1
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Herb D, Rossini M, Ankerhold J. Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. Phys Rev E 2024; 109:064413. [PMID: 39020927 DOI: 10.1103/physreve.109.064413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/21/2024] [Indexed: 07/20/2024]
Abstract
After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.
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2
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Kashida H, Kawai H, Azuma H, Araki Y, Wada T, Asanuma H. Quantitative Analyses of Förster Resonance Energy Transfer between Identical Pyrene Chromophores (Homo‐FRET) In DNA Scaffolds. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hidenori Azuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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3
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Burns JR, Wood JW, Stulz E. A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution. Front Chem 2020; 8:113. [PMID: 32175308 PMCID: PMC7054460 DOI: 10.3389/fchem.2020.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
DNA-based molecular rulers enable scientists to determine important parameters across biology, from the measurement of protein binding interactions, to the study of membrane dynamics in cells. However, existing rulers can suffer from poor nanometre resolution due to the flexible nature of linkers used to tether to the DNA framework. We aimed to overcome this problem using zinc and free-base porphyrin chromophores attached via short and rigid acetylene linkers. This connectivity enables the distance and angle between the porphyrins to be fine-tuned along the DNA scaffold. The porphyrins undergo favorable energy transfer and chiral exciton coupling interactions to act as highly sensitive molecular ruler probes. To validate the system, we monitored the detection of small changes in DNA structure upon intercalation of ethidium bromide. CD spectroscopy showed the porphyrins undergo highly sensitive changes in excitation coupling to facilitate base pair resolution of the novel system.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London, London, United Kingdom
| | - James W Wood
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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4
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Fritz Y, Wagenknecht HA. Influences of Linker and Nucleoside for the Helical Self-Assembly of Perylene Along DNA Templates. Front Chem 2019; 7:659. [PMID: 31696102 PMCID: PMC6817502 DOI: 10.3389/fchem.2019.00659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
Six different conjugates of perylene with 2'-deoxyuridine and with 2-amino-2'-deoxyadenosine were synthesized and applied for DNA-templated assembly in aqueous buffer solutions. They differ by the linkers ethynylene, phenylene, and phenylene-ethynylene between nucleoside and chromophore. The nucleosides were investigated as monomers in CHCl3 and dimethyl sulfoxide by optical spectroscopy. The properties of the four phenylene-linked conjugates are similar to that of perylene as reference because these linkers separate both aromatic parts. The ethynylene linker electronically couples the chromophore with the respective nucleoside and thus red shifts the absorbance. The DNA-templated assembly properties were elucidated by mixing the templates in aqueous buffer with the perylene-nucleoside conjugates from a dimethyl sulfoxide stock solution. Specific binding of the nucleosides was probed by comparing the results with dA20 and T20 as single-stranded DNA templates. Our studies reveal the structural parameters that are important for the DNA-templated assembly of perylenes. First, perylene-2'-deoxyuridine conjugates do not form DNA-templated helical assemblies, regardless of the choice of linker. Second, the ethynylene linker is crucial for successful DNA-templated chromophore assemblies of perylene-2-amino-2'-deoxyadenosine conjugates. Third, in contrast, the phenylene linker inhibits self-assembly along single-stranded DNA templates. In conclusion, the 2-amino-2'-deoxyadenosin in combination with the ethynylene linker provides the best structural feature for specific and helical DNA-templated assembly of perylenes. This result is important for the design of future DNA-based supramolecular architectures with chromophores, in particular DNA-based light-harvesting systems and DNA systems for emitting or sensing circularly polarized luminescence.
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Affiliation(s)
- Yannic Fritz
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
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5
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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6
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Hofsäß R, Sinn S, Biedermann F, Wagenknecht HA. Programmable and Sequence-Selective Supramolecular Assembly of Two Different Chromophores along DNA Templates. Chemistry 2018; 24:16257-16261. [DOI: 10.1002/chem.201804314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Robert Hofsäß
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan Sinn
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Frank Biedermann
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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7
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Brown KE, Singh APN, Wu YL, Ma L, Mishra AK, Phelan BT, Young RM, Lewis FD, Wasielewski MR. Fluorescent excimers and exciplexes of the purine base derivative 8-phenylethynyl-guanine in DNA hairpins. Faraday Discuss 2018; 207:217-232. [PMID: 29362748 DOI: 10.1039/c7fd00186j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ground- and excited-state electronic interactions between the nucleobase analog 8-(4'-phenylethynyl)deoxyguanosine, EG, with natural nucleobases and 7-deazaguanine, as well as between adjacent EG base analogs, have been characterized using a combination of steady-state spectroscopy and time-resolved fluorescence, absorption, and stimulated Raman spectroscopies. The properties of the nucleoside EG-H2 are only weakly perturbed upon incorporation into synthetic DNA hairpins in which thymine, cytosine or adenine are the bases flanking EG. Incorporation of the nucleoside to be adjacent to guanine or deazaguanine results in the formation of short-lived (40-80 ps) exciplexes, the charge transfer character of which increases as the oxidation potential of the donor decreases. Hairpins possessing two or three adjacent EG base analogs display exciton-coupled circular dichroism in the ground state and form long-lived fluorescent excited states upon electronic excitation. Incorporation of EG into the helical scaffold of the DNA hairpins places it adjacent to its neighboring nucleobases or a second EG, thus providing the close proximity required for the formation of exciplex or excimer intermediates upon geometric relaxation of the short-lived EG excited state. The three time-resolved spectroscopic methods employed permit both the characterization of the several intermediates and the kinetics of their formation and decay.
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Affiliation(s)
- Kristen E Brown
- Department of Chemistry, Argonne-Northwestern Solar Energy Research (ANSER) Center, Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, USA.
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8
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Jabłoński A, Fritz Y, Wagenknecht HA, Czerwieniec R, Bernaś T, Trzybiński D, Woźniak K, Kowalski K. Pyrene-nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies. Beilstein J Org Chem 2017; 13:2521-2534. [PMID: 29259662 PMCID: PMC5727867 DOI: 10.3762/bjoc.13.249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022] Open
Abstract
Fluorescent pyrene–linker–nucleobase (nucleobase = thymine, adenine) conjugates with carbonyl and hydroxy functionalities in the linker were synthesized and characterized. X-ray single-crystal structure analysis performed for the pyrene–C(O)CH2CH2–thymine (2) conjugate reveals dimers of molecules 2 stabilized by hydrogen bonds between the thymine moieties. The photochemical characterization showed structure-dependent fluorescence properties of the investigated compounds. The conjugates bearing a carbonyl function represent weak emitters as compared to compounds with a hydroxy function in the linker. The self-assembly properties of pyrene nucleobases were investigated in respect to their binding to single and double strand oligonucleotides in water and in buffer solution. In respect to the complementary oligothymidine T10 template in water, compounds 3 and 5 both show a self-assembling behavior according to canonical base–base pairing. However, in buffer solution, derivative 5 was much more effective than 3 in binding to the T10 template. Furthermore the adenine derivative 5 binds to the double-stranded (dA)10–T10 template with a self-assembly ratio of 112%. Such a high value of a self-assembly ratio can be rationalized by a triple-helix-like binding, intercalation, or a mixture of both. Remarkably, compound 5 also shows dual staining pattern in living HeLa cells. Confocal microscopy confirmed that 5 predominantly stains mitochondria but it also accumulates in the nucleoli of the cells.
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Affiliation(s)
- Artur Jabłoński
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, PL-91403 Łódź, Poland
| | - Yannic Fritz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Rafał Czerwieniec
- Universität Regensburg, Institut für Physikalische und Theoretische Chemie, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Tytus Bernaś
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, ul. Pasteura 3, 02-093 Warsaw, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki and Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki and Wigury 101, 02-089 Warszawa, Poland
| | - Konrad Kowalski
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, PL-91403 Łódź, Poland
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9
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Han JH, Yamamoto S, Park S, Sugiyama H. Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair. Chemistry 2017; 23:7607-7613. [PMID: 28411372 DOI: 10.1002/chem.201701118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 12/12/2022]
Abstract
A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.
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Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Seigi Yamamoto
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University,Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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10
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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11
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Reuss AJ, Grünewald C, Braun M, Engels JW, Wachtveitl J. The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers. Chemphyschem 2016; 17:1369-76. [PMID: 26635201 DOI: 10.1002/cphc.201500958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 01/22/2023]
Abstract
This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential. These features in the ultrafast dynamics are indicative of the rotational energy barriers in the first excited state.
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Affiliation(s)
- Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Joachim W Engels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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12
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Trojanowski P, Plötner J, Grünewald C, Graupner FF, Slavov C, Reuss AJ, Braun M, Engels JW, Wachtveitl J. Photo-physical properties of 2-(1-ethynylpyrene)-adenosine: influence of hydrogen bonding on excited state properties. Phys Chem Chem Phys 2014; 16:13875-88. [PMID: 24894337 DOI: 10.1039/c4cp01148a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-physical properties of 2-(1-ethynylpyrene)-adenosine (PyA), a fluorescent probe for RNA dynamics, were examined by solvation studies. The excited-state dynamics display the influence of the vicinity on the spectral features. Combining improved transient absorption and streak camera measurements along with a new analysis method provide a detailed molecular picture of the photophysics. After intramolecular vibrational energy redistribution (IVR), two distinct states are observed. Solvent class (protic/aprotic) and permittivity strongly affect the properties of these states and their population ratio. As a result their emission spectrum is altered, while the fluorescence quantum yield and the overall lifetime remain nearly unchanged. Consequently, the hitherto existing model of the photophysics is herein refined and extended. The findings can serve as basis for improving the information content of measurements with PyA as a label in RNA.
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Affiliation(s)
- P Trojanowski
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt/Main, Germany.
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13
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Plasser F, Lischka H. Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution. Photochem Photobiol Sci 2014; 12:1440-52. [PMID: 23737069 DOI: 10.1039/c3pp50032b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.
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Affiliation(s)
- Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria.
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14
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013; 52:12937-41. [DOI: 10.1002/anie.201306017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/11/2013] [Indexed: 11/08/2022]
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16
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Toppari JJ, Wirth J, Garwe F, Stranik O, Csaki A, Bergmann J, Paa W, Fritzsche W. Plasmonic coupling and long-range transfer of an excitation along a DNA nanowire. ACS NANO 2013; 7:1291-1298. [PMID: 23305550 DOI: 10.1021/nn304789w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We demonstrate an excitation transfer along a fluorescently labeled dsDNA nanowire over a length of several micrometers. Launching of the excitation is done by exciting a localized surface plasmon mode of a 40 nm silver nanoparticle by 800 nm femtosecond laser pulses via two-photon absorption. The plasmonic mode is subsequently coupled or transformed to excitation in the nanowire in contact with the particle and propagated along it, inducing bleaching of the dyes on its way. In situ as well as ex situ fluorescence microscopy is utilized to observe the phenomenon. In addition, transfer of the excitation along the nanowire to another nanoparticle over a separation of 5.7 μm was clearly observed. The nature of the excitation coupling and transfer could not be fully resolved here, but injection of an electron into the DNA from the excited nanoparticle and subsequent coupled transfer of charge (Dexter) and delocalized exciton (Frenkel) is the most probable mechanism. However, a direct plasmonic or optical coupling and energy transfer along the nanowire cannot be totally ruled out either. By further studies the observed phenomenon could be utilized in novel molecular systems, providing a long-needed communication method between molecular devices.
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Affiliation(s)
- J Jussi Toppari
- Institute of Photonic Technology, Albert-Einstein-Strasse 9, Jena 07745, Germany
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17
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Sezi S, Wagenknecht HA. DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun (Camb) 2013; 49:9257-9. [DOI: 10.1039/c3cc44733b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Sezi S, Varghese R, Vilaivan T, Wagenknecht HA. Conformational Control of Dual Emission by Pyrrolidinyl PNA-DNA Hybrids. ChemistryOpen 2012; 1:173-6. [PMID: 24551507 PMCID: PMC3922446 DOI: 10.1002/open.201200016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 01/09/2023] Open
Affiliation(s)
- Sabrina Sezi
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Reji Varghese
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University Phyathai Road, Pathumwan, Bangkok 10330 (Thailand) E-mail:
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
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19
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Tanaka M, Oguma K, Saito Y, Saito I. Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines. Bioorg Med Chem Lett 2012; 22:4103-5. [PMID: 22578464 DOI: 10.1016/j.bmcl.2012.04.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/07/2012] [Accepted: 04/13/2012] [Indexed: 12/30/2022]
Abstract
5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength.
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Affiliation(s)
- Makiko Tanaka
- Department of Chemical Biology and Applied Chemistry, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
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20
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Berndt F, Ioffe I, Granovsky AA, Mahrwald R, Tannert S, Kovalenko SA, Ernsting NP. 7-Amino-dibenzofuran-3-carboxylate: A new probe for femtosecond dynamic microsolvation studies of biomolecules. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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Tanaka M, Oguma K, Saito Y, Saito I. Drastic enhancement of excess electron-transfer efficiency through DNA by inserting consecutive 5-phenylethynyl-2′-deoxyuridines as a modulator. Chem Commun (Camb) 2012; 48:9394-6. [DOI: 10.1039/c2cc34661c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Förster U, Grünewald C, Engels JW, Wachtveitl J. Ultrafast dynamics of 1-ethynylpyrene-modified RNA: a photophysical probe of intercalation. J Phys Chem B 2010; 114:11638-45. [PMID: 20707369 DOI: 10.1021/jp103176q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The photophysics of pyrene attached to an adenine base within RNA single strands and duplexes is examined with respect to the position of the pyrene within the strand and the number of pyrenes attached to one duplex. Compounds with pyrenes intercalating sequence specifically are examined, as well as a doubly modified compound, where the two pyrenes are located close enough to each other for significant excimer interaction. Femtosecond transient absorption measurements and time correlated single photon counting measurements allow a thorough examination of the local influences on the pyrene photophysics. Our results suggest that optical excitation establishes an equilibration between two molecular states of different spectroscopic properties and lifetimes that are coupled only via the excited state as a gateway. One of them is a neutral pyrene-adenine excited state, S*, while the second one is connected to an excited charge transfer state, S*(CT). In all compounds, an ultrafast sub-ps decay from a higher excited state into the lowest excited state S* occurs, and an excited charge transfer species S*(CT) is formed within picoseconds. The fluorescence behavior of the pyrene-modified adenine, however, is strongly dependent on RNA conformation. Both S* and S*(CT) states are fluorescent, and decay within hundreds of picoseconds and approximately 2 ns, respectively. The ratio between S* and S*(CT) fluorescence depends strongly on pyrene intercalation, and it is found that the S* state is quenched selectively upon intercalation of the pyrene into RNA. The doubly modified duplex exhibits an additional fluorescent state with a lifetime of 18.7 ns, which is associated with the pyrene excimer state. This state coexists with a significant population of the pyrene monomer, since the characteristic features of the latter can still be observed. Formation of the excimer occurs on femtosecond time scales. The pyrene label thus provides a sensitive tool to monitor the local structural dynamics of RNA with the chromophore acting as a molecular beacon.
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Affiliation(s)
- Ute Förster
- Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
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24
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Förster U, Lommel K, Sauter D, Grünewald C, Engels JW, Wachtveitl J. 2-(1-Ethynylpyrene)-adenosine as a folding probe for RNA - pyrene in or out. Chembiochem 2010; 11:664-72. [PMID: 20183842 DOI: 10.1002/cbic.200900778] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of short RNA duplexes containing one or two 1-ethynylpyrene-modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature-dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene-rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A-U base pairs. Flanking G-C base pairs, even only in the 5'-direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene-pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.
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Affiliation(s)
- Ute Förster
- Institute of Biophysics, Institute of Physical and Theoretical Chemistry, Goethe-University, Max-von-Laue-Strasse 1, 60438 Frankfurt, Germany
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25
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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: 658] [Impact Index Per Article: 47.0] [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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26
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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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27
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Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Fluorescent analysis of excess electron transfer through DNA. Bioorg Med Chem Lett 2010; 20:994-6. [DOI: 10.1016/j.bmcl.2009.12.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/10/2009] [Accepted: 12/11/2009] [Indexed: 11/23/2022]
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29
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30
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Filichev V, Astakhova I, Malakhov A, Korshun V, Pedersen E. 1-, 2-, and 4-Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship. Chemistry 2008; 14:9968-80. [DOI: 10.1002/chem.200800380] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Roca-Sanjuán D, Merchán M, Serrano-Andrés L. Modeling hole transfer in DNA: Low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Wanninger-Weiss C, Valis L, Wagenknecht HA. Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer. Bioorg Med Chem 2008; 16:100-6. [PMID: 17509886 DOI: 10.1016/j.bmc.2007.04.064] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 04/27/2007] [Indexed: 11/24/2022]
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods. The fluorescence enhancement upon DNA hybridization can be improved significantly by the presence of 7-deazaguanin as an additional modification and charge acceptor three bases away from the Py-G modification site. Moreover, Py-G in DNA can be applied as a photoinducable donor for charge transfer processes when indol is present as an artificial DNA base and charge acceptor. Correctly base-paired duplexes can be discriminated from mismatched ones by comparison of their fluorescence quenching.
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Affiliation(s)
- Claudia Wanninger-Weiss
- University of Regensburg, Institute for Organic Chemistry, Universitätstr. 31, D-93053 Regensburg, Germany
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33
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Wagenknecht HA. Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept. Ann N Y Acad Sci 2007; 1130:122-30. [PMID: 18096856 DOI: 10.1196/annals.1430.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There is an increasing need for fluorescent nucleic acid probes that are able to sense genetic variations without the application of enzymes. The incorporation of organic fluorophores either as DNA base modifications or as DNA base substitutions represents a powerful and versatile method for such new fluorescent DNA assays. Multiple labeling of oligonucleotides using several adjacent chromophore-modified DNA bases yields fluorescence enhancement and modulation that are sensitive to single-base mismatches in the complementary oligonucleotide. Charge transfer processes that cause fluorescence quenching are DNA-base mediated and occur over several base pairs distance. Our "DETEQ" setup, consisting of a fluorescence DNA base substitution and the charge acceptor as a second modification two base pairs away, allows the homogeneous detection of single-base mutations simply by fluorescence readout. This could lead to new DNA microarrays which are based on charge transfer processes and can be analyzed by commonly used fluorescence readout techniques.
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34
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Kwok WM, Ma C, Phillips DL. Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J Am Chem Soc 2007; 128:11894-905. [PMID: 16953630 DOI: 10.1021/ja0622002] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By employing broadband femtosecond Kerr-gated time-resolved fluorescence (KTRF) and transient absorption (TA) techniques, we report the first (to our knowledge) femtosecond combined time- and wavelength-resolved study on an ultraviolet-excited nucleoside and a single-stranded oligonucleotide (namely adenosine (Ado) and single-stranded adenine oligomer (dA)(20)) in aqueous solution. With the advantages of the ultrafast time resolution, the broad spectral and temporal probe window, and a high sensitivity, our KTRF and TA results enable the real time monitoring and spectral characterization of the excited-state relaxation processes of the Ado nucleoside and (dA)(20) oligonucleotide investigated. The temporal evolution of the 267 nm excited Ado KTRF spectra indicates there are two emitting components with lifetimes of approximately 0.13 ps and approximately 0.45 ps associated with the L(a) and L(b) pipi* excited states, respectively. These Ado results reveal no obvious evidence for the involvement of the npi* state along the irradiative internal conversion pathway. A distinct mechanism involving only the two pipi* states has been proposed for the ultrafast Ado deactivation dynamics in aqueous solution. The time dependence of the 267 nm excited (dA)(20) KTRF and TA spectra reveals temporal evolution from an ultrafast "A-like" state (with a approximately 0.39 ps decay time) to a relatively long-lived E(1) "excimer" (approximately 4.3 ps decay time) and an E(2) "excimer-like" (approximately 182 ps decay time) state. The "A-like" state has a spectral character closely resembling the excited state of Ado. Comparison of the spectral evolution between the results for Ado and (dA)(20) provides unequivocal evidence for the local excitation character of the initially photoexcited (dA)(20). The rapid transformation of the locally excited (dA)(20) component into the delocalized E(1) "excimer" state which then further evolves into the E(2) "excimer-like" state indicates that base stacking has a high ability to modify the excited-state deactivation pathway. This modification appears to occur by suppressing the internal conversion pathway of an individually excited base component where the stacking interaction mediates efficient interbase energy transfer and promotes formation of the collective excited states. This feature of the local excitation that is subsequently followed by rapid energy delocalization into nearby bases may occur in many base multimer systems. Our results provide an important new contribution to better understanding DNA photophysics.
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Affiliation(s)
- Wai-Ming Kwok
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S. A. R., P. R. China
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35
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Grünewald C, Kwon T, Piton N, Förster U, Wachtveitl J, Engels JW. RNA as scaffold for pyrene excited complexes. Bioorg Med Chem 2007; 16:19-26. [PMID: 17512739 DOI: 10.1016/j.bmc.2007.04.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 02/26/2007] [Accepted: 04/27/2007] [Indexed: 11/15/2022]
Abstract
Synthesis and spectral properties of 1-ethynylpyrene base modified RNA are reported. The fluorophore attached to the 2-position of adenosine is directed into the easily accessible minor groove in RNA. Through an intermolecular interaction of the pyrene residues in twofold labelled RNA, single and double strands can be distinguished by their fluorescence maxima around 450 and 480 nm, respectively. This behaviour allows the kinetic investigation of RNA hybridisation and folding by fluorescence spectroscopy.
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Affiliation(s)
- Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60348 Frankfurt, Germany
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36
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The spectroscopy, dynamics, and electronic structure of pyrenyl–dU nucleosides: P+/dU− charge transfer state photophysics. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.11.095] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Hariharan M, Joseph J, Ramaiah D. Novel Bifunctional Viologen-Linked Pyrene Conjugates: Synthesis and Study of Their Interactions with Nucleosides and DNA. J Phys Chem B 2006; 110:24678-86. [PMID: 17134231 DOI: 10.1021/jp063079o] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the objective of developing efficient DNA oxidizing agents, a new series of viologen-linked pyrene conjugates with the general formula PYLnV(2+), having a different number of methylene spacer units (Ln) was synthesized, and their interactions with nucleosides and DNA have been investigated through photophysical and biophysical techniques. The viologen-linked pyrene derivatives PYL1V(2+) (n =equals; 1), PYL7V(2+) (n = 7), and PYL12V(2+) (n = 12) exhibited characteristic fluorescence emission of the pyrene chromophore centered around 380 nm but with significantly reduced yields when compared to those of the model compound PYL1Et(3)(+). The fluorescence quenching observed in these systems is explained through an electron-transfer mechanism based on a calculated favorable change in free energy (DeltaG(ET) = -1.59 eV), and the redox species characterized through laser flash photolysis studies. Intramolecular electron-transfer rate constants (k(ET)) were calculated from the observed fluorescence yields, and the singlet lifetimes of the model compound and are found to decrease with increasing spacer length. The DNA binding studies of these systems through photophysical, chiroptical, and viscometric techniques demonstrated that these systems effectively undergo DNA intercalation with association constants (KDNA) in the range of 1.1-2.6 x 10(4) M(-1) and exhibit 2:1 sequence selectivity for poly(dG) x poly(dC) over poly(dA) x poly(dT). Photoactivation of these systems initiates electron transfer from the singlet excited state of the pyrene chromophore to the viologen moiety followed by an electron transfer from DNA to the oxidized pyrene. This results in the formation of stable charge-separated species such as radical cations of both DNA and reduced viologen as characterized by laser flash photolysis studies and subsequently the oxidized DNA modifications. These novel systems are soluble in buffer media, stable under irradiation conditions, and oxidize DNA efficiently and selectively through a cosensitization mechanism and hence can be useful as photoactivated DNA cleaving agents.
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Affiliation(s)
- Mahesh Hariharan
- Photosciences and Photonics, Chemical Sciences and Technology Division, Regional Research Laboratory, Council of Scientific and Industrial Research, Trivandrum 695019, India
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38
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Abbou J, Anne A, Demaille C. Accessing the Dynamics of End-Grafted Flexible Polymer Chains by Atomic Force-Electrochemical Microscopy. Theoretical Modeling of the Approach Curves by the Elastic Bounded Diffusion Model and Monte Carlo Simulations. Evidence for Compression-Induced Lateral Chain Escape. J Phys Chem B 2006; 110:22664-75. [PMID: 17092014 DOI: 10.1021/jp064559i] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.
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Affiliation(s)
- Jeremy Abbou
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université-CNRS No. 7591, Université de Paris 7-Denis Diderot, 2 place Jussieu, 75251 Paris Cedex 05, France
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39
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Valis L, Wang Q, Raytchev M, Buchvarov I, Wagenknecht HA, Fiebig T. Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proc Natl Acad Sci U S A 2006; 103:10192-10195. [PMID: 16801552 PMCID: PMC1502433 DOI: 10.1073/pnas.0600957103] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.
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Affiliation(s)
- Linda Valis
- Institute for Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Qiang Wang
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Milen Raytchev
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | - Ivan Buchvarov
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
| | | | - Torsten Fiebig
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467; and
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40
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Valis L, Mayer-Enthart E, Wagenknecht HA. 8-(Pyren-1-yl)-2′-deoxyguanosine as an optical probe for DNA hybridization and for charge transfer with small peptides. Bioorg Med Chem Lett 2006; 16:3184-7. [PMID: 16621544 DOI: 10.1016/j.bmcl.2006.03.063] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 03/14/2006] [Accepted: 03/16/2006] [Indexed: 11/28/2022]
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as an optical probe into oligonucleotides. The Py-G group in DNA does not discriminate between any of the four natural nucleosides as a counterbase and exhibits altered optical properties in single strands versus double strands. Thus, the duplex hybridization of Py-G-modified DNA can be observed by both fluorescence and absorption spectroscopy. Moreover, Py-G in DNA can be applied as photoinducable donor for charge transfer processes with small peptides.
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Affiliation(s)
- Linda Valis
- University of Regensburg, Institute for Organic Chemistry, D-93040 Regensburg, Germany
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41
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Skorobogatyi MV, Malakhov AD, Pchelintseva AA, Turban AA, Bondarev SL, Korshun VA. Fluorescent 5-Alkynyl-2′-Deoxyuridines: High Emission Efficiency of a Conjugated Perylene Nucleoside in a DNA Duplex. Chembiochem 2006; 7:810-6. [PMID: 16572492 DOI: 10.1002/cbic.200600040] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Four fluorescent 5-alkynyl-2'-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2'-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2'-deoxyuridine), which is quenched upon duplex formation.
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Affiliation(s)
- Mikhail V Skorobogatyi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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42
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Barbaric J, Wagenknecht HA. DNA as a supramolecular scaffold for the helical arrangement of a stack of 1-ethynylpyrene chromophores. Org Biomol Chem 2006; 4:2088-90. [PMID: 16729121 DOI: 10.1039/b605251g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly organized helical pi-stacked arrangement of 1-ethynylpyrene moieties along the major groove of duplex DNA can only be achieved if more than three chromophores have been synthetically incorporated adjacent to each other.
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Affiliation(s)
- Janez Barbaric
- University of Regensburg, Institute for Organic Chemistry, D-93040 Regensburg, Germany
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43
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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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