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Schmitt HC, Fischer I, Ji L, Merz J, Marder TB, Hoche J, Röhr MIS, Mitric R. Isolated 2-hydroxypyrene and its dimer: a frequency- and time-resolved spectroscopic study. NEW J CHEM 2021. [DOI: 10.1039/d0nj02391d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated isolated 2-hydroxypyrene and its dimer in the gas phase by time- and frequency-resolved photoionisation with picosecond time-resolution.
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Affiliation(s)
- Hans-Christian Schmitt
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Ingo Fischer
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Lei Ji
- Institut für Anorganische Chemie, and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Julia Merz
- Institut für Anorganische Chemie, and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Todd B. Marder
- Institut für Anorganische Chemie, and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
| | - Merle I. S. Röhr
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Julius-Maximilians-Universität Würzburg, Theodor-Boveri-Weg, D-97074 Würzburg, Germany
| | - Roland Mitric
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, D-97074 Würzburg, Germany
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Padalkar VS, Patil VS, D. Telore R, Sekar N. Synthesis of novel fluorescent 1,3,5-trisubstituted triazine derivatives and photophysical property evaluation of fluorophores and their BSA conjugates. HETEROCYCL COMMUN 2012. [DOI: 10.1515/hc-2012-0024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractCyanuric chloride was allowed to react with
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Crovetto L, Rios R, Alvarez-Pez JM, Paredes JM, Lozano-Velez P, del Valle C, Talavera EM. Synthesis of a Fluorescent Xanthenic Derivative Useful for Labeling Amine Residues. J Phys Chem B 2008; 112:10082-5. [DOI: 10.1021/jp803970c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis Crovetto
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Ramon Rios
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Jose M. Alvarez-Pez
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Jose M. Paredes
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Patricia Lozano-Velez
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Carmen del Valle
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
| | - Eva M. Talavera
- Department of Physical Chemistry, Cartuja Campus, University of Granada, Granada 18071, Spain
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Crovetto L, Paredes JM, Rios R, Talavera EM, Alvarez-Pez JM. Photophysics of a Xanthenic Derivative Dye Useful as an “On/Off” Fluorescence Probe. J Phys Chem A 2007; 111:13311-20. [DOI: 10.1021/jp077249o] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Crovetto
- Department of Physical Chemistry, University of Granada, Cartuja Campus, Granada 18071, Spain, and Department of Organic Chemistry, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Jose M. Paredes
- Department of Physical Chemistry, University of Granada, Cartuja Campus, Granada 18071, Spain, and Department of Organic Chemistry, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Ramon Rios
- Department of Physical Chemistry, University of Granada, Cartuja Campus, Granada 18071, Spain, and Department of Organic Chemistry, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Eva M. Talavera
- Department of Physical Chemistry, University of Granada, Cartuja Campus, Granada 18071, Spain, and Department of Organic Chemistry, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Jose M. Alvarez-Pez
- Department of Physical Chemistry, University of Granada, Cartuja Campus, Granada 18071, Spain, and Department of Organic Chemistry, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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Hrdlicka PJ, Babu BR, Sørensen MD, Harrit N, Wengel J. Multilabeled pyrene-functionalized 2'-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays. J Am Chem Soc 2005; 127:13293-9. [PMID: 16173760 DOI: 10.1021/ja052887a] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Homogeneous fluorescence assays for detection of nucleic acids are widely used in biological sciences. Typically, probes such as molecular beacons that rely on distance-dependent fluorescence quenching are used for such assays. Less attention has been devoted to tethering a single kind of fluorophores to oligonucleotides and exploiting hybridization-induced modulation of fluorescence intensity for nucleic acid detection. Herein, thermal denaturation experiments and fluorescence properties of oligodeoxyribonucleotides containing one or more 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA monomer(s) X are described. These pyrene-functionalized 2'-amino-LNAs display large increases in thermal stability against DNA/RNA complements with excellent Watson-Crick mismatch discrimination. Upon duplex formation of appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA probes and complementary DNA/RNA, intensive fluorescence emission with quantum yields between 0.28 and 0.99 are observed. Quantum yields of such magnitudes are unprecedented among pyrene-labeled oligonucleotides. Molecular modeling studies suggest that the dioxabicyclo[2.2.1]heptane skeleton and amide linkage of monomer X fix the orientation of the pyrene moiety in the minor groove of a nucleic acid duplex. Interactions between pyrene and nucleobases, which typically lead to quenching of fluorescence, are thereby reduced. Duplexes between multiple modified probes and DNA/RNA complements exhibit additive increases in fluorescence intensity, while the fluorescence of single stranded probes becomes increasingly quenched. Up to 69-fold increase in fluorescence intensity (measured at lambda(em) = 383 nm) is observed upon hybridization to DNA/RNA. The emission from duplexes of multiple modified probes and DNA/RNA at concentrations down to less than 500 nM can easily be seen by the naked eye using standard illumination intensities.
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Affiliation(s)
- Patrick J Hrdlicka
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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Guarnaccia C, Raman B, Zahariev S, Simoncsits A, Pongor S. DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains. Nucleic Acids Res 2004; 32:4992-5002. [PMID: 15388801 PMCID: PMC521646 DOI: 10.1093/nar/gkh827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The specificity of DNA-mediated protein assembly was studied in two in vitro systems, based on (i) the DNA-binding domain of bacteriophage 434 repressor cI (amino acid residues 1-69), or (ii) the DNA-binding domain of the yeast transcription factor GCN4, (amino acids 1-34) and their respective oligonucleotide cognates. In vivo, both of these peptides are part of larger protein molecules that also contain dimerization domains, and the resulting dimers recognize cognate palindromic DNA sequences that contain two half-sites of 4 bp each. The dimerization domains were not included in the peptides tested, so in solution-in the presence or absence of non-cognate DNA oligonucleotides-these molecules did not show appreciable dimerization, as determined by pyrene excimer fluorescence spectroscopy and oxidative cross-linking monitored by mass spectrometry. Oligonucleotides with only one 4 bp cognate half-site were able to initiate measurable dimerization, and two half-sites were able to select specific dimers even from a heterogeneous pool of molecules of closely related specificity (such as DNA-binding domains of the 434 repressor and their engineered mutants that mimic the binding helix of the related P22 phage repressor). The fluorescent technique allowed us to separately monitor the unspecific, ionic interaction of the peptides with DNA which produced a roughly similar signal in the case of both cognate and non-cognate oligonucleotides. But in the former case, a concomitant excimer fluorescence signal showed the formation of correctly positioned dimers. The results suggest that DNA acts as a highly specific template for the recruitment of weakly interacting protein molecules that can thus build up highly specific complexes.
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Affiliation(s)
- Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
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Talavera EM, Bermejo R, Crovetto L, Orte A, Alvarez-Pez JM. Fluorescence energy transfer between fluorescein label and DNA intercalators to detect nucleic acids hybridization in homogeneous media. APPLIED SPECTROSCOPY 2003; 57:208-215. [PMID: 14610959 DOI: 10.1366/000370203321535132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A general approach to detecting nucleic acid sequences in homogeneous media by means of steady-state fluorescence measurements is proposed. The methodology combines the use of a fluorescence-labeled single-strand DNA model probe, the complementary single-strand DNA target, and a DNA intercalator. The probe was fluorescein labeled to a spacer arm at the N4 position of the cytosine amino groups in polyribocytidylic acid (5'), poly(C), which acts as a model DNA probe. The complementary strand was polyriboinosinic acid (5'), poly(I), as a model of the target, and the energy transfer acceptor was an intercalator, either ethidium bromide or ethidium homodimer. In previous papers we have shown that the fluorescence intensity of the fluorescein label decreases when labeled poly(C) hybridizes with poly(I), and this fluorescence quenching can be used to detect DNA hybridization or renaturation in homogeneous media. In this paper we demonstrate that fluorescence resonance energy transfer (FRET) between fluorescein labeled to poly(C) and an intercalator agent takes place when single-stranded poly(C) hybridizes with poly(I), and we show how the fluorescence energy transfer further decreases the steady-state fluorescence intensity of the label, thus increasing the detection limit of the method. The main aim of this work was to develop a truly homogeneous detection system for specific nucleic acid hybridization in solution using steady-state fluorescence and FRET, but with the advantage of only having to label the probe with the energy donor since the energy acceptor is intercalated spontaneously. Moreover, the site label is not critical and can be labeled randomly in the DNA strand. Thus, the method is simpler than those published previously based on FRET. The experiments were carried out in both direct and competitive formats.
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Affiliation(s)
- Eva M Talavera
- Department of Physical Chemistry, Cartuja Campus, Granada University, 18071 Granada, Spain
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Synthesis and spectroscopic characterisation of 2-(2′-hydroxyphenyl)benzazole isothiocyanates as new fluorescent probes for proteins. J Photochem Photobiol A Chem 2002. [DOI: 10.1016/s1010-6030(02)00008-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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