1
|
Monari A, Burger A, Dumont E. Rationalizing the environment-dependent photophysical behavior of a DNA luminescent probe by classical and non-adiabatic molecular dynamics simulations. Photochem Photobiol Sci 2023; 22:2081-2092. [PMID: 37166569 DOI: 10.1007/s43630-023-00431-3] [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: 02/09/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
Environment-sensitive fluorescent nucleoside analogs are of utmost importance to investigate the structure of nucleic acids, their intrinsic flexibility, and sequence-specific DNA- and RNA-binding proteins. The latter play indeed a key role in transcription, translation as well as in the regulation of RNA stability, localization and turnover, and many other cellular processes. The sensitivity of the embedded fluorophore to polarity, hydration, and base stacking is clearly dependent on the specific excited-state relaxation mechanism and can be rationalized combining experimental and computational techniques. In this work, we elucidate the mechanisms leading to the population of the triplet state manifold for a versatile nucleobase surrogate, namely the 2-thienyl-3-hydroxychromone in gas phase, owing to non-adiabatic molecular dynamics simulations. Furthermore, we analyze its behavior in the B-DNA environment via classical molecular dynamics simulations, which evidence a rapid extrusion of the adenine facing the 2-thienyl-3-hydroxychromone nucleobase surrogate. Our simulations provide new insights into the dynamics of this family of chromophores, which could give rise to an integrated view and a fine tuning of their photochemistry, and namely the role of excited-state intramolecular proton transfer for the rational design of the next generation of fluorescent nucleoside analogs.
Collapse
Affiliation(s)
- Antonio Monari
- Université Paris Cité and CNRS, ITODYS, 75006, Paris, France.
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, 06108, Nice, France
| | - Elise Dumont
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, 06108, Nice, France.
- Institut Universitaire de France, 5 Rue Descartes, 75005, Paris, France.
| |
Collapse
|
2
|
Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| |
Collapse
|
3
|
Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
4
|
Paterson KA, Arlt J, Jones AC. Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution. Methods Appl Fluoresc 2020; 8:025002. [PMID: 32000159 DOI: 10.1088/2050-6120/ab71c3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
2-aminopurine (2AP) is a responsive fluorescent base analogue that is used widely as a probe of the local molecular environment in DNA. The ability of 2AP to report changes in local conformation and base-stacking interactions arises from the efficient quenching of its fluorescence by the natural DNA bases. However, the mechanism of this inter-base quenching remains imperfectly understood. Two previous studies of the collisional quenching of 2AP by the natural bases, in different buffer solutions, showed that dynamic quenching efficiency depends on the identity of the natural base, but disagreed on the relative quenching efficiencies of the bases. We report a comprehensive investigation of inter-base quenching of 2AP by the natural nucleoside monophosphates (NMPs), replicating the buffer conditions used in the previous studies. Using time-resolved fluorescence measurements to distinguish between dynamic and static quenching, we find that the dynamic quenching rate constants of the different bases show a consistent trend across both buffers, and this is in line with a charge-transfer mechanism. Time-resolved measurements also provide insight into static quenching, revealing formation of 2AP-NMP ground-state complexes in which 2AP displays a very short fluorescence lifetime, comparable to that seen in oligonucleotides. In these complexes, the dependence of the rate of quenching on the partner base also supports a charge-transfer mechanism.
Collapse
Affiliation(s)
- Kyle A Paterson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | | | | |
Collapse
|
5
|
Sardana D, Yadav K, Shweta H, Clovis NS, Alam P, Sen S. Origin of Slow Solvation Dynamics in DNA: DAPI in Minor Groove of Dickerson-Drew DNA. J Phys Chem B 2019; 123:10202-10216. [PMID: 31589442 DOI: 10.1021/acs.jpcb.9b09275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The measurement and understanding of collective solvation dynamics in DNA have vital biological implications, as protein and ligand binding to DNA can be directly controlled by complex electrostatic interactions of anionic DNA and surrounding dipolar water, and ions. Time-resolved fluorescence Stokes shift (TRFSS) experiments revealed anomalously slow solvation dynamics in DNA much beyond 100 ps that follow either power-law or slow multiexponential decay over several nanoseconds. The origin of such dispersed dynamics remains difficult to understand. Here we compare results of TRFSS experiments to molecular dynamics (MD) simulations of well-known 4',6-diamidino-2-phenylindole (DAPI)/Dickerson-Drew DNA complex over five decades of time from 100 fs to 10 ns to understand the origin of such dispersed dynamics. We show that the solvation time-correlation function (TCF) calculated from 200 ns simulation trajectory (total 800 ns) captures most features of slow dynamics as measured in TRFSS experiments. Decomposition of TCF into individual components unravels that slow dynamics originating from dynamically coupled DNA-water motion, although contribution from coupled water-Na+ motion is non-negligible. The analysis of residence time of water molecules around the probe (DAPI) reveals broad distribution from ∼6 ps to ∼3.5 ns: Several (49 nos.) water molecules show residences time greater than 500 ps, of which at least 14 water molecules show residence times of more than 1 ns in the first solvation shell of DAPI. Most of these slow water molecules are found to occupy two hydration sites in the minor groove near DAPI binding site. The residence time of Na+, however, is found to vary within ∼17-120 ps. Remarkably, we find that freezing the DNA fluctuations in simulation eliminates slower dynamics beyond ∼100 ps, where water and Na+ dynamics become faster, although strong anticorrelation exists between them. These results indicate that primary origin of slow dynamics lies within the slow fluctuations of DNA parts that couple with nearby slow water and ions to control the dispersed collective solvation dynamics in DNA minor groove.
Collapse
Affiliation(s)
- Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences , Jawaharlal Nehru University , New Delhi 110067 , India
| |
Collapse
|
6
|
|
7
|
O'Brien E, Holt ME, Thompson MK, Salay LE, Ehlinger AC, Chazin WJ, Barton JK. The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport. Science 2017; 355:355/6327/eaag1789. [PMID: 28232525 DOI: 10.1126/science.aag1789] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023]
Abstract
DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.
Collapse
Affiliation(s)
- Elizabeth O'Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marilyn E Holt
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew K Thompson
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren E Salay
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Aaron C Ehlinger
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
8
|
Beall E, Ulku S, Liu C, Wierzbinski E, Zhang Y, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes. J Am Chem Soc 2017; 139:6726-6735. [PMID: 28434220 DOI: 10.1021/jacs.7b02260] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G0, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.
Collapse
Affiliation(s)
- Edward Beall
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Selma Ulku
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Chaoren Liu
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Emil Wierzbinski
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Yuqi Zhang
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Yookyung Bae
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Catalina Achim
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - David H Waldeck
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
9
|
Remington JM, Philip AM, Hariharan M, Kohler B. On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides. J Chem Phys 2017; 145:155101. [PMID: 27782452 DOI: 10.1063/1.4964718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.
Collapse
Affiliation(s)
- Jacob M Remington
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
| | - Abbey M Philip
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Bern Kohler
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
| |
Collapse
|
10
|
Levine AD, Iv M, Peskin U. Length-independent transport rates in biomolecules by quantum mechanical unfurling. Chem Sci 2016; 7:1535-1542. [PMID: 28808530 PMCID: PMC5530864 DOI: 10.1039/c5sc03495g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/19/2015] [Indexed: 11/22/2022] Open
Abstract
Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-independent transfer rate. We show that the rigid molecular structure of a poly-A bridge supports single step transitions from a localized hole state to delocalized states, spread over the entire bridge. Since propagation to the bridge end is a single step process (termed quantum unfurling) the transfer rate becomes independent of the bridge length. This explanation is consistent with experimental results, and emphasizes the importance of structural order in charge transfer through bio-molecular systems.
Collapse
Affiliation(s)
- Ariel D Levine
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Michael Iv
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Uri Peskin
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| |
Collapse
|
13
|
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Collapse
|
14
|
Sholokh M, Sharma R, Shin D, Das R, Zaporozhets OA, Tor Y, Mély Y. Conquering 2-aminopurine's deficiencies: highly emissive isomorphic guanosine surrogate faithfully monitors guanosine conformation and dynamics in DNA. J Am Chem Soc 2015; 137:3185-8. [PMID: 25714036 DOI: 10.1021/ja513107r] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The archetypical fluorescent nucleoside analog, 2-aminopurine (2Ap), has been used in countless assays, though it suffers from very low quantum yield, especially when included in double strands, and from the fact that its residual emission frequently does not represent biologically relevant conformations. To conquer 2Ap's deficiencies, deoxythienoguanosine (d(th)G) was recently developed. Here, steady-state and time-resolved fluorescence spectroscopy was used to compare the ability of 2Ap and d(th)G, to substitute and provide relevant structural and dynamical information on a key G residue in the (-) DNA copy of the HIV-1 primer binding site, (-)PBS, both in its stem loop conformation and in the corresponding (-)/(+)PBS duplex. In contrast to 2Ap, this fluorescent nucleoside when included in (-)PBS or (-)/(+)PBS duplex fully preserves their stability and exhibits a respectable quantum yield and a simple fluorescence decay, with marginal amounts of dark species. In further contrast to 2Ap, the fluorescently detected d(th)G species reflect the predominantly populated G conformers, which allows exploring their relevant dynamics. Being able to perfectly substitute G residues, d(th)G will transform nucleic acid biophysics by allowing, for the first time, to selectively and faithfully monitor the conformations and dynamics of a given G residue in a DNA sequence.
Collapse
Affiliation(s)
- Marianna Sholokh
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch, France
| | | | | | | | | | | | | |
Collapse
|
15
|
Sengupta C, Basu S. A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains. RSC Adv 2015. [DOI: 10.1039/c5ra13035b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.
Collapse
Affiliation(s)
- Chaitrali Sengupta
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| |
Collapse
|
16
|
Khan A. Effect of guanine–cytosine base pair orientation and cluster size on ionization energy and charge distribution: A theoretical study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Wang X, You Z, Sha H, Cheng Y, Zhu H, Sun W. Sensitive electrochemical detection of dopamine with a DNA/graphene bi-layer modified carbon ionic liquid electrode. Talanta 2014; 128:373-8. [DOI: 10.1016/j.talanta.2014.04.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 04/22/2014] [Accepted: 04/29/2014] [Indexed: 11/28/2022]
|
18
|
St-Pierre P, McCluskey K, Shaw E, Penedo JC, Lafontaine DA. Fluorescence tools to investigate riboswitch structural dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1005-1019. [PMID: 24863161 DOI: 10.1016/j.bbagrm.2014.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 11/15/2022]
Abstract
Riboswitches are novel regulatory elements that respond to cellular metabolites to control gene expression. They are constituted of highly conserved domains that have evolved to recognize specific metabolites. Such domains, so-called aptamers, are folded into intricate structures to enable metabolite recognition. Over the years, the development of ensemble and single-molecule fluorescence techniques has allowed to probe most of the mechanistic aspects of aptamer folding and ligand binding. In this review, we summarize the current fluorescence toolkit available to study riboswitch structural dynamics. We fist describe those methods based on fluorescent nucleotide analogues, mostly 2-aminopurine (2AP), to investigate short-range conformational changes, including some key steady-state and time-resolved examples that exemplify the versatility of fluorescent analogues as structural probes. The study of long-range structural changes by Förster resonance energy transfer (FRET) is mostly discussed in the context of single-molecule studies, including some recent developments based on the combination of single-molecule FRET techniques with controlled chemical denaturation methods. This article is part of a Special Issue entitled: Riboswitches.
Collapse
Affiliation(s)
- Patrick St-Pierre
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Kaley McCluskey
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - Euan Shaw
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom
| | - J C Penedo
- SUPA, School of Physics and Astronomy University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom; Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, United Kingdom.
| | - D A Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| |
Collapse
|
19
|
Kratochvílová I, Golan M, Vala M, Špérová M, Weiter M, Páv O, Šebera J, Rosenberg I, Sychrovský V, Tanaka Y, Bickelhaupt FM. Theoretical and Experimental Study of Charge Transfer through DNA: Impact of Mercury Mediated T-Hg-T Base Pair. J Phys Chem B 2014; 118:5374-81. [DOI: 10.1021/jp501986a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Irena Kratochvílová
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Faculty of Nuclear Physics
and Physical Engineering, Czech Technical University in Prague, Zikova 1, 160 00 Prague 6, Czech Republic
| | - Martin Golan
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Physics,
Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Martin Vala
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Miroslava Špérová
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Martin Weiter
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Jakub Šebera
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale
Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and
Materials (IMM), Radboud University Nijmegen, Comeniuslaan 4, 6525 HP Nijmegen, The Netherlands
| |
Collapse
|
20
|
Merz T, Wenninger M, Weinberger M, Riedle E, Wagenknecht HA, Schütz M. Conformational control of benzophenone-sensitized charge transfer in dinucleotides. Phys Chem Chem Phys 2014; 15:18607-19. [PMID: 24084688 DOI: 10.1039/c3cp52344f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Charge transfer in DNA cannot be understood without addressing the complex conformational flexibility, which occurs on a wide range of timescales. In order to reduce this complexity four dinucleotide models 1X consisting of benzophenone linked by a phosphodiester to one of the natural nucleosides X = A, G, T, C were studied in water and methanol. The theoretical work focuses on the dynamics and electronic structure of 1G. Predominant conformations in the two solvents were obtained by molecular dynamics simulations. 1G in MeOH adopts mainly an open geometry with a distance of 12–16 Å between the two aromatic parts. In H2O the two parts of 1G form primarily a stacked conformation yielding a distance of 5–6 Å. The low-lying excited states were investigated by electronic structure theory in a QM/MM environment for representative snapshots of the trajectories. Photo-induced intramolecular charge transfer in the S1 state occurs exclusively in the stacked conformation. Ultrafast transient absorption spectroscopy with 1X reveals fast charge transfer from S1 in both solvents with varying yields. Significant charge transfer from the T1 state is only found for the nucleobases with the lowest oxidation potential: in H2O, charge transfer occurs with 3.2 × 10(9) s(-1) for 1A and 6.0 × 10(9) s(-1) for 1G. The reorganization energy remains nearly unchanged going from MeOH to the more polar H2O. The electronic coupling is rather low even for the stacked conformation with H(AB) = 3 meV and explains the moderate charge transfer rates. The solvent controls the conformational distribution and therefore gates the charge transfer due to differences in distance and stacking.
Collapse
Affiliation(s)
- Thomas Merz
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany.
| | | | | | | | | | | |
Collapse
|
21
|
Adhikary A, Kumar A, Palmer BJ, Todd AD, Sevilla MD. Formation of S-Cl phosphorothioate adduct radicals in dsDNA S-oligomers: hole transfer to guanine vs disulfide anion radical formation. J Am Chem Soc 2013; 135:12827-38. [PMID: 23885974 DOI: 10.1021/ja406121x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In phosphorothioate-containing dsDNA oligomers (S-oligomers), one of the two nonbridging oxygen atoms in the phosphate moiety of the sugar-phosphate backbone is replaced by sulfur. In this work, electron spin resonance (ESR) studies of one-electron oxidation of several S-oligomers by Cl2(•-) at low temperatures are performed. Electrophilic addition of Cl2(•-) to phosphorothioate with elimination of Cl(-) leads to the formation of a two-center three-electron σ(2)σ*(1)-bonded adduct radical (-P-S-̇Cl). In AT S-oligomers with multiple phosphorothioates, i.e., d[ATATAsTsAsT]2, -P-S-̇Cl reacts with a neighboring phosphorothioate to form the σ(2)σ*(1)-bonded disulfide anion radical ([-P-S-̇S-P-](-)). With AT S-oligomers with a single phosphorothioate, i.e., d[ATTTAsAAT]2, reduced levels of conversion of -P-S-̇Cl to [-P-S-̇S-P-](-) are found. For guanine-containing S-oligomers containing one phosphorothioate, -P-S-̇Cl results in one-electron oxidation of guanine base but not of A, C, or T, thereby leading to selective hole transfer to G. The redox potential of -P-S-̇Cl is thus higher than that of G but is lower than those of A, C, and T. Spectral assignments to -P-S-̇Cl and [-P-S-̇S-P-](-) are based on reaction of Cl2(•-) with the model compound diisopropyl phosphorothioate. The results found for d[TGCGsCsGCGCA]2 suggest that [-P-S-̇S-P-](-) undergoes electron transfer to the one-electron-oxidized G, healing the base but producing a cyclic disulfide-bonded backbone with a substantial bond strength (50 kcal/mol). Formation of -P-S-̇Cl and its conversion to [-P-S-̇S-P-](-) are found to be unaffected by O2, and this is supported by the theoretically calculated electron affinities and reduction potentials of [-P-S-S-P-] and O2.
Collapse
Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
| | | | | | | | | |
Collapse
|
22
|
Liang J, Nguyen QL, Matsika S. Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases. Photochem Photobiol Sci 2013; 12:1387-400. [PMID: 23625036 PMCID: PMC5006741 DOI: 10.1039/c3pp25449f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 03/29/2013] [Indexed: 12/26/2022]
Abstract
Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.
Collapse
Affiliation(s)
- JingXin Liang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Quynh L. Nguyen
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | | |
Collapse
|
23
|
Reorganization, activation and ionization energies for hole transfer reactions through inosine–cytosine, 2-aminopurine – Thymine, adenine–thymine, and guanine–cytosine base pairs: A computational study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Osakada Y, Kawai K, Majima T. Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| |
Collapse
|
25
|
Wohlgamuth CH, McWilliams MA, Slinker JD. Temperature dependence of electrochemical DNA charge transport: influence of a mismatch. Anal Chem 2013; 85:1462-7. [PMID: 23252597 DOI: 10.1021/ac302508f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge transfer through DNA is of interest as DNA is both the quintessential biomolecule of all living organisms and a self-organizing element in bioelectronic circuits and sensing applications. Here, we report the temperature-dependent properties of DNA charge transport in an electronically relevant arrangement of DNA monolayers on gold under biologically relevant conditions, and we track the effects of incorporating a CA single base pair mismatch. Charge transfer (CT) through double stranded, 17mer monolayers was monitored by following the yield of electrochemical reduction of a Nile blue redox probe conjugated to a modified thymine. Analysis with cyclic voltammetry and square wave voltammetry shows that DNA CT increases significantly with temperature, indicative of more DNA bridges becoming active for transport. The mismatch was found to attenuate DNA CT at lower temperatures, but the effect of the mismatch diminished as temperature was increased. Voltammograms were analyzed to extract the electron transfer rate k(0), the electron transfer coefficient α, and the redox-active surface coverage Γ*. Arrhenius behavior was observed, with activation energies of 100 meV for electron transfer through well-matched DNA. Single CA mismatches increased the activation energy by 60 meV. These results have clear implications for sensing applications and are evaluated with respect to the prominent models of DNA CT.
Collapse
Affiliation(s)
- Chris H Wohlgamuth
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | | | | |
Collapse
|
26
|
Muren NB, Olmon ED, Barton JK. Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport. Phys Chem Chem Phys 2012; 14:13754-71. [PMID: 22850865 PMCID: PMC3478128 DOI: 10.1039/c2cp41602f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.
Collapse
Affiliation(s)
- Natalie B. Muren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Eric D. Olmon
- 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
| |
Collapse
|
27
|
Kawai K, Hayashi M, Majima T. Hole transfer in LNA and 5-Me-2'-deoxyzebularine-modified DNA. J Am Chem Soc 2012; 134:9406-9. [PMID: 22591000 DOI: 10.1021/ja302641e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the measurement of hole-transfer rate constants (k(ht)) in locked nucleic acid (LNA) and 5-Me-2'-deoxyzebularine (B)-modified DNA. LNA modification, which makes DNA more rigid, caused a decrease of more than 2 orders of magnitude in k(ht), whereas B modification, which increases DNA flexibility, increased k(ht) by more than 20-fold. The present results clearly showed that hole-transfer efficiency in DNA can be increased by increasing DNA flexibility.
Collapse
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan.
| | | | | |
Collapse
|
28
|
Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Reppireddy S, Venkatramani R, Keinan S, Ly DH, Madrid M, Beratan DN, Achim C, Waldeck DH. Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes. J Am Chem Soc 2012; 134:9335-42. [DOI: 10.1021/ja301677z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emil Wierzbinski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Arnie de Leon
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Xing Yin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Alexander Balaeff
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Kathryn L. Davis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Srinivas Reppireddy
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Ravindra Venkatramani
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Shahar Keinan
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Danith H. Ly
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Marcela Madrid
- Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
| | - David N. Beratan
- Departments of Chemistry, Biochemistry,
and Physics, Duke University, Durham, North
Carolina 27708, United States
| | - Catalina Achim
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - David H. Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| |
Collapse
|
29
|
Kawai K, Hayashi M, Majima T. HOMO energy gap dependence of hole-transfer kinetics in DNA. J Am Chem Soc 2012; 134:4806-11. [PMID: 22335550 DOI: 10.1021/ja2109213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).
Collapse
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | | | | |
Collapse
|
30
|
Kodali G, Narayanan M, Stanley RJ. Excited-state electronic properties of 6-methylisoxanthopterin (6-MI): an experimental and theoretical study. J Phys Chem B 2012; 116:2981-9. [PMID: 22276652 DOI: 10.1021/jp2110083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Methylisoxanthopterin (6-MI) is a pteridine-based guanine analog that has a red-shifted absorption and high fluorescence quantum yield. Its Watson-Crick base-pairing and base stacking properties are similar to guanine. The fluorescence quantum yield of 6-MI is sensitive to its nearest neighbors and base stacking, making it a very useful real-time probe of DNA structure. The fundamental photophysics underlying this fluorescence quenching by base stacking is not well understood. We have explored the excited-state electronic structure of the 6-MI in frozen 77 K LiCl glasses using Stark spectroscopy. These measurements yielded the direction and degree of charge redistribution for the S(0)→S(1) transition as manifested in the difference dipole moment, Δμ(01), and difference static polarizability, TrΔα. TDDFT (time-dependent density functional theory) was employed to calculate the transition energy, oscillator strength, and the dipole moments of the ground and lowest optically bright excited state of 6-MI (S(0)→S(1)). The direction of Δμ(01) was assigned in the molecular frame based on the Stark data and calculations. These results suggest that the C4═O and C2-NH(2) groups are electron-deficient in the excited state, a very different outcome compared with guanine. This implies that Watson-Crick hydrogen bonding in 6-MI may be modulated by absorption of a photon so as to strengthen base pairing, if only transiently. Solvatochromism was also obtained for the absorption and emission spectra of 6-MI in various solvents and compared with the Stark spectroscopic results using both the Lippert-Mataga and Bakhshiev models.
Collapse
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | | | | |
Collapse
|
31
|
Wang Y, Fleurence A, Yamada-Takamura Y, Friedlein R. Intermolecular band dispersion in quasi-one-dimensional adenine assemblies. Chem Commun (Camb) 2011; 47:12349-51. [PMID: 22005662 DOI: 10.1039/c1cc14942c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly-ordered, hydrated adenine multilayer films grown on the surface of highly-oriented pyrolytic graphite, HOPG(0001), display extended electronic states, affording anisotropic band-like charge transport along the π-π stacking direction.
Collapse
Affiliation(s)
- Ying Wang
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, 923-1292, Japan.
| | | | | | | |
Collapse
|
32
|
Olmon ED, Hill MG, Barton JK. Using metal complex reduced states to monitor the oxidation of DNA. Inorg Chem 2011; 50:12034-44. [PMID: 22043853 PMCID: PMC3277451 DOI: 10.1021/ic201511y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Metallointercalating photooxidants interact intimately with the base stack of double-stranded DNA and exhibit rich photophysical and electrochemical properties, making them ideal probes for the study of DNA-mediated charge transport (CT). The complexes [Rh(phi)(2)(bpy')](3+) (phi = 9,10-phenanthrenequinone diimine; bpy' = 4-methyl-4'-(butyric acid)-2,2'-bipyridine), [Ir(ppy)(2)(dppz')](+) (ppy = 2-phenylpyridine; dppz' = 6-(dipyrido[3,2-a:2',3'-c]phenazin-11-yl)hex-5-ynoic acid), and [Re(CO)(3)(dppz)(py')](+) (dppz = dipyrido[2,3-a:2',3'-c]phenazine; py' = 3-(pyridin-4-yl)-propanoic acid) were each covalently tethered to DNA to compare their photooxidation efficiencies. Biochemical studies show that upon irradiation, the three complexes oxidize guanine by long-range DNA-mediated CT with the efficiency: Rh > Re > Ir. Comparison of spectra obtained by spectroelectrochemistry after bulk reduction of the free metal complexes with those obtained by transient absorption (TA) spectroscopy of the conjugates suggests that the reduced metal states form following excitation of the conjugates at 355 nm. Electrochemical experiments and kinetic analysis of the TA decays indicate that the thermodynamic driving force for CT, variations in the efficiency of back electron transfer, and coupling to DNA are the primary factors responsible for the trend observed in the guanine oxidation yields of the three complexes.
Collapse
Affiliation(s)
- Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California 91125, USA
| | - Michael G. Hill
- Department of Chemistry, Occidental College, Los Angeles, California 90041, USA
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California 91125, USA
| |
Collapse
|
33
|
Cornicchi E, Sebastiani F, De Francesco A, Orecchini A, Paciaroni A, Petrillo C, Sacchetti F. Collective density fluctuations of DNA hydration water in the time-window below 1 ps. J Chem Phys 2011; 135:025101. [PMID: 21766968 DOI: 10.1063/1.3609101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coherent density fluctuations propagating through DNA hydration water were studied by neutron scattering spectroscopy. Two collective modes were found to be sustained by the aqueous solvent: a propagating excitation, characterised by a speed of about 3500 m/s, and another one placed at about 6 meV. These results globally agree with those previously found for the coherent excitations in bulk water, although in DNA hydration water the speed of propagating modes is definitely higher than that of the pure solvent. The short-wavelength collective excitations of DNA hydration water are reminiscent of those observed in protein hydration water and in the amorphous forms of ice.
Collapse
Affiliation(s)
- Elena Cornicchi
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy.
| | | | | | | | | | | | | |
Collapse
|
34
|
Multi-walled carbon nanotube-chitosan/poly(amidoamine)/DNA nanocomposite modified gold electrode for determination of dopamine and uric acid under coexistence of ascorbic acid. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2011.01.024] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
35
|
Liang J, Matsika S. Pathways for Fluorescence Quenching in 2-Aminopurine π-Stacked with Pyrimidine Nucleobases. J Am Chem Soc 2011; 133:6799-808. [DOI: 10.1021/ja2007998] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- JingXin Liang
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
36
|
Khanduri D, Adhikary A, Sevilla MD. Highly oxidizing excited states of one-electron-oxidized guanine in DNA: wavelength and pH dependence. J Am Chem Soc 2011; 133:4527-37. [PMID: 21381665 PMCID: PMC3063320 DOI: 10.1021/ja110499a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Excited states of one-electron-oxidized guanine in DNA are known to induce hole transfer to the sugar moiety and on deprotonation result in neutral sugar radicals that are precursors of DNA strand breaks. This work carried out in a homogeneous aqueous glass (7.5 M LiCl) at low temperatures (77-175 K) shows the extent of photoconversion of one-electron-oxidized guanine and the associated yields of individual sugar radicals are crucially controlled by the photon energy, protonation state, and strandedness of the oligomer. In addition to sugar radical formation, highly oxidizing excited states of one-electron-oxidized guanine are produced with 405 nm light at pH 5 and below that are able to oxidize chloride ion in the surrounding solution to form Cl(2)(•-) via an excited-state hole transfer process. Among the various DNA model systems studied in this work, the maximum amount of Cl(2)(•-) is produced with ds (double-stranded) DNA, where the one-electron-oxidized guanine exists in its cation radical form (G(•+):C). Thus, via excited-state hole transfer, the dsDNA is apparently able to protect itself from cation radical excited states by transfer of damage to the surrounding environment.
Collapse
Affiliation(s)
- Deepti Khanduri
- Department of Chemistry Oakland University Rochester, MI 48309
| | | | | |
Collapse
|
37
|
Genereux JC, Wuerth SM, Barton JK. Single-step charge transport through DNA over long distances. J Am Chem Soc 2011; 133:3863-8. [PMID: 21348520 DOI: 10.1021/ja107033v] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.
Collapse
Affiliation(s)
- Joseph C Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | | |
Collapse
|
38
|
Fogarty AC, Jones AC, Camp PJ. Extraction of lifetime distributions from fluorescence decays with application to DNA-base analogues. Phys Chem Chem Phys 2011; 13:3819-30. [DOI: 10.1039/c0cp01779e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
39
|
Affiliation(s)
- Joseph C. Genereux
- 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
| |
Collapse
|
40
|
Khan A. Substituent group effects on reorganization and activation energies: Theoretical study of charge transfer reaction through DNA. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
41
|
Genereux JC, Boal AK, Barton JK. DNA-mediated charge transport in redox sensing and signaling. J Am Chem Soc 2010; 132:891-905. [PMID: 20047321 PMCID: PMC2902267 DOI: 10.1021/ja907669c] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The transport of charge through the DNA base-pair stack offers a route to carry out redox chemistry at a distance. Here we describe characteristics of this chemistry that have been elucidated and how this chemistry may be utilized within the cell. The shallow distance dependence associated with these redox reactions permits DNA-mediated signaling over long molecular distances in the genome and facilitates the activation of redox-sensitive transcription factors globally in response to oxidative stress. The long-range funneling of oxidative damage to sites of low oxidation potential in the genome also may provide a means of protection within the cell. Furthermore, the sensitivity of DNA charge transport to perturbations in base-pair stacking, as may arise with base lesions and mismatches, may be used as a route to scan the genome for damage as a first step in DNA repair. Thus, the ability of double-helical DNA in mediating redox chemistry at a distance provides a natural mechanism for redox sensing and signaling in the genome.
Collapse
Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Amie K. Boal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
| |
Collapse
|
42
|
Adhikary A, Kumar A, Munafo SA, Khanduri D, Sevilla MD. Prototropic equilibria in DNA containing one-electron oxidized GC: intra-duplex vs. duplex to solvent deprotonation. Phys Chem Chem Phys 2010; 12:5353-68. [PMID: 21491657 PMCID: PMC4677782 DOI: 10.1039/b925496j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
By use of ESR and UV-vis spectral studies, this work identifies the protonation states of one-electron oxidized G:C (viz. G˙+:C, G(N1–H)˙:C(+H+), G(N1–H)˙:C, and G(N2-H)˙:C) in a DNA oligomer d[TGCGCGCA]2. Benchmark ESR and UV-vis spectra from one electron oxidized 1-Me-dGuo are employed to analyze the spectral data obtained in one-electron oxidized d[TGCGCGCA]2 at various pHs. At pH ≥7, the initial site of deprotonation of one-electron oxidized d[TGCGCGCA]2 to the surrounding solvent is found to be at N1 forming G(N1–H)˙:C at 155 K. However, upon annealing to 175 K, the site of deprotonation to the solvent shifts to an equilibrium mixture of G(N1–H)˙:C and G(N2–H)˙:C. For the first time, the presence of G(N2–H)˙:C in a ds DNA-oligomer is shown to be easily distinguished from the other prototropic forms, owing to its readily observable nitrogen hyperfine coupling (Azz(N2) = 16 G). In addition, for the oligomer in H2O, an additional 8 G N2–H proton HFCC is found. This ESR identification is supported by a UV-vis absorption at 630 nm which is characteristic for G(N2–H)˙ in model compounds and oligomers. We find that the extent of photo-conversion to the C1′ sugar radical (C1′˙) in the one-electron oxidized d[TGCGCGCA]2 allows for a clear distinction among the various G:C protonation states which can not be easily distinguished by ESR or UV-vis spectroscopies with this order for the extent of photo-conversion: G˙+:C > G(N1–H)˙:C(+H+) ≫ G(N1–H)˙:C. We propose that it is the G˙+:C form that undergoes deprotonation at the sugar and this requires reprotonation of G within the lifetime of exited state
Collapse
Affiliation(s)
| | - Anil Kumar
- Department of Chemistry Oakland University Rochester, MI 48309
| | - Shawn A. Munafo
- Department of Chemistry Oakland University Rochester, MI 48309
| | - Deepti Khanduri
- Department of Chemistry Oakland University Rochester, MI 48309
| | | |
Collapse
|
43
|
Wang Y, Li J, Liu Y, Ma R, Jia W, Cui H, Wang H. Fabrication of the DNA/poly(3-methylthiophene) composite film modified electrode and its application for the study on the voltammetric behavior and determination of 8-hydroxy-2′-deoxyguanosine. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0241-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
44
|
Kawai K, Osakada Y, Majima T. Importance of protonation state of guanine radical cation during hole transfer in DNA. Chemphyschem 2009; 10:1766-9. [PMID: 19437477 DOI: 10.1002/cphc.200900148] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kiyohiko Kawai
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
| | | | | |
Collapse
|
45
|
Adhikary A, Khanduri D, Sevilla MD. Direct observation of the hole protonation state and hole localization site in DNA-oligomers. J Am Chem Soc 2009; 131:8614-9. [PMID: 19469533 DOI: 10.1021/ja9014869] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, it is shown that the incorporation of an 8-deuteroguanine (G*) moiety in DNA-oligomers allows for direct determination at 77 K of (i) the location of holes (i.e., the radical site) within dsDNA at specific base sites, even within stacks of G, as well as (ii) the protonation state of the hole at that site. These findings are based on our work and demonstrate that selective deuteration at C-8 on a guanine moiety in dGuo results in an ESR signal from the guanine cation radical (G**(+)) which is easily distinguishable from that of the undeuterated guanine cation radical (G*(+)). G**(+) is also found to be easily distinguishable from its conjugate base, the N1-deprotonated radical, G*(-H)*. Our ESR results clearly establish that at 77 K (i) one-electron oxidized guanine in double stranded DNA-oligomers exists as the deprotonated neutral radical G(-H)* as a result of facile proton transfer to the hydrogen bonded cytosine and (ii) the hole is preferentially located at the 5'-end in several ds DNA-oligomers with a GGG sequence.
Collapse
Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
| | | | | |
Collapse
|
46
|
Campbell CJ, Mountford CP, Stoquert HC, Buck AH, Dickinson P, Ferapontova E, Terry JG, Beattie JS, Walton AJ, Crain J, Ghazal P, Mount AR. A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets. Analyst 2009; 134:1873-9. [PMID: 19684913 DOI: 10.1039/b900325h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.
Collapse
Affiliation(s)
- Colin J Campbell
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, UK EH16 4SB.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Gutiérrez R, Caetano RA, Woiczikowski BP, Kubar T, Elstner M, Cuniberti G. Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches. PHYSICAL REVIEW LETTERS 2009; 102:208102. [PMID: 19519078 DOI: 10.1103/physrevlett.102.208102] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Indexed: 05/27/2023]
Abstract
We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.
Collapse
Affiliation(s)
- R Gutiérrez
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, D-01062, Dresden, Germany
| | | | | | | | | | | |
Collapse
|
48
|
Okamoto S, Morita T, Kimura S. Electron transfer through a self-assembled monolayer of a double-helix peptide with linking the terminals by ferrocene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3297-3304. [PMID: 19437730 DOI: 10.1021/la8034962] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A unique molecular structure, a double-helix peptide, was self-assembled on gold, and the electron transfer through the monolayer was studied. The double-helix peptide consists of two 9mer 3(10)-helical peptide chains having a disulfide group at each N terminal and being linked by a ferrocene dicarboxylic acid between the C terminals. Each helical peptide chain has three naphthyl groups in a linear arrangement along the helix. The monolayer properties and the electron transfer from the ferrocene unit to gold were studied with reference peptides with a similar double helix but without naphthyl groups, a single helix with a dicarboxylic ferrocene unit, and a single helix with a monocarboxylic ferrocene unit. It was demonstrated that the naphthyl groups on the side chains had no effect on electron transfer, and the electron-transfer rate in the double-helix monolayer was not promoted, despite the two electron pathways in the molecule. We propose that in the double-helix monolayer, molecular motions are suppressed, possibly by its rigid structure tethered by the two linkers on gold to cancel out acceleration effects of the 2-fold electron pathways and the ferrocene substitution number. The factors that affect the electron-transfer reaction across the helical peptide SAMs are discussed in depth.
Collapse
Affiliation(s)
- Shinpei Okamoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | |
Collapse
|
49
|
Genereux JC, Augustyn KE, Davis ML, Shao F, Barton JK. Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts. J Am Chem Soc 2008; 130:15150-6. [PMID: 18855390 PMCID: PMC2663386 DOI: 10.1021/ja8052738] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging pi-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N 2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain.
Collapse
Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Katherine E. Augustyn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Molly L. Davis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Fangwei Shao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| |
Collapse
|
50
|
Bonnist EYM, Jones AC. Long-wavelength fluorescence from 2-aminopurine-nucleobase dimers in DNA. Chemphyschem 2008; 9:1121-9. [PMID: 18446915 DOI: 10.1002/cphc.200700813] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
When 2-aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long-wavelength emission and excitation bands, in addition to the familiar short-wavelength spectra, as a result of formation of a ground-state heterodimer with an adjacent, pi-stacked, natural base. The observation of dual emission from 2AP in a variety of oligodeoxynucleotide duplexes and single strands demonstrates the generality of this phenomenon. The photophysical and conformational properties of the long-wavelength-emitting 2AP-nucleobase dimer are examined. Analogous long-wavelength fluorescence is seen when 2AP pi-stacks with aromatic amino acid sidechains in the active sites of methyltransferase enzymes during DNA nucleotide flipping.
Collapse
Affiliation(s)
- Eleanor Y M Bonnist
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | | |
Collapse
|