51
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Ultrafast investigation of photoinduced charge transfer in aminoanthraquinone pharmaceutical product. Sci Rep 2017; 7:43419. [PMID: 28233835 PMCID: PMC5324068 DOI: 10.1038/srep43419] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/24/2017] [Indexed: 01/03/2023] Open
Abstract
We investigated the mechanism of intramolecular charge transfer and the following radiationless dynamics of the excited states of 1-aminoanthraquinone using steady state and time-resolved absorption spectroscopy combined with quantum chemical calculations. Following photoexcitation with 460 nm, conformational relaxation via twisting of the amino group, charge transfer and the intersystem crossing (ISC) processes have been established to be the major relaxation pathways responsible for the ultrafast nonradiative of the excited S1 state. Intramolecular proton transfer, which could be induced by intramolecular hydrogen bonding is inspected and excluded. Time-dependent density functional theory (TDDFT) calculations reveal the change of the dipole moments of the S0 and S1 states along the twisted coordinate of the amino group, indicating the mechanism of twisted intra-molecular charge transfer (TICT). The timescale of TICT is measured to be 5 ps due to the conformational relaxation and a barrier on the S1 potential surface. The ISC from the S1 state to the triplet manifold is a main deactivation pathway with the decay time of 28 ps. Our results observed here have yield a physically intuitive and complete picture of the photoinduced charge transfer and radiationless dynamics in anthraquinone pharmaceutial products.
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52
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Schütz M, Matsumoto Y, Bouchet A, Öztürk M, Dopfer O. Microsolvation of the pyrrole cation (Py+) with nonpolar and polar ligands: infrared spectra of Py+–Ln with L = Ar, N2, and H2O (n ≤ 3). Phys Chem Chem Phys 2017; 19:3970-3986. [DOI: 10.1039/c6cp07251h] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR spectra and dispersion-corrected density functional calculations of pyrrole cluster ions with Ar, N2, and H2O reveal the competition between H-bonding and π-stacking motifs of this prototypical heterocyclic aromatic cation in a hydrophobic and hydrophilic solvent.
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Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | | | - Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Murat Öztürk
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
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53
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Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
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Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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54
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Arnold AR, Grodick MA, Barton JK. DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016; 23:183-197. [PMID: 26933744 DOI: 10.1016/j.chembiol.2015.11.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 11/30/2022]
Abstract
The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.
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Affiliation(s)
- Anna R Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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55
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Kowalczyk A, Sadowska M, Krasnodebska-Ostrega B, Nowicka AM. Selective and sensitive electrochemical device for direct VB 2 determination in real products. Talanta 2016; 163:72-77. [PMID: 27886772 DOI: 10.1016/j.talanta.2016.10.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/20/2016] [Accepted: 10/23/2016] [Indexed: 11/29/2022]
Abstract
The developed by us electrochemical device for vitamin B2 (VB2; riboflavin) determination, without preconcentration step, in real products exhibits high sensitivity, selectivity, stability and low detection limit compared to those described in the literature. The determination procedure was based on the monitoring of the reduction current signal of VB2 bound with dsDNA anchored to the electrode surface through intermediary - carboxyphenyl layer. The application of such intermediary layer formed during electroreduction of appropriate diazonium salt at CV peak potential guarantees high efficiency of hybridization process and thus fully available places for VB2 interaction. Moreover, such intermediary layer provides good electrical contact, what is very important in the case of electrochemical sensors. The analytical range of work of the proposed VB2 sensor was between 0.08-1µM (30-377μgL-1) of riboflavin concentration. The obtained detection (LOD) and quantification limits (LOQ) were 24±2 and 55±5μgL-1, respectively. The proposed VB2 detection method was used for determination of riboflavin content in commercially available dietary supplements and yolk of hen egg samples. The accuracy of the obtained data was proved using comparison with an independent method (HPLC FLD).
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Affiliation(s)
- Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, PL-02-093 Warsaw, Poland.
| | - Monika Sadowska
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, PL-02-093 Warsaw, Poland
| | | | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, PL-02-093 Warsaw, Poland
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56
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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57
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Recent advances of folded tetraphenylethene derivatives featuring through-space conjugation. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.06.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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58
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Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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59
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Harris MA, Mishra AK, Young RM, Brown KE, Wasielewski MR, Lewis FD. Direct Observation of the Hole Carriers in DNA Photoinduced Charge Transport. J Am Chem Soc 2016; 138:5491-4. [DOI: 10.1021/jacs.6b00702] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michelle A. Harris
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Kristen E. Brown
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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60
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Dutta D, Nagapradeep N, Zhu H, Forsyth M, Verma S, Bhattacharyya AJ. N7-(carboxymethyl)guanine-Lithium Crystalline Complex: A Bioinspired Solid Electrolyte. Sci Rep 2016; 6:24499. [PMID: 27091631 PMCID: PMC4835778 DOI: 10.1038/srep24499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/30/2016] [Indexed: 11/23/2022] Open
Abstract
Electrochemical device with components having direct significance to biological life
processes is a potent futuristic strategy for the realization of all-round green and
sustainable development. We present here synthesis design, structural analysis and
ion transport of a novel solid organic electrolyte (G7Li), a compound reminiscent of
ion channels, derived from regioisomeric N7-guanine-carboxylate conjugate and
Li-ions. G7Li, with it’s in-built supply of Li+-ions,
exhibited remarkably high lithium-ion transference number (= 0.75) and
tunable room temperature ionic conductivity spanning three decades
(≈10−7 to
10−3 Ω−1 cm−1)
as a function of moisture content. The ionic conductivity show a distinct reversible
transition around 80–100 °C, from a dual
Li+ and H+
(<100 °C) to a pure Li+ conductor
(>100 °C). Systematic studies reveal a transition
from water-assisted Li-ion transport to Li hopping-like mechanism involving
guanine-Li coordination. While as-synthesized G7Li has potential in humidity
sensors, the anhydrous G7Li is attractive for rechargeable batteries.
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Affiliation(s)
- Dipak Dutta
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012 (Karnataka), India
| | - N Nagapradeep
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur-208016 (UP), India
| | - Haijin Zhu
- Institute for Frontier Materials, Deakin University, Waurn Ponds, VIC3216, Australia
| | - Maria Forsyth
- Institute for Frontier Materials, Deakin University, Waurn Ponds, VIC3216, Australia
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur-208016 (UP), India.,Centre for Nanosciences, Indian Institute of Technology, Kanpur, Kanpur-208016 (UP), India.,Centre for Environmental Science and Technology, Indian Institute of Technology, Kanpur, Kanpur-208016 (UP), India
| | - Aninda J Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012 (Karnataka), India
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61
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Changenet-Barret P, Gustavsson T, Markovitsi D, Manet I. Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy. Chemphyschem 2016; 17:1264-72. [PMID: 26790038 DOI: 10.1002/cphc.201501091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 01/23/2023]
Abstract
Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.
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Affiliation(s)
- Pascale Changenet-Barret
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France. .,LOB, CNRS, INSERM, Université Paris Saclay, 91128, Palaiseau, France.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, CNR, via P. Gobetti 101, 40129, Bologna, Italy.
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62
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Zhang F, Wang HW, Tominaga K, Hayashi M. Characteristics of Low-Frequency Molecular Phonon Modes Studied by THz Spectroscopy and Solid-State ab Initio Theory: Polymorphs I and III of Diflunisal. J Phys Chem B 2016; 120:1698-710. [PMID: 26808927 DOI: 10.1021/acs.jpcb.5b08798] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
THz absorption spectra of two polymorphs of diflunisal, form I and form III, exhibit distinct features due to the influence of packing conformations on the frequency distributions and IR activities of gamma point phonon modes within the 100 cm(-1) region. In order to understand the origins of these THz modes, we perform a detailed mode analysis. The result shows that although the spectral features are different, these low-frequency phonon modes of the two molecular polymorphs have similar vibrational characteristics in terms of harmonic couplings of intermolecular and intramolecular vibrations.
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Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center, Kobe University , Kobe 657-8501, Japan
| | - Houng-Wei Wang
- Center for Condensed Matter Sciences, National Taiwan University , 1 Roosevelt Road Sec. 4, Taipei 10617, Taiwan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University , Kobe 657-8501, Japan
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences, National Taiwan University , 1 Roosevelt Road Sec. 4, Taipei 10617, Taiwan
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63
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Low-dose carbon-based nanoparticle-induced effects in A549 lung cells determined by biospectroscopy are associated with increases in genomic methylation. Sci Rep 2016; 6:20207. [PMID: 26831369 PMCID: PMC4735790 DOI: 10.1038/srep20207] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/23/2015] [Indexed: 11/17/2022] Open
Abstract
Nanotechnology has introduced many manufactured carbon-based nanoparticles (CNPs) into our environment, generating a debate into their risks and benefits. Numerous nanotoxicology investigations have been carried, and nanoparticle-induced toxic effects have been reported. However, there remain gaps in our knowledge, primarily regarding mechanism. Herein, we assessed the global alterations induced by CNPs in A549 lung cells using biospectroscopy techniques, including attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and surface-enhanced Raman spectroscopy (SERS). A549 cells were treated with fullerene (C60), long or short multi-walled carbon nanotubes, or single-walled carbon nanotubes at concentrations of 0.1 mg/L, 0.01 mg/L and 0.001 mg/L. Exposed cells were then analysed by ATR-FTIR spectroscopy and SERS. Spectra were pre-processed via computational analysis, and information on biochemical alterations in exposed cells were identified. Additionally, global DNA methylation levels in cells exposed to CNPs at 0.1 mg/L were determined using HPLC-MS and genetic regulators (for DNA methylation) were checked by quantitative real-time RT-PCR. It was found that CNPs exert marked effects in A549 cells and also contribute to increases in global DNA methylation. For the first time, this study highlights that real-world levels of nanoparticles can alter the methylome of exposed cells; this could have enormous implications for their regulatory assessment.
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64
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Kuss-Petermann M, Wenger OS. Electron Transfer Rate Maxima at Large Donor-Acceptor Distances. J Am Chem Soc 2016; 138:1349-58. [PMID: 26800279 DOI: 10.1021/jacs.5b11953] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Because of their low mass, electrons can transfer rapidly over long (>15 Å) distances, but usually reaction rates decrease with increasing donor-acceptor distance. We report here on electron transfer rate maxima at donor-acceptor separations of 30.6 Å, observed for thermal electron transfer between an anthraquinone radical anion and a triarylamine radical cation in three homologous series of rigid-rod-like donor-photosensitizer-acceptor triads with p-xylene bridges. Our experimental observations can be explained by a weak distance dependence of electronic donor-acceptor coupling combined with a strong increase of the (outer-sphere) reorganization energy with increasing distance, as predicted by electron transfer theory more than 30 years ago. The observed effect has important consequences for light-to-chemical energy conversion.
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Affiliation(s)
- Martin Kuss-Petermann
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Oliver S Wenger
- Department of Chemistry, University of Basel , St. Johanns-Ring 19, 4056 Basel, Switzerland
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65
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Lin SH, Fujitsuka M, Majima T. Excess-Electron Transfer in DNA by a Fluctuation-Assisted Hopping Mechanism. J Phys Chem B 2016; 120:660-6. [DOI: 10.1021/acs.jpcb.5b10857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
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66
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Liu W, Liu J, Zheng G, Ke S, Miao M, Kioussis N. Electronic Structure Change in DNA Caused by Base Pair Motions and Its Effect on Charge Transfer in DNA Chains. Aust J Chem 2016. [DOI: 10.1071/ch15177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
One important aspect of carrier transfer in DNA is its coupling with atomic motions. The collective motion of the base pairs can either improve the charge transfer by enhancing the π stacking between the bases, or trap the carriers due to strong coupling. By utilizing a pseudo-helical base pair stack model, we systematically studied the electronic structure and its dependence to geometry changes that represent the important DNA motions, including the translation, the twist and the torsion of the base pairs. Our calculations reveal that the above motions may significantly change the electron structure and affect their transport properties. In order to improve the transport of carriers in DNA so that it can become a prospective material in future electronics, it is necessary to make large changes to the atomic structure. Our calculations of the electronic structure under large geometry variation, including large base pair stacking deformation and the insertion of phenyl rings in the bases, can provide good guidelines for such structural modifications of DNA.
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67
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Yoo-Kong S, Liewrian W. Double path integral method for obtaining the mobility of the one-dimensional charge transport in molecular chain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:135. [PMID: 26701710 DOI: 10.1140/epje/i2015-15135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
We report on a theoretical investigation concerning the polaronic effect on the transport properties of a charge carrier in a one-dimensional molecular chain. Our technique is based on the Feynman's path integral approach. Analytical expressions for the frequency-dependent mobility and effective mass of the carrier are obtained as functions of electron-phonon coupling. The result exhibits the crossover from a nearly free particle to a heavily trapped particle. We find that the mobility depends on temperature and decreases exponentially with increasing temperature at low temperature. It exhibits large polaronic-like behaviour in the case of weak electron-phonon coupling. These results agree with the phase transition (A.S. Mishchenko et al., Phys. Rev. Lett. 114, 146401 (2015)) of transport phenomena related to polaron motion in the molecular chain.
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Affiliation(s)
- Sikarin Yoo-Kong
- Theoretical and Computational Physics (TCP) Group, Department of Physics, Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Theoretical and Computational Science Centre (TaCS), Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Ratchaburi Campus, King Mongkut's University of Technology Thonburi, 70510, Ratchaburi, Thailand.
| | - Watchara Liewrian
- Theoretical and Computational Physics (TCP) Group, Department of Physics, Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Theoretical and Computational Science Centre (TaCS), Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- ThEP Center, Commission of Higher Education, 328 Si Ayuthaya Rd., 10400, Bangkok, Thailand.
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68
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Huang YC, Yu HZ, Sen D. DNA mechatronic devices switched by K+and by Sr2+are structurally, topologically, and electronically distinct. Biopolymers 2015; 103:460-8. [DOI: 10.1002/bip.22595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Yu Chuan Huang
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
| | - Hua-Zhong Yu
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
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69
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Wong JR, Lee KJ, Shu JJ, Shao F. Magnetic Fields Facilitate DNA-Mediated Charge Transport. Biochemistry 2015; 54:3392-9. [DOI: 10.1021/acs.biochem.5b00295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiun Ru Wong
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Kee Jin Lee
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Jian-Jun Shu
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Fangwei Shao
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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70
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Capobianco A, Caruso T, D'Ursi AM, Fusco S, Masi A, Scrima M, Chatgilialoglu C, Peluso A. Delocalized hole domains in Guanine-rich DNA oligonucleotides. J Phys Chem B 2015; 119:5462-6. [PMID: 25839102 DOI: 10.1021/acs.jpcb.5b02940] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential pulse voltammetries of guanine-rich single- and double-stranded oligonucleotides containing up to six consecutive guanines are reported. The observed progressive lowering of the first voltammetric peak potential as the number of adjacent guanines increases unambiguously points toward the establishment of delocalized hole domains; the hole stabilization energy is ca. 0.1 eV per GG step, significantly lower than that observed for AA steps.
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Affiliation(s)
| | | | | | | | - Annalisa Masi
- §Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy
| | | | - Chryssostomos Chatgilialoglu
- §Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy.,∥National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology, 15341 Agia Paraskevi, Athens, Greece
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71
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Karamtzioti P, Papastergiou A, Stefanakis JG, Koumbis AE, Anastasiou I, Koffa M, Fylaktakidou KC. O-Benzoyl pyridine aldoxime and amidoxime derivatives: novel efficient DNA photo-cleavage agents. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00548a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyridine oxime esters are effective DNA photocleavers, causing single-/double-stranded DNA cleavage at concentrations as low as 1 μM.
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Affiliation(s)
- Paraskevi Karamtzioti
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Asterios Papastergiou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - John G. Stefanakis
- Laboratory of Organic Chemistry
- Chemistry Department
- Aristotle University of Thessaloniki
- Thessaloniki
- Greece
| | - Alexandros E. Koumbis
- Laboratory of Organic Chemistry
- Chemistry Department
- Aristotle University of Thessaloniki
- Thessaloniki
- Greece
| | - Ioanna Anastasiou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Maria Koffa
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Konstantina C. Fylaktakidou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
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72
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Borrelli R, Capobianco A, Landi A, Peluso A. Vibronic couplings and coherent electron transfer in bridged systems. Phys Chem Chem Phys 2015; 17:30937-45. [DOI: 10.1039/c5cp01190f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A computational strategy to analyze the dynamics of coherent electron transfer processes in bridged systems, involving three or more electronic states, is presented.
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Affiliation(s)
- Raffaele Borrelli
- Department of Agricultural
- Forestry and Food Science
- University of Torino
- I-10095 Grugliasco
- Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
| | - Alessandro Landi
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
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73
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Wu L, Liu K, Jie J, Song D, Su H. Direct observation of guanine radical cation deprotonation in G-quadruplex DNA. J Am Chem Soc 2014; 137:259-66. [PMID: 25506785 DOI: 10.1021/ja510285t] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G(+•)) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2-H instead of imino proton N1-H) and slower (1-2 orders of magnitude) deprotonation rate of G(+•) within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, mechanistic insights have been further achieved, showing that it should be the non-hydrogen-bonded free proton to be released during deprotonation in G-quadruplexes, which is the N2-H exposed to solvent for G bases in G-quartets or the free N1-H for G base in the loop. The slower N2-H deprotonation rate can thus ensure less interruption of the hole transfer. The unique deprotonation features observed here for G-quadruplexes open possibilities for their interesting applications as molecular electronic devices, while the elucidated mechanisms can provide illuminations for the rational design of G-quadruplex structures toward such applications and enrich the fundamental understandings of DNA radical chemistry.
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Affiliation(s)
- Lidan Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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74
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Karimata A, Suzuki S, Kozaki M, Kimoto K, Nozaki K, Matsushita H, Ikeda N, Akiyama K, Kosumi D, Hashimoto H, Okada K. Direct observation of hole shift and characterization of spin states in radical ion pairs generated from photoinduced electron transfer of (phenothiazine)(n)-anthraquinone (n = 1, 3) dyads. J Phys Chem A 2014; 118:11262-71. [PMID: 25347200 DOI: 10.1021/jp509643q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Photoinduced intramolecular electron transfer of dyad PTZ3-PTZ2-PTZ1-B-AQ consisting of phenothiazine trimer (PTZ3-PTZ2-PTZ1), bicyclo[2.2.2]octane (B), and anthraquinone (AQ) was investigated. After excitation (∼20 ps) of the AQ moiety in THF, a metastable radical ion pair (RIP) PTZ3-PTZ2-PTZ1(+)-B-AQ(-) appeared at ∼620 nm. From 500 ps to 6 ns the spectrum changed to a new absorption (∼950 nm), which was assigned to the hole-shifted stable RIP state PTZ3-PTZ2(+)-PTZ1-B-AQ(-). The time constant of the hole-shift process was determined to be 6.0 ns. The hole-shifted RIP state had a lifetime (τ) of 250 ns and was characterized by spin-polarized signals as a spin-correlated radical pair (SCRP) by means of time-resolved ESR. These results were compared with those for the phenothiazine monomer analog PTZ-B-AQ, which also produced the RIP state PTZ(+)-B-AQ(-) with τ = 1.9 μs. Time-resolved ESR showed an all emission signal pattern showing the triplet mechanism of PTZ-B-(3)AQ* → (3)[PTZ(+)-B-AQ(-)]. The origin of the difference in the lifetimes between the trimer and the monomer RIP states was discussed from various points of view, including free energy difference in the RIP states, reorganization energy difference in the charge recombination process, and the spin-state difference. Of these, the spin-state difference effect provided the most reasonable explanation.
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Affiliation(s)
- Ayumu Karimata
- Department of Chemistry, Graduate School of Science and ⊥Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University , Sumiyoshi-ku, Osaka, 558-8585, Japan
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75
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Brizhik LS, Piette BMAG, Zakrzewski WJ. Donor-acceptor electron transport mediated by solitons. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:052915. [PMID: 25493866 DOI: 10.1103/physreve.90.052915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 06/04/2023]
Abstract
We study the long-range electron and energy transfer mediated by solitons in a quasi-one-dimensional molecular chain (conjugated polymer, alpha-helical macromolecule, etc.) weakly bound to a donor and an acceptor. We show that for certain sets of parameter values in such systems an electron, initially located at the donor molecule, can tunnel to the molecular chain, where it becomes self-trapped in a soliton state, and propagates to the opposite end of the chain practically without energy dissipation. Upon reaching the end, the electron can either bounce back and move in the opposite direction or, for suitable parameter values of the system, tunnel to the acceptor. We estimate the energy efficiency of the donor-acceptor electron transport depending on the parameter values. Our calculations show that the soliton mechanism works for the parameter values of polypeptide macromolecules and conjugated polymers. We also investigate the donor-acceptor electron transport in thermalized molecular chains.
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Affiliation(s)
- L S Brizhik
- Bogolyubov Institute for Theoretical Physics, 03680 Kyiv, Ukraine
| | - B M A G Piette
- Department of Mathematical Sciences, University of Durham, Durham DH1 3LE, United Kingdom
| | - W J Zakrzewski
- Department of Mathematical Sciences, University of Durham, Durham DH1 3LE, United Kingdom
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76
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Quinoxaline-walled π-stacking molecules: synthesis, conformation, and luminescence properties. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.08.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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78
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Huang YC, Sen D. A Twisting Electronic Nanoswitch Made of DNA. Angew Chem Int Ed Engl 2014; 53:14055-9. [DOI: 10.1002/anie.201407729] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/03/2014] [Indexed: 01/12/2023]
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79
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Jalilov AS, Young RM, Eaton SW, Wasielewski MR, Lewis FD. Electronic Interactions of Michler's Ketone with DNA Bases in Synthetic Hairpins. Photochem Photobiol 2014; 91:739-47. [PMID: 25296568 DOI: 10.1111/php.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/30/2014] [Indexed: 11/26/2022]
Abstract
The mechanism and dynamics of photoinduced electron transfer in two families of DNA hairpins possessing Michler's ketone linkers have been investigated by means of steady state and time-resolved transient absorption and emission spectroscopies. The excited state behavior of the diol linker employed in hairpin synthesis is similar to that of Michler's ketone in methanol solution. Hairpins possessing only a Michler's ketone linker undergo fast singlet state charge separation and charge recombination with an adjacent purine base, attributed to well-stacked ground state conformations, and intersystem crossing to the triplet state, attributed to poorly stacked ground state conformations. The failure of the triplet to undergo electron transfer reactions on the 7 ns time scale of our measurements is attributed to the low triplet energy and reduction potential of the twisted triplet state. Hairpins possessing both a Michler's ketone linker and a perylenediimide base surrogate separated by four base pairs undergo photoinduced hole transport from the diimide to Michler's ketone upon excitation of the diimide. The efficiency of hole transport is dependent upon the sequence of the intervening purine bases.
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Affiliation(s)
- Almaz S Jalilov
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, IL
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80
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Electronic transport through oligopeptide chains: An artificial prototype of a molecular diode. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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81
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82
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Yin X, Kong J, De Leon A, Li Y, Ma Z, Wierzbinski E, Achim C, Waldeck DH. Luminescence quenching by photoinduced charge transfer between metal complexes in peptide nucleic acids. J Phys Chem B 2014; 118:9037-45. [PMID: 24975518 DOI: 10.1021/jp5027042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.
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Affiliation(s)
- Xing Yin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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83
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Mechatronic DNA devices driven by a G-quadruplex-binding platinum ligand. Bioorg Med Chem 2014; 22:4376-83. [PMID: 24909681 DOI: 10.1016/j.bmc.2014.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 01/18/2023]
Abstract
Contractile duplexes are DNA double helices that incorporate two strategically placed patches of guanine-guanine (G·G) base mismatches. Such duplexes are cation-driven mechatronic devices, able to toggle between states with distinct mechanical and charge conduction properties. In aqueous lithium chloride solution contractile duplexes have an extended (E) and poorly conductive conformation; however, potassium ions drive them to a relatively conductive and structurally contracted (C) conformation, via intramolecular G-quadruplex formation. Here, we report that even in the absence of K(+) ions, a known G-quadruplex binding ligand, Pt-PIP [phenylphenanthroimidazole ethylenediamine platinum(II)] efficiently promotes the E→C transition, while a poor binder, Pt-bpy [bipyridine ethylenediamine platinum(II)], does not promote this transition. An examination of E→C transitions within two different designs for DNA contractile helices found an unexpected complexity: the formation of distinct C states, both electrically conductive, but possessing dissimilar DNA topologies. Ligand-driven DNA mechatronic devices such as these may constitute prototypes for electronic biosensors that identify G-quadruplex binding ligands.
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84
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Behmand B, Wagner JR, Sanche L, Hunting DJ. Cisplatin intrastrand adducts sensitize DNA to base damage by hydrated electrons. J Phys Chem B 2014; 118:4803-8. [PMID: 24779712 PMCID: PMC4623755 DOI: 10.1021/jp5014913] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oligonucleotide TTTTTGTGTTT with or without a cisplatin adduct was reacted with hydrated electrons generated by ionizing radiation. Hydroxyl radicals were quenched with ethylenediaminetetraacetic acid (EDTA), and the solutions were bubbled with wet nitrogen to eliminate oxygen, a scavenger of hydrated electrons. Prior to irradiation, the structure of the initial cisplatin adduct was identified by mass spectrometry as G-cisplatin-G. Radiation damage to DNA bases was quantified by high-performance liquid chromatography (HPLC), after enzymatic digestion of the TTTTTGTGTTT-cisplatin complex to deoxyribonucleosides. The masses of the platinum adducts following digestion and separation by HPLC were measured by mass spectrometry. Our results demonstrate that hydrated electrons induce damage to thymines as well as detachment of the cisplatin moiety from both guanines in the oligonucleotide. This detachment regenerates both unmodified guanine and damaged guanine, in equimolar amounts. At 1000 Gy, a net average of 2.5 thymines and 1 guanine are damaged for each platinum lost from the oligonucleotide. Given the extensive base damage that occurs for each cisplatin adduct lost, it is clear that, prior to undergoing detachment, these adducts must catalyze several cycles of reactions of hydrated electrons with DNA bases. It is likely that a single reaction leads to the loss of the cisplatin adduct and the damage observed on the guanine base; however, the damage to the thymine bases must require the continued presence of the cisplatin adduct, acting as a catalyst. To our knowledge, this is the first time that platinum-DNA adducts have been shown to have catalytic activity. We propose two pathways for the interaction of hydrated electrons with TTTTTGTGTTT-cisplatin: (1) the hydrated electron is initially captured by a thymine base and transferred by base to base electron hopping to the guanine site, where the cisplatin moiety detaches from the oligonucleotide via dissociative electron attachment, and (2) the hydrated electron interacts directly with the platinum-guanine adduct and induces detachment of the cisplatin moiety via dissociative electron attachment. Although the precise mechanism remains to be elucidated, our results provide important insights into the radiosensitization of DNA by cisplatin.
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Affiliation(s)
- B. Behmand
- Groupe en sciences des radiations, Faculté de médicine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - J. R. Wagner
- Groupe en sciences des radiations, Faculté de médicine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - L. Sanche
- Groupe en sciences des radiations, Faculté de médicine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - D. J. Hunting
- Groupe en sciences des radiations, Faculté de médicine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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85
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Zhang F, Hayashi M, Wang HW, Tominaga K, Kambara O, Nishizawa JI, Sasaki T. Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes. J Chem Phys 2014; 140:174509. [DOI: 10.1063/1.4873421] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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86
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Wong JR, Shao F. 8-Cyclopropyl-2′-Deoxyguanosine: A Hole Trap for DNA-Mediated Charge Transport. Chembiochem 2014; 15:1171-5. [DOI: 10.1002/cbic.201402018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 11/08/2022]
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87
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Rokhlenko Y, Cadet J, Geacintov NE, Shafirovich V. Mechanistic aspects of hydration of guanine radical cations in DNA. J Am Chem Soc 2014; 136:5956-62. [PMID: 24689701 PMCID: PMC4004273 DOI: 10.1021/ja412471u] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The mechanistic aspects of hydration of guanine radical cations, G(•+) in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G(•+) radical one-electron oxidation products were generated by SO4(•-) radical anions derived from the photolysis of S2O8(2-) anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4(•-) radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)(•) with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)(•) radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)(•) decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)(•) radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)(•) radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G(•+):C] base pair. This [G(-H)(•):H(+)C ⇆ G(•+):C] equilibrium allows for the hydration of G(•+) followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G(•+) and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally.
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Affiliation(s)
- Yekaterina Rokhlenko
- Chemistry Department, New York University , 31 Washington Place, New York, New York 10003-5180, United States
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88
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Hu T, Liu X, Liu S, Wang Z, Tang Z. Toward Understanding of Transfer Mechanism between Electrochemiluminescent Dyes and Luminescent Quantum Dots. Anal Chem 2014; 86:3939-46. [DOI: 10.1021/ac5004823] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Tao Hu
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Xuefeng Liu
- National Center for Nanoscience and Technology, Beijing 100090, China
| | - Shaoqin Liu
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Zhenlong Wang
- Key
Laboratory of Microsystems and Micronanostructures Manufacturing,
Ministry of Education, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiyong Tang
- National Center for Nanoscience and Technology, Beijing 100090, China
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89
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Bose A, Basu S. Effect of phosphate group in switching off electron transfer in different media. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2013.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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90
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Cheng HB, Zhang YM, Xu C, Liu Y. Photoresponsive supramolecular complexes as efficient DNA regulator. Sci Rep 2014; 4:4210. [PMID: 24572680 PMCID: PMC3936212 DOI: 10.1038/srep04210] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/11/2014] [Indexed: 12/04/2022] Open
Abstract
Two supramolecular complexes of trans-1⊂CB[8] and trans-2⊂CB[8] were successfully achieved by the controlled selective complexation process of cucurbit[8]uril (CB[8]) with hetero-guest pair containing azobenzene and bispyridinium moieties in aqueous solution, exhibiting the reversibly light-driven movements of CB[8] upon the photocontrollable isomerization of azophenyl axle components. Significantly, the obtained bistable supramolecular complexes and their corresponding [2]pseudorotaxanes could act as a promising concentrator and cleavage agent to regulate the binding behaviors with DNA molecules.
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Affiliation(s)
- Hong-Bo Cheng
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, P. R. China
| | - Ying-Ming Zhang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, P. R. China
| | - Chao Xu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, P. R. China
| | - Yu Liu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, P. R. China
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91
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Devereux SJ, Keane PM, Vasudevan S, Sazanovich IV, Towrie M, Cao Q, Sun XZ, George MW, Cardin CJ, Kane-Maguire NAP, Kelly JM, Quinn SJ. Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods. Dalton Trans 2014; 43:17606-9. [DOI: 10.1039/c4dt01989j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excited-state quenching of DNA intercalated [Cr(phen)2(dppz)]3+ by guanine proceeds by rapid forward and back electron transfer of <3 ps.
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Affiliation(s)
- Stephen J. Devereux
- School of Chemistry and Chemical Biology
- Centre for Synthesis and Chemical Biology
- University College Dublin
- Dublin 4, Ireland
| | - Páraic M. Keane
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
- Department of Chemistry
- University of Reading
| | - Suni Vasudevan
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
| | - Igor V. Sazanovich
- Central Laser Facility
- Research Complex at Harwell
- Science & Technology Facilities Council
- Rutherford Appleton Laboratory
- Didcot, UK
| | - Michael Towrie
- Central Laser Facility
- Research Complex at Harwell
- Science & Technology Facilities Council
- Rutherford Appleton Laboratory
- Didcot, UK
| | - Qian Cao
- Department of Chemistry
- University of Nottingham
- , UK
| | | | | | | | | | - John M. Kelly
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
| | - Susan J. Quinn
- School of Chemistry and Chemical Biology
- Centre for Synthesis and Chemical Biology
- University College Dublin
- Dublin 4, Ireland
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92
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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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93
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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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94
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Yin C, Zhang J, Huo F. Combined spectral experiment and theoretical calculation to study the interaction of 1,4-dihydroxyanthraquinone for metal ions in solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:772-777. [PMID: 23892118 DOI: 10.1016/j.saa.2013.06.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/23/2013] [Accepted: 06/27/2013] [Indexed: 06/02/2023]
Abstract
The interaction between 1,4-dihydroxyanthraquinone (1,4-DHA) and metal ions was studied by UV-Visible and fluorescence spectroscopies in solution. Time-dependent density functional theory calculations confirmed complex structures. The investigation results showed 1,4-DHA can selectively respond some metal ions and can be monitored by UV-Vis, fluorescence spectra and naked-eye. So 1,4-DHA has a potential application in the design of metal ions probe. More, as typical metal ions, Hg(2+) and Er(3+), their reaction abilities for 1,4-DHA were studied in detailed. Experimental results showed they have better response for 1,4-DHA. And theoretical calculation concluded that Er(3+) easily reacts with 1,4-DHA over Hg(2+) attributed to the low reaction energy of Er(3+)-1,4-DHA than Hg(2+)-1,4-DHA.
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Affiliation(s)
- Caixia Yin
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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95
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Koyanagi K, Kita Y, Shigeta Y, Tachikawa M. Binding of a positron to nucleic base molecules and their pairs. Chemphyschem 2013; 14:3458-62. [PMID: 24030868 DOI: 10.1002/cphc.201300549] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Indexed: 11/09/2022]
Abstract
Hole attack: A theoretical one-electron oxidation of nucleic base molecules and their pairs by positron is proposed, based on the calculations for positron-attached neutral forms of species, adenine (A), thymine (T), guanine (G), cytosine (C), and their Watson-Crick base pairs (A-T and G-C). The results reveal that binding of a positron to neutral isolated nucleic base molecules is base-selective.
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Affiliation(s)
- Katsuhiko Koyanagi
- Quantum Chemistry Division, Yokohama City University, Kanazawa-ku, Yokohama 236-0027 (Japan)
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96
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Kratochvílová I, Vala M, Weiter M, Špérová M, Schneider B, Páv O, Šebera J, Rosenberg I, Sychrovský V. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies. Biophys Chem 2013; 180-181:127-34. [DOI: 10.1016/j.bpc.2013.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 12/31/2022]
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97
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Karimata A, Kawauchi H, Suzuki S, Kozaki M, Ikeda N, Keyaki K, Nozaki K, Akiyama K, Okada K. Photoinduced Charge Separation of 10-Phenyl-10H-phenothiazine–2-Phenylanthraquinone Dyad Bridged by Bicyclo[2.2.2]octane. CHEM LETT 2013. [DOI: 10.1246/cl.130062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ayumu Karimata
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Hidetoshi Kawauchi
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Shuichi Suzuki
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Masatoshi Kozaki
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Noriaki Ikeda
- Department of Chemistry and Materials Technology, Kyoto Institute of Technology
| | - Kazutoshi Keyaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama
| | - Koichi Nozaki
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama
| | - Kimio Akiyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
| | - Keiji Okada
- Department of Chemistry, Graduate School of Science, Osaka City University
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98
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Cerreta A, Vobornik D, Dietler G. Fine DNA structure revealed by constant height frequency modulation AFM imaging. Eur Polym J 2013. [DOI: 10.1016/j.eurpolymj.2013.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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99
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Capobianco A, Caruso T, Celentano M, D'Ursi AM, Scrima M, Peluso A. Stacking interactions between adenines in oxidized oligonucleotides. J Phys Chem B 2013; 117:8947-53. [PMID: 23837863 DOI: 10.1021/jp404133a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effects of stacking interactions on the oxidation potentials of single strand oligonucleotides containing up to four consecutive adenines, alternated with thymines and cytosines in different sequences and ratios, have been determined by means of differential pulse voltammetry. Voltammetric measurements point toward the establishment in solution of structured oligonucleotide conformations, in which the nucleobases are well stacked altogether. Molecular dynamics simulations confirm that finding, indicating that single strands assume geometrical parameters characteristic of the B-DNA form. The analysis of the voltammetric signals in terms of a simple effective tight binding quantum model leads one to infer a robust set of parameters for treating hole transfer in one-electron-oxidized DNA containing adenines and thymines.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia, Università di Salerno, I-84084 Fisciano, Salerno, Italy
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100
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Horn A, Fernandes C, Parrilha GL, Kanashiro MM, Borges FV, de Melo EJT, Schenk G, Terenzi H, Pich CT. Highly efficient synthetic iron-dependent nucleases activate both intrinsic and extrinsic apoptotic death pathways in leukemia cancer cells. J Inorg Biochem 2013; 128:38-47. [PMID: 23933562 DOI: 10.1016/j.jinorgbio.2013.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 07/01/2013] [Accepted: 07/08/2013] [Indexed: 12/28/2022]
Abstract
The nuclease activity and the cytotoxicity toward human leukemia cancer cells of iron complexes, [Fe(HPClNOL)Cl2]NO3 (1), [Cl(HPClNOL)Fe(μ-O)Fe(HPClNOL)Cl]Cl2·2H2O (2), and [(SO4)(HPClNOL)Fe(μ-O)Fe(HPClNOL)(SO4)]·6H2O (3) (HPClNOL=1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol), were investigated. Each complex was able to promote plasmid DNA cleavage and change the supercoiled form of the plasmid to circular and linear ones. Kinetic data revealed that (1), (2) and (3) increase the rate of DNA hydrolysis about 278, 192 and 339 million-fold, respectively. The activity of the complexes was inhibited by distamycin, indicating that they interact with the minor groove of the DNA. The cytotoxic activity of the complexes toward U937, HL-60, Jukart and THP-1 leukemia cancer cells was studied employing 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), fluorescence and electronic transmission microscopies, flow cytometry and a cytochrome C release assay. Compound (2) has the highest activity toward cancer cells and is the least toxic for normal ones (i.e. peripheral blood mononuclear cells (PBMCs)). In contrast, compound (1) is the least active toward cancer cells but displays the highest toxicity toward normal cells. Transmission electronic microscopy indicates that cell death shows features typical of apoptotic cells, which was confirmed using the annexin V-FITC/PI (fluorescein isothiocyanate/propidium iodide) assay. Furthermore, our data demonstrate that at an early stage during the treatment with complex (2) mitochondria lose their transmembrane potential, resulting in cytochrome C release. A quantification of caspases 3, 9 (intrinsic apoptosis pathway) and caspase 8 (extrinsic apoptosis pathway) indicated that both the intrinsic (via mitochondria) and extrinsic (via death receptors) pathways are involved in the apoptotic stimuli.
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Affiliation(s)
- Adolfo Horn
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, 28013-602 RJ, Brazil.
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