1
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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2
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Huang G, Xiao Z, Zhen W, Fan Y, Zeng C, Li C, Liu S, Wong PK. Hydrogen production from natural organic matter via cascading oxic-anoxic photocatalytic processes: An energy recovering water purification technology. WATER RESEARCH 2020; 175:115684. [PMID: 32171099 DOI: 10.1016/j.watres.2020.115684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Photocatalysis provides a "green" strategy to produce the clean energy of H2. However, the realization of efficient H2 production is usually accomplished by the consumption of electron donors, which are costly energy carriers themselves. Here, we attempted to utilize the naturally abundant humic acid (HA), a representative natural organic matter (NOM), as the source of electron donor in a cascading oxic-anoxic photocatalytic system. Results showed that degradation of HA and remarkable H2 yield (1660.9 μmol g-1 h-1 at optimal condition) were obtained successively, whereas the anoxic photocatalytic treatment of pristine HA did not improve H2 yield but substantially eliminated the H2 production and HA degradation efficiency. These phenomena suggested the preoxidation process played a vital role in counteracting the detrimental effect of HA on photocatalytic H2 production. Electrochemical measurement indicated that the preoxidized HA harbored more redox-active moieties than the untreated HA and thus leading to a higher photo-induced charge carrier separation efficiency. A variety of advanced spectroscopic analyses revealed that the photocatalytic oxic pre-treatment resulted in breakdown of chemically inert, electron mediating and chromophoric aromatic macrostructure of HA to form smaller sized oxygenated organic intermediates. These intermediates were more nucleophilic than the pristine HA and acted as sacrificial reagent in the subsequent anoxic process for boosting H2 production. This study showcases an energy recovering water remediation process and paves the way for the design of novel photocatalytic technologies for environmental application.
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Affiliation(s)
- Guocheng Huang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Zhengtao Xiao
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Weiqian Zhen
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yaxin Fan
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Cuiping Zeng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Chuanhao Li
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shengwei Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Po Keung Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China; Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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3
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Tao L, Shi M. (CH 3) 2CuLi/Cu(OTf) 2 Mediated N- or O-Cyclization of Urea-Tethered Cyclobuta[ b]indolines. Org Lett 2019; 21:129-133. [PMID: 30571130 DOI: 10.1021/acs.orglett.8b03565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A (CH3)2CuLi/Cu(OTf)2 mediated N- or O-cyclization of urea-tethered cyclobuta[ b]indolines has been reported in this paper, giving a new synthetic protocol for the construction of pyrimido[1,6- a]indolone and cyclic imidate derivatives in moderate to good yields with a broad substrate scope under mild conditions. A plausible reaction mechanism has been also proposed on the basis of previous reports and the control experiments.
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Affiliation(s)
- Leyi Tao
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, University of Chinese Academy of Sciences , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Min Shi
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, University of Chinese Academy of Sciences , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
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4
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Kochman MA, Bil A, Miller RJD. Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP). J Phys Chem A 2017; 121:8267-8279. [PMID: 28984456 DOI: 10.1021/acs.jpca.7b08334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.
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Affiliation(s)
- Michał A Kochman
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL) , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Andrzej Bil
- Faculty of Chemistry, University of Wrocław , F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL) , Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Chemistry and Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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5
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Dell'Acqua M, Ronda L, Piano R, Pellegrino S, Clerici F, Rossi E, Mozzarelli A, Gelmi ML, Abbiati G. MediaChrom: Discovering a Class of Pyrimidoindolone-Based Polarity-Sensitive Dyes. J Org Chem 2015; 80:10939-54. [PMID: 26473465 DOI: 10.1021/acs.joc.5b02066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A small library of six polarity-sensitive fluorescent dyes, nicknamed MediaChrom, was prepared. This class of dyes is characterized by a pyrimidoindolone core fitted out with a conjugated push-pull system and a carboxy linker for a conceivable coupling with biomolecules. The optimized eight-step synthetic strategy involves a highly chemo- and regioselective gold-catalyzed cycloisomerization reaction. The photophysical properties of MediaChrom dyes have been evaluated in-depth. In particular, the MediaChrom bearing a diethylamino as an electron-donating group and a trifluoromethyl as an electron-withdrawing group displays the most interesting and advantageous spectroscopic features (e.g., absorption and emission in the visible range and a good quantum yield). Promising results in terms of sensitivity have been obtained in vitro on this dye as a membrane/lipophilic probe and as a peptide fluorescent label.
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Affiliation(s)
- Monica Dell'Acqua
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | | | | | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Francesca Clerici
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Elisabetta Rossi
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | | | - Maria Luisa Gelmi
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Giorgio Abbiati
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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6
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Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs. Nucleic Acids Res 2015; 43:5675-86. [PMID: 26013815 PMCID: PMC4499124 DOI: 10.1093/nar/gkv496] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/03/2015] [Indexed: 11/28/2022] Open
Abstract
A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2’-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2’-OMegC), 2’-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2’-OMegCs), dgC and 4S-(2-guanidoethyl)-4-thiothymidine (gsT). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine (DANac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing DANac, dgC, 2’-OMe-2-thiothymidine (2’-OMesT) and 2’-OMe-8-thioxoadenosine (2’-OMesA) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kenji Yamada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yu Ito
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kiichi Yoshimura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Koichiro Miyauchi
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
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7
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Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
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Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
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8
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Abstract
![]()
A family
of extended 5-modified-6-aza-uridines was obtained via
Suzuki coupling reactions with a common brominated precursor. Extending
the conjugated-6-aza-uridines with substituted aryl rings increases
the push–pull interactions yielding enhanced bathochromic shifts
and solvatochromism compared to the parent nucleosides. For example,
the methoxy substituted derivative 1d displays λmax abs around 375 nm, with visible emission maxima at
486 nm (Φ = 0.74) and 525 nm (Φ = 0.02) in dioxane and
water, respectively.
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Affiliation(s)
- Patrycja A Hopkins
- Department of Chemistry and Biochemistry, University of California , San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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9
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Zilbershtein-Shklanovsky L, Kafri P, Shav-Tal Y, Yavin E, Fischer B. Development of fluorescent double-strand probes labeled with 8-(p-CF3-cinnamyl)-adenosine for the detection of cyclin D1 breast cancer marker. Eur J Med Chem 2014; 79:77-88. [DOI: 10.1016/j.ejmech.2014.03.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/24/2014] [Accepted: 03/29/2014] [Indexed: 12/14/2022]
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10
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Sato K. [Development of selective detection method for 5-formyl-2'-deoxyuridine in DNA using a fluorogenic reagent]. YAKUGAKU ZASSHI 2013; 133:1041-53. [PMID: 24088348 DOI: 10.1248/yakushi.13-00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is important that various lesions in DNA were detected selectively and conveniently to know mechanisms of carcinogenicity and/or aging of cells. However, most detection methods of DNA lesion are complicated and take a long time for enzymatic hydrolysis and analysis by HPLC and/or mass spectrometry. This review shows the new concept for detection of DNA lesion by "fluorogenic reagent". Inspired by the unique bis-heteroaryl structure of luciferin and 5-heteroaryl-2'-deoxyuridine having good fluorescence properties, we designed and synthesized fluorogenic reagent 4,5-dimethoxy-2-aminothiophenol for a selective and convenient detection for 5-formyl-2'-deoxyuridine, which is generated in yields comparable to that of 2'-deoxy-8-oxoguanosine, in DNA. Generated 5-(5,6-dimethoxybenzothiazol-2-yl)-2'-deoxyuridine has a high quantum yield and larger Stokes shift in aqueous solution. This derivatization of 5-formyl-2'-deoxyuridine in oligodeoxynucleotide occurred quickly and quantitatively. The fluorogenic reagent was also revealed to detect 5-formyl-2'-deoxyuridine in γ-irradiated calf thymus DNA with irradiation dose dependent manner. Thus, our fluorogenic strategy enables to selective and convenient detection of lesion in DNA exposed to various forms of oxidative stress.
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Affiliation(s)
- Kousuke Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University
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11
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Gupta S, Koley D, Ravikumar K, Kundu B. Counter Ion Effect in Au/Ag-Catalyzed Chemoselective 6-endo-dig N- and O-Cyclizations of Enyne–Urea System: Diversity-Oriented Synthesis of Annulated Indoles. J Org Chem 2013; 78:8624-33. [DOI: 10.1021/jo4013332] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sahaj Gupta
- Medicinal and Process
Chemistry
Division, CSIR-Central Drug Research Institute, Lucknow 226001, India
| | - Dipankar Koley
- Medicinal and Process
Chemistry
Division, CSIR-Central Drug Research Institute, Lucknow 226001, India
- Academy of Scientific and Innovative Research, New Delhi 110001, India
| | - Krishnan Ravikumar
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Tarnaka,
Hyderabad 500607, India
| | - Bijoy Kundu
- Medicinal and Process
Chemistry
Division, CSIR-Central Drug Research Institute, Lucknow 226001, India
- Academy of Scientific and Innovative Research, New Delhi 110001, India
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12
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Seio K, Kanamori T, Tokugawa M, Ohzeki H, Masaki Y, Tsunoda H, Ohkubo A, Sekine M. Fluorescent properties of oligonucleotides doubly modified with an indole-fused cytosine analog and 2-aminopurine. Bioorg Med Chem 2013; 21:3197-201. [PMID: 23628471 DOI: 10.1016/j.bmc.2013.03.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 11/16/2022]
Abstract
Single- and double-stranded oligodeoxynucleotides (ODNs) incorporating both 2-aminopurine (2AP) and an indole-fused cytosine analog (PPI) were prepared and studied for their fluorescence properties. PPI and 2AP can be excited simultaneously by irradiation at 300 nm, with emission observed at 500 nm for PPI and 370 nm for 2AP. We demonstrated the utility of these properties in the dual fluorescence labeling of ODNs giving well-separated emission peaks. In addition, both of the fluorescence signals of a doubly modified ODN changed independently, reflecting the local duplex formation at the regions containing 2AP or PPI. Potential applications of this strategy for the dual fluorescence labeling of oligonucleotides with 2AP and PPI include monitoring local structure alterations of functional nucleic acids and the multiplex detection of biologically important nucleic acids.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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13
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Kanamori T, Masaki Y, Mizuta M, Tsunoda H, Ohkubo A, Sekine M, Seio K. DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes. Org Biomol Chem 2011; 10:1007-13. [PMID: 22146807 DOI: 10.1039/c1ob06411h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.
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14
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Hirose W, Sato K, Matsuda A. Fluorescence Properties of 5-(5,6-Dimethoxybenzothiazol-2-yl)-2′-deoxyuridine (dbtU) and Oligodeoxyribonucleotides Containing dbtU. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100818] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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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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16
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Preus S, Kilså K, Wilhelmsson LM, Albinsson B. Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family. Phys Chem Chem Phys 2010; 12:8881-92. [PMID: 20532361 DOI: 10.1039/c000625d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tC(O) and tC(nitro); all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tC(nitro) is an internal conversion of a different origin than the decay pathways of tC and tC(O). tC(nitro) is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S(0) potential energy surfaces of tC and tC(nitro) possess two global minima corresponding to geometries folded along the middle sulfur-nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311+G(2d,p) level. The ground-state potential energy surface of tC(O) is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tC(O) in various confined (biological) environments. The S(1) equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Wang ZJ, Yang JG, Yang F, Bao W. One-Pot Synthesis of Pyrimido[1,6-a]indol-1(2H)-one Derivatives by a Nucleophilic Addition/Cu-Catalyzed N-Arylation/Pd-Catalyzed C−H Activation Sequential Process. Org Lett 2010; 12:3034-7. [PMID: 20527777 DOI: 10.1021/ol101041e] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi-Jing Wang
- Department of Chemistry, Zhejiang University, Xixi Campus, Hangzhou 310028, P. R. China, and School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou 317000, P. R. China
| | - Jian-Guo Yang
- Department of Chemistry, Zhejiang University, Xixi Campus, Hangzhou 310028, P. R. China, and School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou 317000, P. R. China
| | - Fan Yang
- Department of Chemistry, Zhejiang University, Xixi Campus, Hangzhou 310028, P. R. China, and School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou 317000, P. R. China
| | - Weiliang Bao
- Department of Chemistry, Zhejiang University, Xixi Campus, Hangzhou 310028, P. R. China, and School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou 317000, P. R. China
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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Preus S, Börjesson K, Kilså K, Albinsson B, Wilhelmsson LM. Characterization of nucleobase analogue FRET acceptor tCnitro. J Phys Chem B 2010; 114:1050-6. [PMID: 20039634 DOI: 10.1021/jp909471b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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