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Aydemir M, Haykir G, Selvitopi H, Yildirim OC, Arslan ME, Abay B, Turksoy F. Exploring the potential of anthracene derivatives as fluorescence emitters for biomedical applications. J Mater Chem B 2023; 11:4287-4295. [PMID: 37144344 DOI: 10.1039/d3tb00449j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Two novel anthracene derivatives were synthesized, and detailed photo-physical and biological investigations were carried out using a variety of spectroscopy techniques. The effect of cyano (-CN) substitution was found to be effective to alter the charge population and frontier orbital energy levels via Density Functional Theory (DFT) calculations. Particularly, the introduction of styryl and triphenylamine groups attached to the anthracene core helped to increase the conjugation relative to the anthracene moiety. The results revealed that the molecules have intramolecular charge transfer (ICT) properties, occurring from the electron donating triphenylamine to the electron accepting anthracene moiety in solutions. In addition, the photo-physical properties are strongly cyano-dependent, where the cyano-substituted (E/Z)-(2-anthracen-9-yl)-3-(4'-(diphenylamino)biphenyl-4yl)acrylonitrile molecule showed stronger electron affinity due to the enhanced internal steric hindrance compared to the (E)-4'-(2-(anthracen-9-yl)vinyl)-N,N-diphenylbiphenyl-4-amine molecule, which resulted in a lower photoluminescence quantum yield (PLQY) value and a shorter lifetime in the molecule. Besides, the Molecular Docking approach was used to investigate possible cellular staining targets to confirm cellular imaging potential of the compounds. Moreover, cell viability analyses put forth that synthesized molecules do not exhibit significant cytotoxicity under 125 μg mL-1 concentration on the human dermal fibroblast cell line (HDFa). Moreover, both of the compounds showed great potential in cellular imaging of HDFa cells. Compared to Hoechst 33258, a common fluorescent dye used for nuclear staining, the compounds showed higher magnification of cellular structure imaging capacity by staining the whole cellular compartment. On the other hand, bacterial staining showed that ethidium bromide has higher resolution in monitoring Staphylococcus aureus (S. aureus) cell culture.
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Affiliation(s)
- Murat Aydemir
- Department of Fundamental Sciences, Faculty of Science, Erzurum Technical University, Erzurum, Turkey.
| | - Gulcin Haykir
- TUBITAK Marmara Research Centre, Institute of Chemical Technology, p.b.21,41470, Gebze, Turkey.
| | - Harun Selvitopi
- Department of Mathematics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Ozge Caglar Yildirim
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Mehmet Enes Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Bahattin Abay
- Department of Physics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Figen Turksoy
- TUBITAK Marmara Research Centre, Institute of Chemical Technology, p.b.21,41470, Gebze, Turkey.
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2
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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3
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Lee SY, Hong SW, Yeo H, Hwang GT. The linkers in fluorene-labeled 2′-deoxyuridines affect fluorescence discriminating phenomena upon duplex formation. RSC Adv 2020; 10:18853-18859. [PMID: 35518342 PMCID: PMC9053879 DOI: 10.1039/d0ra01651a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 11/29/2022] Open
Abstract
Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers—UF (without linker), UFL (with ethynyl linker), and UDF (with diethynyl linker)—have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the fluorescence emission properties upon duplex formation with fully matched and single-base-mismatched targets. Here, we describe the influence of the linkers on the emission behavior, the intramolecular electron transfer between the fluorene moiety and the uracil base after photoexcitation, and the structural stability upon duplex formation. The probe containing the UFL residue (with an ethynyl linker) and cytosine residues as flanking bases exhibited the greatest fluorescence turn-on selective behavior toward the perfectly matched target. Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the emission properties upon duplex formations.![]()
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Affiliation(s)
- So Young Lee
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Hyeonuk Yeo
- Department of Chemistry Education
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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4
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Yang R, Deng S, Dong XY, Song X, Cai H, Bai J, Xiao Q. Metal-free synthesis of 1, N6-ethenoadenines from N6-propargyl-adenines via NIS mediated radical cascade reaction. RSC Adv 2019; 9:38897-38901. [PMID: 35540232 PMCID: PMC9075968 DOI: 10.1039/c9ra09198j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
In the present paper, an efficient approach for the construction of 1,N6-ethenoadenines from conveniently prepared N6-propargyl-adenines is developed. This reaction merges N-iodosuccinimide radical initiation and aerobic aminooxygenation in dioxane. This mild, 5-exo-dig, and metal-free cascade reaction could be applied to a wide substrate scope to provide 1,N6-ethenoadenines in moderate to good yields. The reaction mechanism was proposed and tested using radical inhibitor (butylated hydroxytoluene) and isotopic labelling (18O2) experiments. An efficient approach for the construction of 1,N6-ethenoadenines is developed through the metal-free mediated radical cascade cyclization of conveniently prepared N6-propargyl-adenines.![]()
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Affiliation(s)
- Ruchun Yang
- Institute of Chemistry
- Nanchang University
- Nanchang 330031
- China
- Institute of Organic Chemistry
| | - Si Deng
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Xiang-you Dong
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Xianrong Song
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Hu Cai
- Institute of Chemistry
- Nanchang University
- Nanchang 330031
- China
| | - Jiang Bai
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Qiang Xiao
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
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5
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Kamoto S, Hyuga M, Kato T. Fluorescence detection of single-nucleotide differences using aptamer-forming binary DNA probes. Analyst 2018; 141:6087-6092. [PMID: 27540601 DOI: 10.1039/c6an00912c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a simple method for fluorescence detection of single-nucleotide alterations in a long target DNA, which is based on the formation of a three-way-junction-structured cholic-acid-binding DNA aptamer by the hybridization of the target with binary DNA probes. The new method was successfully exploited for SNP genotyping of human CYP2C19 gene.
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Affiliation(s)
- Saori Kamoto
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Masumi Hyuga
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Teru Kato
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
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6
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Schwarze T, Riemer J, Holdt HJ. A Ratiometric Fluorescent Probe for K + in Water Based on a Phenylaza-18-Crown-6 Lariat Ether. Chemistry 2018; 24:10116-10121. [PMID: 29863303 DOI: 10.1002/chem.201802306] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 01/24/2023]
Abstract
This work presents two molecular fluorescent probes 1 and 2 for the selective determination of physiologically relevant K+ levels in water based on a highly K+ /Na+ selective building block, the o-(2-methoxyethoxy)phenylaza-18-crown-6 lariat ether unit. Fluorescent probe 1 showed a high K+ -induced fluorescence enhancement (FE) by a factor of 7.7 of the anthracenic emission and a dissociation constant (Kd ) value of 38 mm in water. Further, for 2+K+ , we observed a dual emission behavior at 405 and 505 nm. K+ increases the fluorescence intensity of 2 at 405 nm by a factor of approximately 4.6 and K+ decreases the fluorescence intensity at 505 nm by a factor of about 4.8. Fluorescent probe 2+K+ exhibited a Kd value of approximately 8 mm in Na+ -free solutions and in combined K+ /Na+ solution a similar Kd value of about 9 mm was found, reflecting the high K+ /Na+ selectivity of 2 in water. Therefore, 2 is a promising fluorescent tool to measure ratiometrically and selectively physiologically relevant K+ levels.
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Affiliation(s)
- Thomas Schwarze
- Institut für Chemie, Anorganische Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Golm, Germany
| | - Janine Riemer
- Institut für Chemie, Anorganische Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Golm, Germany
| | - Hans-Jürgen Holdt
- Institut für Chemie, Anorganische Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Golm, Germany
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7
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Lee KF, Bai W, Sung HHY, Williams ID, Lin Z, Jia G. Rhenium-Promoted C-C Bond-Cleavage Reactions of Internal Propargyl Alcohols. Chemistry 2018; 24:9760-9764. [PMID: 29878488 DOI: 10.1002/chem.201801448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 12/14/2022]
Abstract
The first examples of C-C bond cleavage reactions of internal propargyl alcohols to give vinylidene complexes are described. Treatment of [Re(dppm)3 ]I with RC≡CC(OH)R'R'' (R=aryl, alkyl; C(OH)R'R''=C(OH)Ph2, C(OH)Me2 , C(OH)HPh, C(OH)H2 ) produced the vinylidene complexes ReI(=C=CHR)(dppm)2 with the elimination of C(O)R'R''. Computational studies support that the reactions proceed through a β-alkynyl elimination of alkoxide intermediates Re{OC(R')(R'')C≡CR}(dppm)2 .
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Affiliation(s)
- Kui Fun Lee
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei Bai
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Herman H Y Sung
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ian D Williams
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhenyang Lin
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Guochen Jia
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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8
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Xie P, Yuan N, Li S, Ouyang Y, Zhu Y, Liang H. Synthesis and properties of blue luminescent bipolar materials constructed with carbazole and anthracene units with 4-cyanophenyl substitute at the 9-position of the carbazole unit. LUMINESCENCE 2018; 33:604-610. [PMID: 29377545 DOI: 10.1002/bio.3452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 11/11/2022]
Abstract
With carbazole and p-cyanobromobenzene as raw materials, 4-(3,6-di (anthracen-9-yl)-9H-carbazol-9-yl)benzonitrile (DACB) and 4-(3,6-bis(anthracene -9-ylethynyl)-9H-carbazol-9-yl)benzonitrile (BACB) were synthesized through the Suzuki coupling reaction and the Sonogashira coupling reaction, respectively. These structures were characterized using 1 H nuclear magnetic resonance (NMR), elemental analysis and mass spectrometry. Their thermal properties, ultraviolet-visible (UV-vis) absorption, fluorescence emission, fluorescence quantum yields and electrochemical properties were also investigated systematically. In addition, a electroluminescence (EL) device was made with BACB as the emitting layer and performance of the EL device was studied. Results showed that: (1) the temperature points with 5% and 10% of DACB weight loss were 443°C and 461°C, respectively, and were 475°C and 506°C with BACB weight loss of 5% and 10%, respectively. When the temperature was 50-300°C, no significantly thermal transition was observed which suggested that they had excellent thermal stability. (2) DACB and BACB had single emission peaks at 415 nm, and 479 nm with fluorescence quantum yields of 0.61 and 0.87, respectively, indicating that both compounds could emit strong blue light. (3) According to electrochemical measurement on BACB and DACB, their gaps were 3.07 eV and 2.76 eV, respectively, which further showed that these two compounds were very stable and acted as efficient blue light materials. (4) The turn-on voltage of the device was 5 V, and the device emitted dark blue light with Commission Internationale de L'Eclairage (CIE) coordinates of (0.157, 0.079).
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Affiliation(s)
- Pengbo Xie
- Petrochemical Engineering Department of Guangzhou Institute of Technology, Guangzhou, China
| | - Ningning Yuan
- Petrochemical Engineering Department of Guangzhou Institute of Technology, Guangzhou, China
| | - Shanji Li
- Petrochemical Engineering Department of Guangzhou Institute of Technology, Guangzhou, China
| | - Ying Ouyang
- Petrochemical Engineering Department of Guangzhou Institute of Technology, Guangzhou, China
| | - Yongju Zhu
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, China
| | - Hui Liang
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, China
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9
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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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10
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Szyszkowska M, Czaplewski C, Wiczk W. Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Chistov AA, Ivanov NM, Kutyakov SV, Ustinov AV, Glybin AV, Streshnev PP, Mikhura IV, Korshun VA. Fluorescent nucleosides with an elongated rigid linker: attaching perylene to a nucleobase via a one-pot desilylation/Sonogashira reaction. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Imincan G, Pei F, Yu L, Jin H, Zhang L, Yang X, Zhang L, Tang X. Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA. Anal Chem 2016; 88:4448-55. [PMID: 27021236 DOI: 10.1021/acs.analchem.6b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (U(p)) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes successfully distinguished target RNA from single-mutated RNA analyte during an in vitro assay of RNA synthesis.
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Affiliation(s)
- Gülnur Imincan
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Fen Pei
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Xiaoda Yang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
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13
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Morihiro K, Hasegawa O, Mori S, Tsunoda S, Obika S. C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability. Org Biomol Chem 2016; 13:5209-14. [PMID: 25853508 DOI: 10.1039/c5ob00477b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.
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Affiliation(s)
- K Morihiro
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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14
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Byrne S, Mullen KM. Sensing anions on surfaces: tethering triazolium based anion receptors to polymer resins. RSC Adv 2016. [DOI: 10.1039/c6ra03569h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Herein we report the development of a new series of surface bound triazolium based anion sensors. Differences in the chemical reactivity and anion binding properties were observed; highlighting the need for good surface characterisation techniques such as HR MAS NMR.
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Affiliation(s)
- S. Byrne
- School of Chemistry, Physics and Mechanical Engineering
- Queensland University of Technology
- Brisbane
- Australia
| | - K. M. Mullen
- School of Chemistry, Physics and Mechanical Engineering
- Queensland University of Technology
- Brisbane
- Australia
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15
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Wierzbicka M, Bylińska I, Czaplewski C, Wiczk W. Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives. RSC Adv 2015. [DOI: 10.1039/c5ra01077b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A series of symmetrically substituted diphenylacetylene derivatives possessing electron-donating or electron-accepting character were prepared and studied with respect to their spectral and photophysical properties.
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16
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Barthes NPF, Karpenko IA, Dziuba D, Spadafora M, Auffret J, Demchenko AP, Mély Y, Benhida R, Michel BY, Burger A. Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues. RSC Adv 2015. [DOI: 10.1039/c5ra02709h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.
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Affiliation(s)
- N. P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - I. A. Karpenko
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - D. Dziuba
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - M. Spadafora
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - J. Auffret
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | | | - Y. Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - R. Benhida
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - B. Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - A. Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
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17
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Park S, Otomo H, Zheng L, Sugiyama H. Highly emissive deoxyguanosine analogue capable of direct visualization of B-Z transition. Chem Commun (Camb) 2014; 50:1573-5. [PMID: 24382561 DOI: 10.1039/c3cc48297a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside, (th)dG, was synthesized and incorporated readily into oligonucleotides as a versatile fluorescent guanine analogue. We demonstrate that (th)dG enables the visual detection of Z-DNA successfully based on different π-stacking of B- and Z-DNA.
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Affiliation(s)
- Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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18
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Kovaliov M, Wachtel C, Yavin E, Fischer B. Synthesis and evaluation of a photoresponsive quencher for fluorescent hybridization probes. Org Biomol Chem 2014; 12:7844-58. [PMID: 25177827 DOI: 10.1039/c4ob01185f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nowadays, most nucleic acid detections using fluorescent probes rely on quenching of fluorescence by energy transfer from one fluorophore to another or to a non-fluorescent molecule (quencher). The most widely used quencher in fluorescent probes is 4-((4-(dimethylamino)phenyl)azo)benzoic acid (DABCYL). We targeted a nucleoside-DABCYL analogue which could be incorporated anywhere in an oligonucleotide sequence and in any number, and used as a quencher in different hybridization sensitive probes. Specifically, we introduced a 5-(4-((dimethylamino)phenyl)azo)benzene)-2'-deoxy-uridine (dU(DAB)) quencher. The photoisomerization and dU(DAB)'s ability to quench fluorescein emission have been investigated. We incorporated dU(DAB) into a series of oligonucleotide (ON) probes including strand displacement probes, labeled with both fluorescein (FAM) and dU(DAB), and TaqMan probes bearing one or two dU(DAB) and a FAM fluorophore. We used these probes for the detection of a DNA target in real-time PCR (RT-PCR). All probes showed amplification of targeted DNA. A dU(DAB) modified TaqMan RT-PCR probe was more efficient as compared to a DABCYL bearing probe (93% vs. 87%, respectively). Furthermore, dU(DAB) had a stabilizing effect on the duplex, causing an increase in Tm up to 11 °C. In addition we showed the photoisomerisation of the azobenzene moiety of dU(DAB) and the dU(DAB) triply-labeled oligonucleotide upon irradiation. These findings suggest that dU(DAB) modified probes are promising probes for gene quantification in real-time PCR detection and as photoswitchable devices.
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Affiliation(s)
- Marina Kovaliov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
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19
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Tanpure AA, Srivatsan SG. Synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue based on the Lucifer chromophore. Chembiochem 2014; 15:1309-16. [PMID: 24861713 DOI: 10.1002/cbic.201402052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/10/2022]
Abstract
The majority of fluorescent nucleoside analogues used in nucleic acid studies have excitation maxima in the UV region and show very low fluorescence within oligonucleotides (ONs); hence, they cannot be utilised with certain fluorescence methods and for cell-based analysis. Here, we describe the synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue, derived by attaching a Lucifer chromophore (1,8-naphthalimide core) at the 5-position of uracil. The emissive nucleoside displays excitation and emission maxima in the visible region and exhibits high quantum yield. Importantly, when incorporated into ON duplexes it retains appreciable fluorescence efficiency and is sensitive to the neighbouring base environment. Notably, the nucleoside signals the presence of purine repeats in ON duplexes with an enhancement in fluorescence intensity, a property rarely displayed by other nucleoside analogues.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008 (India)
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20
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Mori S, Morihiro K, Obika S. C5-azobenzene-substituted 2'-deoxyuridine-containing oligodeoxynucleotides for photo-switching hybridization. Molecules 2014; 19:5109-18. [PMID: 24759071 PMCID: PMC6271114 DOI: 10.3390/molecules19045109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/17/2022] Open
Abstract
A new photoisomeric nucleoside dUAz bearing an azobenzene group at the C5-position of 2'-deoxyuridine was designed and synthesized. Photoisomerization of dUAz in oligodeoxynucleotides can be achieved rapidly and selectively with 365 nm (forward) and 450 nm (backward) irradiation. Thermal denaturation experiments revealed that dUAz stabilized the duplex in the cis-form and destabilized it in the trans-form with mismatch discrimination ability comparable to thymidine. These results indicate that dUAz could be a powerful material for reversibly manipulating nucleic acid hybridization with spatiotemporal control.
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Affiliation(s)
- Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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21
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Dziuba D, Karpenko IA, Barthes NPF, Michel BY, Klymchenko AS, Benhida R, Demchenko AP, Mély Y, Burger A. Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual-Band Ratiometric Response Based on 3-Hydroxychromone. Chemistry 2014; 20:1998-2009. [DOI: 10.1002/chem.201303399] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/24/2022]
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22
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Pawar MG, Srivatsan SG. Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model cell-like compartment. J Phys Chem B 2013; 117:14273-82. [PMID: 24161106 DOI: 10.1021/jp4071168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of fluorescent nucleoside analogue probes that have been used in the in vitro study of nucleic acids are not suitable for cell-based biophysical assays because they exhibit excitation maxima in the UV region and low quantum yields within oligonucleotides. Therefore, we propose that the photophysical characterization of oligonucleotides labeled with a fluorescent nucleoside analogue in reverse micelles (RM), which are good biological membrane models and UV-transparent, could provide an alternative approach to studying the properties of nucleic acids in a cell-like confined environment. In this context, we describe the photophysical properties of an environment-sensitive fluorescent uridine analogue (1), based on the 5-(benzo[b]thiophen-2-yl)pyrimidine core, in micelles and RM. The emissive nucleoside, which is polarity- and viscosity-sensitive, reports the environment of the surfactant assemblies via changes in its fluorescence properties. The nucleoside analogue, incorporated into an RNA oligonucleotide and hybridized to its complementary DNA and RNA oligonucleotides, exhibits a significantly higher fluorescence intensity, lifetime, and anisotropy in RM than in aqueous buffer, which is consistent with the environment of RM. Collectively, our results demonstrate that nucleoside 1 could be utilized as a fluorescent label to study the function of nucleic acids in a model cellular milieu.
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Affiliation(s)
- Maroti G Pawar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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23
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Gutiérrez-Arzaluz L, Guarin CA, Rodríguez-Córdoba W, Peon J. Dynamics of the Formation of a Charge Transfer State in 1,2-Bis(9-anthryl)acetylene in Polar Solvents: Symmetry Reduction with the Participation of an Intramolecular Torsional Coordinate. J Phys Chem B 2013; 117:12175-83. [DOI: 10.1021/jp4038705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, México, 04510, D.F., México
| | - Cesar A. Guarin
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, México, 04510, D.F., México
| | - William Rodríguez-Córdoba
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, México, 04510, D.F., México
- Escuela
de Física, Universidad Nacional de Colombia, Sede Medellín, A.A. 3840, Medellín, Colombia
| | - Jorge Peon
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, México, 04510, D.F., México
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24
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Ast S, Fischer T, Müller H, Mickler W, Schwichtenberg M, Rurack K, Holdt HJ. Integration of the 1,2,3-triazole "click" motif as a potent signalling element in metal ion responsive fluorescent probes. Chemistry 2013; 19:2990-3005. [PMID: 23319382 DOI: 10.1002/chem.201201575] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Indexed: 12/28/2022]
Abstract
In a systematic approach we synthesized a new series of fluorescent probes incorporating donor-acceptor (D-A) substituted 1,2,3-triazoles as conjugative π-linkers between the alkali metal ion receptor N-phenylaza-[18]crown-6 and different fluorophoric groups with different electron-acceptor properties (4-naphthalimide, meso-phenyl-BODIPY and 9-anthracene) and investigated their performance in organic and aqueous environments (physiological conditions). In the charge-transfer (CT) type probes 1, 2 and 7, the fluorescence is almost completely quenched by intramolecular CT (ICT) processes involving charge-separated states. In the presence of Na(+) and K(+) ICT is interrupted, which resulted in a lighting-up of the fluorescence in acetonitrile. Among the investigated fluoroionophores, compound 7, which contains a 9-anthracenyl moiety as the electron-accepting fluorophore, is the only probe which retains light-up features in water and works as a highly K(+)/Na(+)-selective probe under simulated physiological conditions. Virtually decoupled BODIPY-based 6 and photoinduced electron transfer (PET) type probes 3-5, where the 10-substituted anthracen-9-yl fluorophores are connected to the 1,2,3-triazole through a methylene spacer, show strong ion-induced fluorescence enhancement in acetonitrile, but not under physiological conditions. Electrochemical studies and theoretical calculations were used to assess and support the underlying mechanisms for the new ICT and PET 1,2,3-triazole fluoroionophores.
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Affiliation(s)
- Sandra Ast
- Institut für Chemie, Anorganische Chemie, Universität Potsdam, Karl-Liebknecht Str. 24-25, 14467 Golm, Germany
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25
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Madsen AS, Jørgensen AS, Jensen TB, Wengel J. Large scale synthesis of 2'-amino-LNA thymine and 5-methylcytosine nucleosides. J Org Chem 2012; 77:10718-28. [PMID: 23145501 DOI: 10.1021/jo302036h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymine intermediate 17 has been synthesized on a multigram scale (50 g, 70 mmol) from starting sugar 1 in 15 steps in an overall yield of 73%, with only 5 purification steps. The key thymine intermediate 18 was obtained from 17 in a single step in 96% yield, whereas the key 5-methylcytosine intermediate 20 was obtained from 17 in 2 steps in 58% yield. This highly efficient large scale route necessitates only 2 and 3 novel steps to obtain N2'-functionalized thymine and 5-methylcytosine amino-LNA phosphoramidites from these key intermediates, respectively.
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Affiliation(s)
- Andreas Stahl Madsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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26
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Riedl J, Ménová P, Pohl R, Orság P, Fojta M, Hocek M. GFP-like fluorophores as DNA labels for studying DNA-protein interactions. J Org Chem 2012; 77:8287-93. [PMID: 22935023 DOI: 10.1021/jo301684b] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
GFP-like 3,5-difluoro-4-hydroxybenzylideneimidazolinone (FBI) and 3,5-bis(methoxy)-4-hydroxy-benzylideneimidazolinone (MBI) labels were attached to dCTP through a propargyl linker, and the resulting labeled nucleotides (dC(MBI)TP and dC(FBI)TP) were used for a facile enzymatic synthesis of oligonucleotide or DNA probes by polymerase-catalyzed primer extension. The MBI/FBI-labeled DNA probes exerted low fluorescence that was increased 2-3.2 times upon binding of a protein. The concept was demonstrated on sequence-specific binding of p53 to dsDNA and on nonspecific binding of single strand binding protein to an oligonucleotide. The FBI label was also used for a time-resolved experiment monitoring a single-nucleotide incorporation followed by primer extension by Vent(exo-) polymerase.
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Affiliation(s)
- Jan Riedl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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27
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Sari O, Roy V, Balzarini J, Snoeck R, Andrei G, Agrofoglio LA. Synthesis and antiviral evaluation of C5-substituted-(1,3-diyne)-2'-deoxyuridines. Eur J Med Chem 2012; 53:220-8. [PMID: 22578783 DOI: 10.1016/j.ejmech.2012.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/19/2012] [Accepted: 04/03/2012] [Indexed: 11/17/2022]
Abstract
Starting from acetylated 5-ethynyl-2'-deoxyuridine (3), 14 hitherto unknown C5-substituted-(1,3-diyne)-2'-deoxyuridines (with cyclopropyl, hydroxymethyl, methylcyclopentane, p-(substituted)phenyl and disubstituted-phenyl substituents) have been synthesized via a nickel-copper catalyzed C-H activation between two terminal alkynes, in yields ranging from 19% to 67%. Their antiviral activities were measured against a large number of DNA and RNA viruses including herpes simplex virus type 1 and type 2, varicella-zoster virus, human cytomegalovirus and vaccinia virus. The 5-[4-(4-trifluoromethoxyphenyl)buta-1,3-diynyl]-2'-deoxyuridine (26) is the most potent inhibitor of this series against VZV with an EC(50) of ~1 μM and a CC(50) of 55 μM. Their cytostatic activities were determined against murine leukemia cells, human T-lymphocyte cells and cervix carcinoma cells. Compounds were also evaluated on a wide panel of RNA viruses, including influenza virus A (H1N1 and H3N2) and B in MDCK cell cultures, parainfluenza-3 virus, reovirus-1, Sindbis virus and Punta Toro virus in Vero cell cultures and vesicular stomatitis, coxsackie B4 and respiratory syncytial virus in HeLa cell cultures and against human immunodeficiency virus type 1 and 2 in CEM cell cultures, with no specific antiviral effect. This class of compounds could be of further interest for lead optimization as anti-infectious (i.e. herpetic) agents.
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Affiliation(s)
- Ozkan Sari
- Institut de Chimie Organique et Analytique, UMR 7311 CNRS, Université d'Orléans, UFR Science-rue de chartres, 45067 Orléans, France
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28
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Coppock MB, Williams ME. Nucleic Acid Mimetics. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Riedl J, Pohl R, Ernsting NP, Orság P, Fojta M, Hocek M. Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions. Chem Sci 2012. [DOI: 10.1039/c2sc20404e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2′-deoxyuridines. Bioorg Med Chem 2012; 20:480-6. [DOI: 10.1016/j.bmc.2011.10.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/10/2011] [Accepted: 10/14/2011] [Indexed: 11/19/2022]
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31
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Riedl J, Pohl R, Rulíšek L, Hocek M. Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels. J Org Chem 2011; 77:1026-44. [PMID: 22148188 DOI: 10.1021/jo202321g] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.
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Affiliation(s)
- Jan Riedl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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32
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Tanaka M, Kozakai R, Saito Y, Saito I. Stabilization of DNA duplex by 2-substituted adenine as a minor groove modifier. Bioorg Med Chem Lett 2011; 21:7021-4. [DOI: 10.1016/j.bmcl.2011.09.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
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33
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Daniele MA, Bandera YP, Foulger SH. Manipulation of Förster energy transfer of coupled fluorophores through biotransformation by Pseudomonas resinovorans CA10. Photochem Photobiol 2011; 88:129-34. [PMID: 22044050 DOI: 10.1111/j.1751-1097.2011.01023.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An alkyne-terminated anthracene and azide-terminated carbazole were joined through a copper-catalyzed cycloaddition to form a joined donor/acceptor pair. The photonic pair exhibited energy transfer when excited at the peak absorbance of carbazole and fluoresced with an anthracene spectral response. The fluorescent behavior was confirmed as Förster energy transfer (FRET). The lysate of Pseudomonas resinovorans CA10, a member of a predominant group of soil microorganisms that can metabolize a host of substrates, was employed to degrade the pair and alter the luminance spectral characteristics. The FRET was diminished and the corresponding, individual fluorescence of carbazole and anthracene returned. This general approach may find applications in single-cell metabolic studies and bioactivity assays.
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Affiliation(s)
- Michael A Daniele
- Center for Optical Materials Science and Engineering Technologies, School of Materials Science and Engineering, Clemson University, Clemson, SC, USA
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34
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Boonlua C, Vilaivan C, Wagenknecht HA, Vilaivan T. 5-(Pyren-1-yl)uracil as a base-discriminating fluorescent nucleobase in pyrrolidinyl peptide nucleic acids. Chem Asian J 2011; 6:3251-9. [PMID: 21976408 DOI: 10.1002/asia.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 12/15/2022]
Abstract
A pyrene-labeled uridine (U(Py)) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U(Py) base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T(m)) experiments. The fluorescence of the U(Py)-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7-41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U(Py) and dA, making the U(Py)-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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35
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Khan TK, Ravikanth M. Synthesis of covalently linked boron–dipyrromethene–chromophore conjugates using 3-bromo boron–dipyrromethene as a key precursor. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.05.089] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Duprey JLH, Bassani DM, Hyde EI, Ludwig C, Rodger A, Vyle JS, Wilkie J, Zhao ZY, Tucker JH. Anthracene-modified oligonucleotides as fluorescent DNA mismatch sensors: discrimination between various base-pair mismatches. Supramol Chem 2011. [DOI: 10.1080/10610278.2010.523117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Dario M. Bassani
- b Institut des Sciences Moléculaires, CNRS UMR 5255, Université Bordeaux 1 , 33405, Talence, France
| | - Eva I. Hyde
- c School of Biosciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- d Henry Wellcome Building for Biomolecular NMR Spectroscopy , School of Cancer Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK
| | - Alison Rodger
- e Chemistry Department , University of Warwick , Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Joseph S. Vyle
- f School of Chemistry and Chemical Engineering, Queen's University (QUB) , David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - John Wilkie
- a School of Chemistry , University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK
| | - Zheng-Yun Zhao
- a School of Chemistry , University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK
| | - James H.R. Tucker
- a School of Chemistry , University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK
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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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38
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Storr TE, Strohmeier JA, Baumann CG, Fairlamb IJS. A sequential direct arylation/Suzuki-Miyaura cross-coupling transformation of unprotected 2'-deoxyadenosine affords a novel class of fluorescent analogues. Chem Commun (Camb) 2010; 46:6470-2. [PMID: 20714566 DOI: 10.1039/c0cc02043e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Novel rigid 8-biaryl-2'-deoxyadenosines with tuneable fluorescent properties can be accessed by an efficient sequential catalytic Pd(0)-coupling approach.
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Affiliation(s)
- Thomas E Storr
- Department of Chemistry, University of York, York, YO10 5DD, UK
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39
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 665] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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40
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Tanaka M, Elias B, Barton JK. DNA-mediated electron transfer in naphthalene-modified oligonucleotides. J Org Chem 2010; 75:2423-8. [PMID: 20297784 PMCID: PMC2879047 DOI: 10.1021/jo1000862] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Naphthalene-modified oligonucleotides have been synthesized and characterized with respect to electron transfer chemistry. Using the Sonogashira coupling reaction, naphthalene can be covalently anchored onto a modified uridine through an ethynyl linkage. This tethering allows for effective electronic coupling with the DNA bases, resulting in a significant red shift of the absorption bands of the naphthalenic chromophore. Modification with this chromophore does not appear to affect the overall stability and structure of the DNA. Upon selective irradiation of the naphthalene moiety at 340 nm, photoreduction of a distal electron trap, 5-bromouridine, embedded in the DNA base stack occurs. This DNA-mediated reduction from a distance was found to be significantly more efficient with substitution of 5-bromouridine toward the 5'-end than toward the 3'-end. These results support a general preference for electron transfer through DNA toward the 5'-end, irrespective of the donor. In addition, differences in efficiency of photoreduction through intrastrand and interstrand pathways are observed. For DNA-mediated reduction, as with DNA-mediated oxidation, significant differences in the charge transfer reaction are apparent that depend upon subtle differences in coupling into the DNA base stack.
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Affiliation(s)
| | | | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
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41
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Maynard BA, Smith PA, Ladner L, Jaleel A, Beedoe N, Crawford C, Assefa Z, Sykora RE. Emission Enhancement through Dual Donor Sensitization: Modulation of Structural and Spectroscopic Properties in a Series of Europium Tetracyanoplatinates. Inorg Chem 2009; 48:6425-35. [PMID: 19534548 DOI: 10.1021/ic900149v] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Branson A. Maynard
- Department of Chemistry, University of South Alabama, Mobile, Alabama 36688
| | - Philip A. Smith
- Department of Chemistry, University of South Alabama, Mobile, Alabama 36688
| | - LeAnn Ladner
- Department of Chemistry, University of South Alabama, Mobile, Alabama 36688
| | - Ayesha Jaleel
- Department of Chemistry, University of South Alabama, Mobile, Alabama 36688
| | - Nuquie Beedoe
- Department of Chemistry, North Carolina A&T State University, Greensboro, North Carolina 27411
| | - Carlos Crawford
- Department of Chemistry, North Carolina A&T State University, Greensboro, North Carolina 27411
| | - Zerihun Assefa
- Department of Chemistry, North Carolina A&T State University, Greensboro, North Carolina 27411
| | - Richard E. Sykora
- Department of Chemistry, University of South Alabama, Mobile, Alabama 36688
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42
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Bouamaied I, Nguyen T, Rühl T, Stulz E. Supramolecular helical porphyrin arrays using DNA as a scaffold. Org Biomol Chem 2008; 6:3888-91. [PMID: 18931790 DOI: 10.1039/b813584c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A diphenyl porphyrin substituted nucleotide was incorporated site specifically into DNA, leading to helical stacked porphyrin arrays in the major groove of the duplexes. The porphyrins show an electronic interaction which is significantly enhanced compared to the analogous tetraphenyl porphyrin (TPP) as shown in the large exciton coupling of the porphyrin B-band absorbance. Analogous to the TPP-DNA, an induced helical secondary structure is observed in the single strand porphyrin-DNA. The modified DNA can be hybridised to an immobilised complementary strand leading to fluorescent beads.
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Affiliation(s)
- Imenne Bouamaied
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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43
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Jiang L, Gao J, Wang E, Li H, Wang Z, Hu W, Jiang L. Organic Single-Crystalline Ribbons of a Rigid "H"-type Anthracene Derivative and High-Performance, Short-Channel Field-Effect Transistors of Individual Micro/Nanometer-Sized Ribbons Fabricated by an "Organic Ribbon Mask" Technique. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2008; 20:2735-40. [PMID: 25213898 DOI: 10.1002/adma.200800341] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Revised: 03/04/2008] [Indexed: 05/25/2023]
Abstract
The synthesis of a rigid, planar H-type anthracene derivative is described. Single-crystalline ribbons at micro- and nanometer sizes can be controllably produced and transistors based on an individual ribbon can be fabricated in situ through a newly developed "organic ribbon mask" method, in which the channel length of the transistors can be easily scaled down to sub-micrometer level.
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Affiliation(s)
- Lang Jiang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Organic Solids Institute of Chemistry, Chinese Academy of Sciences Beijing 100080 (PR China); Graduate School of Chinese Academy of Sciences Beijing 100039 (PR China)
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44
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Srivatsan SG, Weizman H, Tor Y. A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing. Org Biomol Chem 2008; 6:1334-8. [PMID: 18385838 PMCID: PMC5263222 DOI: 10.1039/b801054d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A highly emissive nucleobase analog, based on a thieno[3,4-d]pyrimidine core, is enzymatically incorporated into RNA oilgonucleotides that function as base discriminating fluorescent probes.
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Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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45
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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46
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5-arylethynyl-2'-deoxyuridines: energy transfer and SNP-detection. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:767-72. [PMID: 18066898 DOI: 10.1080/15257770701501187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Energy transfer between different fluorescent 5-alkynyl-2' -deoxyuridines in complementary and mismatched duplexes was studied.
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47
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Bylińska I, Sikorski A, Wiczk W. 4-(9-Anthryl)-2-methylbutyn-2-ol. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o484-5. [PMID: 21201508 PMCID: PMC2960210 DOI: 10.1107/s1600536808001542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 01/15/2008] [Indexed: 11/22/2022]
Abstract
There are two molecules in the asymmetric unit of the title compound, C19H16O. Neighbouring molecules are linked through O—H⋯O hydrogen bonds into an R44(8) ring motif. There are also C—H⋯π hydrogen and π–π interactions. The molecules are either parallel to each other or are inclined at an angle of 12.5 (1)°.
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Affiliation(s)
- Irena Bylińska
- Faculty of Chemistry, University of Gdańsk, J. Sobieskiego 18, 80-952 Gdańsk, Poland
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48
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Fendt LA, Bouamaied I, Thöni S, Amiot N, Stulz E. DNA as Supramolecular Scaffold for Porphyrin Arrays on the Nanometer Scale. J Am Chem Soc 2007; 129:15319-29. [DOI: 10.1021/ja075711c] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leslie-Anne Fendt
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Imenne Bouamaied
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sandra Thöni
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Nicolas Amiot
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Eugen Stulz
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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