, Jungnick N, Herrmann A, Seitz O. Stammlose PNA-Beacons für die empfindliche DNA- und RNA-Detektion mit geringem Hintergrundrauschen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803549] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bahr M, Gabelica V, Granzhan A, Teulade-Fichou MP, Weinhold E. Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators. Nucleic Acids Res 2008; 36:5000-12. [PMID: 18658249 PMCID: PMC2528167 DOI: 10.1093/nar/gkn392] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Binding of three macrocyclic bis-intercalators, derivatives of acridine and naphthalene, and two acyclic model compounds to mismatch-containing and matched duplex oligodeoxynucleotides was analyzed by thermal denaturation experiments, electrospray ionization mass spectrometry studies (ESI-MS) and fluorescent intercalator displacement (FID) titrations. The macrocyclic bis-intercalators bind to duplexes containing mismatched thymine bases with high selectivity over the fully matched ones, whereas the acyclic model compounds are much less selective and strongly bind to the matched DNA. Moreover, the results from thermal denaturation experiments are in very good agreement with the binding affinities obtained by ESI-MS and FID measurements. The FID results also demonstrate that the macrocyclic naphthalene derivative BisNP preferentially binds to pyrimidine–pyrimidine mismatches compared to all other possible base mismatches. This ligand also efficiently competes with a DNA enzyme (M.TaqI) for binding to a duplex with a TT-mismatch, as shown by competitive fluorescence titrations. Altogether, our results demonstrate that macrocyclic distance-constrained bis-intercalators are efficient and selective mismatch-binding ligands that can interfere with mismatch-binding enzymes.
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Affiliation(s)
- Matthias Bahr
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
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