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Gebhard J, Hirsch L, Schwechheimer C, Wagenknecht HA. Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach. Bioconjug Chem 2022; 33:1634-1642. [PMID: 35995426 PMCID: PMC9501807 DOI: 10.1021/acs.bioconjchem.2c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Fluorescent DNA probes were prepared in a modular approach
using
the “click” post-synthetic modification strategy. The
new glycol-based module and DNA building block place just two carbons
between the phosphodiester bridges and anchor the dye by an additional
alkyne group. This creates a stereocenter in the middle of this artificial
nucleoside substitute. Both enantiomers and a variety of photostable
cyanine–styryl dyes as well as thiazole orange derivatives
were screened as “clicked” conjugates in different surrounding
DNA sequences. The combination of the (S)-configured
DNA anchor and the cyanylated cyanine–styryl dye shows the
highest fluorescence light-up effect of 9.2 and a brightness of approximately
11,000 M–1 cm–1. This hybridization
sensitivity and fluorescence readout were further developed utilizing
electron transfer and energy transfer processes. The combination of
the hybridization-sensitive DNA building block with the nucleotide
of 5-nitroindole as an electron acceptor and a quencher increases
the light-up effect to 20 with the DNA target and to 15 with the RNA
target. The fluorescence readout could significantly be enhanced to
values between 50 and 360 by the use of energy transfer to a second
DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590,
as energy acceptors at the 5′-end. The latter binary probes
shift the fluorescent readout from the range of 500–550 nm
to the range of 610–670 nm. The optical properties make these
fluorescent DNA probes potentially useful for RNA imaging. Due to
the strong light-up effect, they will not require washing procedures
and will thus be suitable for live-cell imaging.
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Affiliation(s)
- Julian Gebhard
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Lara Hirsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Christian Schwechheimer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
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2
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Romanucci V, Oliva R, Petraccone L, Claes S, Schols D, Zarrelli A, Di Fabio G. Synthesis of new riboflavin modified ODNs: Effect of riboflavin moiety on the G-quadruplex arrangement and stability. Bioorg Chem 2020; 104:104213. [PMID: 32919132 DOI: 10.1016/j.bioorg.2020.104213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/31/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
In the panorama of modified G-quadruplexes (G4s) with interesting proprieties, here, it has been reported the synthesis of new modified d(TGGGAG) sequences forming G-quadruplexes, with the insertion of a riboflavin unit (Rf, vitamin B2). Exploiting the flavin similarity with the hydrogen bond pattern of guanine and aiming at mimic a typical nucleoside scaffold, the synthesis of the riboflavin building block 3 it has been efficiently carried out. The effect of insertion of riboflavin mimic nucleoside on the G-quadruplex properties has been here, for the first time investigated. A biophysical characterization of Rf-modified sequences (A-D) has been carried out by circular dichroism (CD), fluorescence spectroscopy, differential scanning calorimetry (DSC) and native gel electrophoresis. CD and electrophoresis data have suggested that Rf-modified sequences are able to form parallel tetramolecular G4 structures similar to that of the unmodified sequence. Analysis of the DSC thermograms has revealed that all modified G-quadruplexes have a higher thermal stability compared with the natural sequence, particularly the stabilisation is higher when the Rf residue is introduced at the 3'-end. Further, DSC analysis has revealed that the Rf residues introduced at the 3'-end are able to form additional stabilising interactions, energetically almost comparable to the enthalpic contribution of a G-tetrad. Fluorescence measurement are consistent with this result showing that the Rf residues introduced at 3'-end are able to form stacking interactions with the adjacent bases within the G-quadruplex structure. The whole of data suggested that the introduction of Rf unit can stabilize G-quadruplex structures and can be a promising candidate for future theranostic applications.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
| | - Rosario Oliva
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy; Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn Strasse 4a, D-44227 Dortmund, Germany
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Sandra Claes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
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3
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Rawtani D, Kuntmal B, Agrawal Y. Charge transfer in DNA and its diverse modelling approaches. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1207570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Deepak Rawtani
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Binal Kuntmal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Y. Agrawal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
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4
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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5
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Iida H, Mizoguchi T, Oh SD, Yashima E. Redox-triggered switching of helical chirality of poly(phenylacetylene)s bearing riboflavin pendants. Polym Chem 2010. [DOI: 10.1039/c0py00044b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Affiliation(s)
- Christoph Behrens
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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7
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Zhu XQ, Dai Z, Yu A, Wu S, Cheng JP. Driving Forces for the Mutual Conversions between Phenothiazines and Their Various Reaction Intermediates in Acetonitrile. J Phys Chem B 2008; 112:11694-707. [DOI: 10.1021/jp8041268] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xiao-Qing Zhu
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhi Dai
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Ao Yu
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Shuai Wu
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jin-Pei Cheng
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
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8
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Gschösser S, Kräutler B. B12-retro-Riboswitches: Guanosyl-Induced Constitutional Switching of B12 Coenzymes. Chemistry 2008; 14:3605-19. [DOI: 10.1002/chem.200701365] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Kino K, Miyazawa H, Sugiyama H. User-friendly Synthesis and Photoirradiation of a Flavin-linked Oligomer. Genes Environ 2007. [DOI: 10.3123/jemsge.29.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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10
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Simon P, Dueymes C, Fontecave M, Décout JL. DNA detection through signal amplification by using NADH: flavin oxidoreductase and oligonucleotide-flavin conjugates as cofactors. Angew Chem Int Ed Engl 2006; 44:2764-2767. [PMID: 15772944 DOI: 10.1002/anie.200461145] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Philippe Simon
- Chimie Bioorganique, Département de Pharmacochimie Moléculaire, UMR CNRS/Université Joseph Fourier 5063, FR CNRS 2607, BP 138, 5 Avenue de Verdun, 38243 Meylan, France, Fax: (+33) 476-04-10-07
| | - Cécile Dueymes
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, UMR Université Joseph Fourier-CNRS-CEA 5047, CEA Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France, Fax: (+33) 438-78-91-24
| | - Marc Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, UMR Université Joseph Fourier-CNRS-CEA 5047, CEA Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France, Fax: (+33) 438-78-91-24
| | - Jean-Luc Décout
- Chimie Bioorganique, Département de Pharmacochimie Moléculaire, UMR CNRS/Université Joseph Fourier 5063, FR CNRS 2607, BP 138, 5 Avenue de Verdun, 38243 Meylan, France, Fax: (+33) 476-04-10-07
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11
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Gschösser S, Gruber K, Kratky C, Eichmüller C, Kräutler B. B12-retro-riboswitches: constitutional switching of B12 coenzymes induced by nucleotides. Angew Chem Int Ed Engl 2006; 44:2284-8. [PMID: 15712313 DOI: 10.1002/anie.200462085] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Mack M, Grill S. Riboflavin analogs and inhibitors of riboflavin biosynthesis. Appl Microbiol Biotechnol 2006; 71:265-75. [PMID: 16607521 DOI: 10.1007/s00253-006-0421-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 11/30/2022]
Abstract
Flavins are active components of many enzymes. In most cases, riboflavin (vitamin B(2)) as a coenzyme represents the catalytic part of the holoenzyme. Riboflavin is an amphiphatic molecule and allows a large variety of different interactions with the enzyme itself and also with the substrate. A great number of active riboflavin analogs can readily be synthesized by chemical methods and, thus, a large number of possible inhibitors for many different enzyme targets is conceivable. As mammalian and especially human biochemistry depends on flavins as well, the target of the inhibiting flavin analog has to be carefully selected to avoid unwanted effects. In addition to flavoproteins, enzymes, which are involved in the biosynthesis of flavins, are possible targets for anti-infectives. Only a few flavin analogs or inhibitors of flavin biosynthesis have been subjected to detailed studies to evaluate their biological activity. Nevertheless, flavin analogs certainly have the potential to serve as basic structures for the development of novel anti-infectives and it is possible that, in the future, the urgent need for new molecules to fight multiresistant microorganisms will be met.
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Affiliation(s)
- Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany.
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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14
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Simon P, Dueymes C, Fontecave M, Décout JL. DNA Detection through Signal Amplification by Using NADH:Flavin Oxidoreductase and Oligonucleotide-Flavin Conjugates as Cofactors. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461145] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Gschösser S, Gruber K, Kratky C, Eichmüller C, Kräutler B. B12-retro-Riboschalter: konstitutionelles Schalten von B12-Coenzymen durch Nucleotide. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462085] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Abstract
Nucleic acids and analogues are suitable building blocks for reliable self-assembly of nanometer-sized two- or three-dimensional materials. In order to mimic or approach nature with respect to size and function, Angstrom-scale chemical engineering is emerging as pivotal for future developments. Efforts within nucleic acid nanotechnology will be focussed on generating rigid and stable low nanometer-sized structures carrying functionalities with predictable spatial positioning allowing, by encoded self-assembly, functional nucleic acid architectures to be built towards applications within the biological and material sciences.
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Affiliation(s)
- Jesper Wengel
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark.
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17
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Kiralj R, Ferreira MMC. On heteroaromaticity of nucleobases. Bond lengths as multidimensional phenomena. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2003; 43:787-809. [PMID: 12767137 DOI: 10.1021/ci0200523] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three hundred and nine carbon-carbon, carbon-nitrogen, and carbon-oxygen pi-bond lengths in high precision crystal structures of 31 purine and pyrimidine nucleobases were related to the Pauling pi-bond order, its analogues corrected to crystal packing effects, the numbers of non-hydrogen atoms around the bond, and the sum of atomic numbers of the bond atoms. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) demonstrated that the bond lengths in the nucleobases are three-dimensional phenomenon, characterized by nine distinct classes of bonds. Bond lengths predicted by Linear Regression models, Pauling Harmonic Potential Curves, Multiple Linear Regression, Principal Component, and Partial Least Squares Regression were compared to those calculated by molecular mechanics, semiempirical, and ab initio methods using PCA-HCA procedure on the calculated bond lengths, statistical parameters, and structural aromaticity indices. Incorporation of crystal packing effects into bond orders makes multivariate models to be competitive to semiempirical results, while further improvement of quantum chemical calculations can be achieved by geometry optimization of molecular clusters.
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Affiliation(s)
- R Kiralj
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
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18
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Rahe N, Rinn C, Carell T. Development of donor–acceptor modified DNA hairpins for the investigation of charge hopping kinetics in DNA. Chem Commun (Camb) 2003. [DOI: 10.1039/b307395e] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Schwögler A, Burgdorf L, Carell T. Selbstreparierende DNA basierend auf einem reduktiven Elektronentransfer durch den Basenstapel. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20001103)112:21<4082::aid-ange4082>3.0.co;2-k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schwögler A, Burgdorf LT, Carell T. Self-Repairing DNA Based on a Reductive Electron Transfer through the Base Stack. Angew Chem Int Ed Engl 2000; 39:3918-3920. [PMID: 29711674 DOI: 10.1002/1521-3773(20001103)39:21<3918::aid-anie3918>3.0.co;2-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2000] [Indexed: 11/09/2022]
Affiliation(s)
- Anja Schwögler
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
| | - Lars T Burgdorf
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
| | - Thomas Carell
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
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