1
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Song Y, Gao Y, Fang H. Unexpected large charge transfer rate mediated by adenine in twisted DNA structure. Phys Rev E 2024; 109:064412. [PMID: 39020924 DOI: 10.1103/physreve.109.064412] [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: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 07/20/2024]
Abstract
DNA exhibits remarkable charge transfer ability, which is crucial for its biological functions and potential electronic applications. The charge transfer process in DNA is widely recognized as primarily mediated by guanine, while the contribution of other nucleobases is negligible. Using the tight-binding models in conjunction with first-principles calculations, we investigated the charge transfer behavior of homogeneous GC and AT pairs. We found that the charge transfer rate of adenine significantly changes. With overstretching, the charge transfer rate of adenine can even surpass that of guanine, by as much as five orders of magnitude at a twist angle of around 26°. Further analysis reveals that it is attributed to the turnover of the relative coupling strength between homogeneous GC and AT base pairs, which is caused by the symmetry exchange between the two highest occupied molecular orbitals of base pairs occurring at different twist angles. Given the high degree of flexibility of DNA in vivo and in vitro conditions, these findings prompt us to reconsider the mechanism of biological functions concerning the charge transfer in DNA molecules and further open the potential of DNA as a biomaterial for electronic applications.
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2
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Deng C, Liu H, Si S, Zhu X, Tu Q, Jin Y, Xiang J. An electrochemical aptasensor for amyloid-β oligomer based on double-stranded DNA as "conductive spring". Mikrochim Acta 2020; 187:239. [PMID: 32189141 DOI: 10.1007/s00604-020-4217-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
Abstract
In order to overcome the antibody-based sensor's shortcomings, an electrochemical aptamer (Apt)-based sensor was developed for amyloid-β40 oligomer (Aβ40-O). The aptasensor was constructed by locating Apt and ferrocence (Fc) on streptavidin-modified gold (SA-gold) nanoparticles. The obtained AptFc@SA-gold nanoparticles were linked onto the Au electrode via the connection of double-stranded DNA (dsDNA) as a "conductive spring." The determination of Aβ40-O was performed with square-wave voltammetry (SWV). Upon bio-recognition between Apt and Aβ40-O, the conformation of Apt changed and the formed Apt/Aβ40-O complex separated from the SA-gold surface. As a result, the surface charge of SA-gold positively shifted, weakening the electrostatic attraction between the SA-gold and the positively charged Au electrode surface (at potential range of 0.1~0.5 V, corresponding to the Fc redox transformation), and stretching the dsDNA chain. Based on the exponential decay of dsDNA's electron transfer efficiency on its chain stretching, the oxidation current density from Fc decreased and displayed linear correlation to the concentration of Aβ40-O. A wide linear range of 0.100 nM to 1.00 μM with a low detection limit of 93.0 pM was obtained. The aptasensor displayed excellent selectivity toward Aβ40-O in contrast to other possible interfering analogs (Aβ40 monomer, Aβ42 monomer, and oligomer) at × 100 higher concentrations. The recoveries for Aβ40-O-spiked artificial cerebrospinal fluid and healthy human serum were 94.0~104% and 92.8~95.4%, respectively. The electrochemical aptasensor meets the demands of clinic determination of Aβ40-O, which is significant for the early diagnosis of AD. Graphical abstract Schematic representation of the electrochemical aptasensor for amyloid-β oligomer based on the surface charge change induced by target binding.
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Affiliation(s)
- Chunyan Deng
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Hui Liu
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Shihui Si
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Xiaojun Zhu
- School of Information Science and Technology, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Qiuyun Tu
- Department of Geratology, The Third Xiangya Hospital, Central South University, Changsha, 410013, People's Republic of China
| | - Yan Jin
- Department of Geratology, The Third Xiangya Hospital, Central South University, Changsha, 410013, People's Republic of China
| | - Juan Xiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
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3
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Cupellini L, Wityk P, Mennucci B, Rak J. Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories. Phys Chem Chem Phys 2019; 21:4387-4393. [PMID: 30729242 DOI: 10.1039/c8cp07700b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 5'-GBrU or 5'-ABrU sequence showed that a much lower reactivity was found for the 5'-GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity has been dubbed a contrathermodynamic one. In the current work, we employ the Marcus and Marcus-Levich-Jortner theory of ET in order to shed light on the observed effect. By using a combination of Density Functional Theory (DFT) and solvation continuum models, we calculated the electronic couplings, reorganization energies, and thermodynamic stimuli for electron transfer which enabled the rates of forward and back ET to be estimated for the two considered sequences. The calculated rates show that the photoreaction could not be efficient if the ET process proceeded within the considered dimers. Only after introducing additional adenines between G and BrU, which accelerates the forward and slows down the back ET, is a significant amount of photodamage expected.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy.
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4
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Iwaura R. Construction of a DNA-Based Supramolecular Nanosheet That Emits Bluish-White Light from Charge-Transfer Excited States of the Nucleobases. Chemistry 2019; 25:2281-2287. [PMID: 30411410 DOI: 10.1002/chem.201804960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/06/2018] [Indexed: 12/26/2022]
Abstract
1,ω-Inosinic acid-bearing bolaamphiphiles dI(18), dI(19), and dI(20) with a 3'-phosphorylated inosine as a universal base connected to each end of an oligomethylene chain were synthesized for the first time. Single-component self-assemblies of these bolaamphiphiles and their binary self-assemblies with salmon sperm DNA were studied by AFM; temperature-dependent UV absorption, fluorescence, and circular dichroism spectroscopy; and gel electrophoresis. The binary self-assembly of dI(20) and salmon sperm DNA (dI(20)-DNA) had a nanosheet structure with a homogeneous thickness of about 6 nm and widths of several micrometers. Interestingly, an aqueous solution of the nanosheets showed a broad absorption band originating from the charge-transfer (CT) states of the nucleobase in the long-wavelength region (>300 nm), and the molar absorptivity per nucleobase was calculated to be approximately 150 times that of single-stranded (dT20 and dA20) and double-stranded (dT20-dA20) oligonucleotides. In addition, a continuous and broad emission band originating from CT excited states of the nucleobases was observed in the visible region. These observations indicate that CT states of the nucleobases were formed and stabilized in the supramolecular nanosheet and that bluish white light was emitted from CT excited states of the nucleobases.
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Affiliation(s)
- Rika Iwaura
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
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5
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Karwowski BT. The AT Interstrand Cross-Link: Structure, Electronic Properties, and Influence on Charge Transfer in dsDNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:665-685. [PMID: 30500729 PMCID: PMC6258832 DOI: 10.1016/j.omtn.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/01/2022]
Abstract
The interaction of chemical and physical agents with genetic material can lead to almost 80 different DNA damage formations. The targeted intentional DNA damage by radiotherapy or chemotherapy is a front-line anticancer therapy. An interstrand cross-link can result from ionization radiation or specific chemical agents, such as trans-/cisplatin activity. Here, the influence of the adenine and thymidine (AT) interstrand linkage, the covalent bond between the adenine N6 and thymidine C5 methylene group, on the isolated base pair as well as double-stranded DNA (dsDNA) was taken into quantum mechanical/molecular mechanical (QM/MM) consideration at the m062x/6-31+G*:UFF level of theory in the aqueous phase. All the results presented in this article, for the first time, show that an AT-interstrand cross-link (ICL) changes the positive and negative charge migration process due to a higher activation energy forced by the cross-link’s presence. However, the final radical cation destination in cross-linked DNA is left in the same place as in a native double-stranded-deoxyoligonucleotide. Additionally, the direction of the radical anion transfer was found to be opposite to that of native dsDNA. Therefore, it can be postulated that the appearance of the AT-ICL does not disturb the hole migration in the double helix, with subsequent effective changes in the electron migration process.
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Affiliation(s)
- Boleslaw T Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland.
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6
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Deng C, Zhang M, Liu C, Deng H, Huang Y, Yang M, Xiang J, Ren B. Electrostatic Force Triggering Elastic Condensation of Double-Stranded DNA for High-Performance One-Step Immunoassay. Anal Chem 2018; 90:11446-11452. [PMID: 30178657 DOI: 10.1021/acs.analchem.8b02556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Current strategies for high-performance immunoassay generally require a sandwich structure for signal amplification. This strategy is limited to multivalent antigens and complicates the detection scheme. Herein we demonstrate a class of simple one-step ultrasensitive immunoassay with the adoption of double-stranded DNA (dsDNA) as "conductive spring" to bridge the electrode and redox-reporter/antibody-receptor comodified gold nanoparticles (AbFc@AuNPs). Upon biorecognition between antigen and antibody, the charge of the AuNPs changes, enhancing the electrostatic interaction between the AuNPs and Au electrode surface, and condensing the dsDNA chain. For the first time, the sensitive response of the electrochemical redox current to the DNA chain length is utilized to achieve an ultrahigh sensitivity down to fM level. Only the primary antibody needed in the recognition interface ensures the one-step immunoreaction works well with monovalent antigens, which ensure this method as a promising general alternative means for fast, high-throughput or point-of-care clinical applications even for very challenging clinically relevant samples.
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Affiliation(s)
- Chunyan Deng
- College of Chemistry and Chemical Engineering , Central South University , Changsha 410083 , P. R. China
| | - Manman Zhang
- College of Chemistry and Chemical Engineering , Central South University , Changsha 410083 , P. R. China
| | - Chunyan Liu
- College of Chemistry and Chemical Engineering , Central South University , Changsha 410083 , P. R. China
| | - Honghua Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Minghui Yang
- College of Chemistry and Chemical Engineering , Central South University , Changsha 410083 , P. R. China
| | - Juan Xiang
- College of Chemistry and Chemical Engineering , Central South University , Changsha 410083 , P. R. China
| | - Bin Ren
- Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, and The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , P. R. China
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7
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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8
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Bruot C, Xiang L, Palma JL, Tao N. Effect of mechanical stretching on DNA conductance. ACS NANO 2015; 9:88-94. [PMID: 25530305 DOI: 10.1021/nn506280t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Studying the structural and charge transport properties in DNA is important for unraveling molecular scale processes and developing device applications of DNA molecules. Here we study the effect of mechanical stretching-induced structural changes on charge transport in single DNA molecules. The charge transport follows the hopping mechanism for DNA molecules with lengths varying from 6 to 26 base pairs, but the conductance is highly sensitive to mechanical stretching, showing an abrupt decrease at surprisingly short stretching distances and weak dependence on DNA length. We attribute this force-induced conductance decrease to the breaking of hydrogen bonds in the base pairs at the end of the sequence and describe the data with a mechanical model.
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Affiliation(s)
- Christopher Bruot
- Center for Bioelectronics and Biosensors, Biodesign Institute, School of Electrical, Energy and Computer Engineering, Arizona State University , Tempe, Arizona 85287-5801, United States
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9
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Mishra AK, Young RM, Wasielewski MR, Lewis FD. Wirelike Charge Transport Dynamics for DNA–Lipid Complexes in Chloroform. J Am Chem Soc 2014; 136:15792-7. [DOI: 10.1021/ja509456q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- 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
| | - 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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10
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Yuan S, Shen Z, Zhang W, Dou Y, Lo GV. Thymine dimer splitting in the T<>T-G trinucleotide model system: a semiclassical dynamics and TD-DFT study. Int J Biol Macromol 2014; 66:267-72. [PMID: 24589472 DOI: 10.1016/j.ijbiomac.2014.02.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
The mechanism leading to bond cleavage of a thymine-thymine cyclobutane dimer (T<>T) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5' and C6C6' bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale.
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Affiliation(s)
- Shuai Yuan
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Zhi Shen
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Wenying Zhang
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Yusheng Dou
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China; Department of Physical Sciences, Nicholls State University, PO Box 2022, Thibodaux, LA 70310, USA.
| | - Glenn V Lo
- Department of Physical Sciences, Nicholls State University, PO Box 2022, Thibodaux, LA 70310, USA
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11
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Berlin YA, Voityuk AA, Ratner MA. DNA base pair stacks with high electric conductance: a systematic structural search. ACS NANO 2012; 6:8216-8225. [PMID: 22901272 DOI: 10.1021/nn3030139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.
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Affiliation(s)
- Yuri A Berlin
- Department of Chemistry, Northwestern University, 1145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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12
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Szalay PG, Watson T, Perera A, Lotrich V, Fogarasi G, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 2. Effect of Biological Environment on the Electronic Excitation Spectrum of Nucleobases. J Phys Chem A 2012; 116:8851-60. [DOI: 10.1021/jp305130q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Péter G. Szalay
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Victor Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
| | - Géza Fogarasi
- Institute
of Chemistry, Eötvös University, H-1518 Budapest, P.O.
Box 32, Hungary
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida, United
States
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13
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Siriwong K, Voityuk AA. Electron transfer in DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1102] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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14
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Davis WB, Bjorklund CC, Deline M. Probing the effects of DNA-protein interactions on DNA hole transport: the N-terminal histone tails modulate the distribution of oxidative damage and chemical lesions in the nucleosome core particle. Biochemistry 2012; 51:3129-42. [PMID: 22409399 DOI: 10.1021/bi201734c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of DNA to transport positive charges, or holes, over long distances is well-established, but the mechanistic details of how this process is influenced by packaging into DNA-protein complexes have not been fully delineated. In eukaryotes, genomic DNA is packaged into chromatin through its association with the core histone octamer to form the nucleosome core particle (NCP), a complex whose structure can be modulated through changes in the local environment and the histone proteins. Because (i) varying the salt concentration and removing the histone tails influence the structure of the NCP in known ways and (ii) previous studies have shown that DNA hole transport (HT) occurs in the nucleosome, we have used our previously described 601 sequence NCPs to test the hypothesis that DNA HT dynamics can be modulated by structural changes in a DNA-protein complex. We show that at low salt concentrations there is a sharp increase in long-range DNA HT efficiency in the NCP as compared to naked DNA. This enhancement of HT can be negated by either removal of the histone tails at low salt concentrations or disruption of the interaction of the packaged DNA and the histone tails by increasing the buffer's ionic strength. Association of the histone tails with 601 DNA at low salt concentrations shifts the guanine damage spectrum to favor lesions like 8-oxoguanine in the NCP, most likely through modulation of the rate of the reaction of the guanine radical cation with oxygen. These experimental results indicate that for most genomic DNA, the influence of DNA-protein interactions on DNA HT will depend strongly on the level of protection of the DNA nucleobases from oxygen. Further, these results suggest that the oxidative damage arising from DNA HT may vary in different genomic regions depending on the presence of either euchromatin or heterochromatin.
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Affiliation(s)
- William B Davis
- School of Molecular Biosciences, Biotechnology/Life Sciences 135, Washington State University, Pullman, Washington 99164-7520, USA.
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15
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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).
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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16
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Tesar SL, Leveritt JM, Kurnosov AA, Burin AL. Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Voityuk AA. Long-Range Electron Transfer in Biomolecules. Tunneling or Hopping? J Phys Chem B 2011; 115:12202-7. [DOI: 10.1021/jp2054876] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alexander A. Voityuk
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institute of Computational Chemistry, Universitat de Girona, Spain
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18
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Shen X, Gu B, Che SA, Zhang FS. Solvent effects on the conformation of DNA dodecamer segment: A simulation study. J Chem Phys 2011; 135:034509. [DOI: 10.1063/1.3610549] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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19
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Venkatramani R, Keinan S, Balaeff A, Beratan DN. Nucleic Acid Charge Transfer: Black, White and Gray. Coord Chem Rev 2011; 255:635-648. [PMID: 21528017 PMCID: PMC3081592 DOI: 10.1016/j.ccr.2010.12.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Theoretical studies of charge transport in deoxyribonucleic acid (DNA) and peptide nucleic acid (PNA) indicate that structure and dynamics modulate the charge transfer rates, and that different members of a structural ensemble support different charge transport mechanisms. Here, we review the influences of nucleobase geometry, electronic structure, solvent environment, and thermal conformational fluctuations on the charge transfer mechanism. We describe an emerging framework for understanding the diversity of charge transport mechanisms seen in nucleic acids.
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Affiliation(s)
| | - Shahar Keinan
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Alexander Balaeff
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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20
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Wu J, Walker VEJ, Boyd RJ. Theoretical study of polaron formation in poly(G)-poly(C) cations. J Phys Chem B 2011; 115:3136-45. [PMID: 21384938 DOI: 10.1021/jp108818u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polaron formation in poly(G)-poly(C) cations is investigated with density functional theory (DFT) and molecular mechanics (MM) employing a two-layer ONIOM method. In these calculations, the high layer, composed of all complementary base pairs, is treated by a DFT method, while the low layer, which includes the sugar-phosphate backbone, counterions and water molecules, is described by the AMBER force field. The high layer is the model system in which the charge transfer takes place. According to our calculations, three or four guanines move in a paddle-like fashion when an electron is removed from the neutral model system. In the cation model system, about 80% of the charge is delocalized onto the guanine residues, and the remaining charge is delocalized onto the cytosine residues. This happens because guanine has a lower ionization potential (IP) than cytosine. The counterions and water molecules in the low layer are important in the geometry optimization. The optimized geometry of the model system is closer to the standard B-form structure when counterions and water molecules are included than when they are omitted. Comparison of the optimized neutral and cationic model systems reveals a polaron in poly(G)-poly(C) cations extending from the first to the third guanine. It is demonstrated that the position of counterions and the number of surrounding water molecules can affect polaron formation.
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Affiliation(s)
- Jian Wu
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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21
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Conron SMM, Thazhathveetil AK, Wasielewski MR, Burin AL, Lewis FD. Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk. J Am Chem Soc 2010; 132:14388-90. [DOI: 10.1021/ja106991f] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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22
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McMahon DP, Troisi A. Organic semiconductors: impact of disorder at different timescales. Chemphyschem 2010; 11:2067-74. [PMID: 20540142 DOI: 10.1002/cphc.201000182] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The charge transport in organic materials, from molecular crystals to polymers, is determined by their degree of disorder. The dynamic disorder in ideal molecular crystals at room temperature and the static disorder in disordered polymers are just two limiting cases of the timescale of the fluctuations in the electronic Hamiltonian caused by nuclear motions. In fact, a very large number of important materials (e.g. liquid crystalline semiconductors) are actually in an intermediate regime where the disorder is neither purely static nor purely dynamic. This Minireview discusses the recent contribution of computational chemistry (molecular dynamics and quantum chemistry) to the characterization of these transport regimes and outlines the theoretical methods that can be used to relate the system characteristics to the measurable mobility.
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Affiliation(s)
- David P McMahon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
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23
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Butchosa C, Simon S, Voityuk AA. Electron transfer from aromatic amino acids to guanine and adenine radical cations in π stacked and T-shaped complexes. Org Biomol Chem 2010; 8:1870-5. [DOI: 10.1039/b927134a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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