51
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Grodick M, Segal HM, Zwang TJ, Barton JK. DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity. J Am Chem Soc 2014; 136:6470-8. [PMID: 24738733 PMCID: PMC4017601 DOI: 10.1021/ja501973c] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Indexed: 02/08/2023]
Abstract
Iron-sulfur clusters have increasingly been found to be associated with enzymes involved in DNA processing. Here we describe a role for these redox clusters in DNA-mediated charge-transport signaling in E. coli between DNA repair proteins from distinct pathways. DNA-modified electrochemistry shows that the 4Fe-4S cluster of DNA-bound DinG, an ATP-dependent helicase that repairs R-loops, is redox-active at cellular potentials and ATP hydrolysis increases DNA-mediated redox signaling. Atomic force microscopy experiments demonstrate that DinG and Endonuclease III (EndoIII), a base excision repair enzyme, cooperate at long-range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Silencing the gene encoding EndoIII in a strain of E. coli where repair by DinG is essential results in a significant growth defect that is rescued by complementation with EndoIII but not with an EndoIII mutant that is enzymatically active but unable to carry out DNA charge transport. This work thus elucidates a fundamental mechanism to coordinate the activities of DNA repair enzymes across the genome.
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Affiliation(s)
- Michael
A. Grodick
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Helen M. Segal
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Theodore J. Zwang
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
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52
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Wong JR, Shao F. 8-Cyclopropyl-2′-Deoxyguanosine: A Hole Trap for DNA-Mediated Charge Transport. Chembiochem 2014; 15:1171-5. [DOI: 10.1002/cbic.201402018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 11/08/2022]
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53
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Kalosakas G, Spanou E. Distance dependence of hole transfer rates from G radical cations to GGG traps in DNA. Phys Chem Chem Phys 2014; 15:15339-46. [PMID: 23928688 DOI: 10.1039/c3cp51062j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relative reaction rates for hole transfer between G radical cations and GGG triplets in DNA, through different bridges of varying lengths, are numerically calculated and the obtained results are compared with corresponding experimental observations [Giese et al., 2001, Nature, 412, 318; Angew. Chem., Int. Ed., 1999, 38, 996]. Hole donors and acceptors are separated either by (T-A)n bridges or by N repeated barriers consisting of (T-A,T-A) double base-pairs which are connected through single G-C base-pairs. In the former case, hole transfer rates show a strong exponential decrease with the length of the bridge for short bridges, while a switching to weak distance dependence has been observed for longer bridges. In the latter case, a power law seems to better describe the distance dependence of charge transfer rates. All these experimental observations are qualitatively reproduced by our simulations without any adjustable parameter, considering only tunneling as the charge transfer mechanism. Physical insights into the mechanism providing the switching behavior in the case of (T-A)n bridges are presented through an analysis of the eigenfunctions of the system.
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Affiliation(s)
- G Kalosakas
- Materials Science Department, University of Patras, Rio GR-26504, Greece.
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54
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Koley Seth B, Ray A, Saha A, Saha P, Basu S. Potency of photoinduced electron transfer and antioxidant efficacy of pyrrole and pyridine based Cu(II)-Schiff complexes while binding with CT-DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 132:72-84. [PMID: 24602815 DOI: 10.1016/j.jphotobiol.2014.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/18/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Here we report a systematic and comparative study to define a correlation between the structure and function of a series of simple, biologically active small inorganic Schiff base copper complexes for the occurrence of charge transfer phenomenon in calf thymus DNA (CT-DNA) using transient absorption spectroscopy corroborated with magnetic field effect. Four copper(II) Schiff base complexes with differently substituted heterocyclic ligands with antioxidant activity have been used. The binding constants of the order of ∼ 10(4) support the moderate binding affinity of the complexes towards CT-DNA. The methyl-substituted pyrrole complex shows maximum binding affinity (Kb: 8.33 × 10(4)) compared to others. The occurrence of photoinduced electron transfer (PET) from CT-DNA to pyrrole containing complexes has been confirmed by identifying the corresponding transient radical ions whereas the extent of PET with pyridine substituted complexes is too small to be observed. The increase of the yield of radical ions in presence of magnetic field depicts that the initial spin correlation in geminate radical ion pair is triplet. The difference between experimental and calculated B½ values, the measure of hyperfine interactions (HFI) present in the system, arises due to hole hopping through intrastrand and interstrand DNA bases. The unsubstituted pyrrole complexes cleave DNA much more than the methyl-substituted one. Therefore, the probability of intrastrand superexchange increases with methyl-substituted complexes, that reduces the rate of hole hopping and hence the B½ value.
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Affiliation(s)
- Banabithi Koley Seth
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Aurkie Ray
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Arpita Saha
- Crystallography and Molecular Biology, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Partha Saha
- Crystallography and Molecular Biology, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Samita Basu
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.
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55
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Liu L, Zhang GM, Zhu RG, Liu YH, Yao HM, Han ZB. Dinuclear Cd(ii), Mn(ii) and Cu(ii) complexes derived from (anthraquinone-1-diyl) benzoate: DNA binding and cleavage studies. RSC Adv 2014. [DOI: 10.1039/c4ra07997c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Three dinuclear Cd(ii), Mn(ii) and Cu(ii) complexes have been successfully synthesized under solvothermal conditions. Among them, only the Cu(ii) complex has the activity for DNA cleavage.
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Affiliation(s)
- Lin Liu
- College of Chemistry
- Liaoning University
- Shenyang 110036, P. R. China
| | - Gong-Ming Zhang
- College of Chemistry
- Liaoning University
- Shenyang 110036, P. R. China
| | - Ru-Gang Zhu
- College of Light Industry
- Liaoning University
- Shenyang 110036, P. R. China
| | - Yong-Hui Liu
- College of Light Industry
- Liaoning University
- Shenyang 110036, P. R. China
| | - Hui-Meng Yao
- College of Chemistry
- Liaoning University
- Shenyang 110036, P. R. China
| | - Zheng-Bo Han
- College of Chemistry
- Liaoning University
- Shenyang 110036, P. R. China
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56
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Angelé-Martínez C, Goodman C, Brumaghim J. Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences. Metallomics 2014; 6:1358-81. [DOI: 10.1039/c4mt00057a] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.
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Affiliation(s)
| | - Craig Goodman
- Department of Chemistry
- Clemson University
- Clemson, USA
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57
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Campbell NP, Rokita SE. Electron transport in DNA initiated by diaminonaphthalene donors alternatively bound by non-covalent and covalent association. Org Biomol Chem 2014; 12:1143-8. [DOI: 10.1039/c3ob42433b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-covalent association can identify active donors for study of charge transfer in DNA but may not establish detailed correlations between donor structure and transfer efficiency.
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Affiliation(s)
- Neil P. Campbell
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park, USA
| | - Steven E. Rokita
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park, USA
- Department of Chemistry
- Johns Hopkins University
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58
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Xia J, Ou YP, Meng XG, Yin J, Yu GA, Liu SH. Synthesis and Characterization of Dithia[3.3]metaparacyclophane-Bridged Dimetallic Ruthenium Acetylide Complexes. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201301304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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59
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Astakhova TY, Likhachev VN, Vinogradov GA. Polaron on a one-dimensional lattice: II. A moving polaron. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2013. [DOI: 10.1134/s199079311305028x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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60
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Arnold AR, Barton JK. DNA protection by the bacterial ferritin Dps via DNA charge transport. J Am Chem Soc 2013; 135:15726-9. [PMID: 24117127 PMCID: PMC3899832 DOI: 10.1021/ja408760w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. Here we examine the mechanism of E. coli Dps protection of DNA, specifically whether this DNA-binding protein can utilize DNA charge transport through the base pair π-stack to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate DNA damage localized to guanine repeats, the sites of lowest potential in DNA. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps, significantly attenuates the yield of oxidative DNA damage. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA charge transport may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.
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Affiliation(s)
- Anna R. Arnold
- 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
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61
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Zhou J, Liu M, Fleming AM, Burrows CJ, Wallace SS. Neil3 and NEIL1 DNA glycosylases remove oxidative damages from quadruplex DNA and exhibit preferences for lesions in the telomeric sequence context. J Biol Chem 2013; 288:27263-27272. [PMID: 23926102 DOI: 10.1074/jbc.m113.479055] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The telomeric DNA of vertebrates consists of d(TTAGGG)n tandem repeats, which can form quadruplex DNA structures in vitro and likely in vivo. Despite the fact that the G-rich telomeric DNA is susceptible to oxidation, few biochemical studies of base excision repair in telomeric DNA and quadruplex structures have been done. Here, we show that telomeric DNA containing thymine glycol (Tg), 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh), or spiroiminodihydantoin (Sp) can form quadruplex DNA structures in vitro. We have tested the base excision activities of five mammalian DNA glycosylases (NEIL1, NEIL2, mNeil3, NTH1, and OGG1) on these lesion-containing quadruplex substrates and found that only mNeil3 had excision activity on Tg in quadruplex DNA and that the glycosylase exhibited a strong preference for Tg in the telomeric sequence context. Although Sp and Gh in quadruplex DNA were good substrates for mNeil3 and NEIL1, none of the glycosylases had activity on quadruplex DNA containing 8-oxoG. In addition, NEIL1 but not mNeil3 showed enhanced glycosylase activity on Gh in the telomeric sequence context. These data suggest that one role for Neil3 and NEIL1 is to repair DNA base damages in telomeres in vivo and that Neil3 and Neil1 may function in quadruplex-mediated cellular events, such as gene regulation via removal of damaged bases from quadruplex DNA.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405-0068
| | - Minmin Liu
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405-0068
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405-0068.
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62
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Rooman M, Wintjens R. Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations. J Biomol Struct Dyn 2013; 32:532-45. [PMID: 23582046 PMCID: PMC3919198 DOI: 10.1080/07391102.2013.783508] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1-10 bases or 1-8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G* hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5'-end for single-stranded Gua-stacks and toward the 3'-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed.
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Affiliation(s)
- Marianne Rooman
- a BioModeling, BioInformatics and BioProcesses Department , CP 165/61 Université Libre de Bruxelles , 50 Roosevelt ave, 1050 Brussels , Belgium
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63
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DAVIS BRETH, PAN JUNHAN, TUNG CHIHKUAN, AUSTIN ROBERTH, RIEHN ROBERT. SENSING DNA WITH ALTERNATING CURRENTS USING A NANOGAP SENSOR EMBEDDED IN A NANOCHANNEL DEVICE. NANO LIFE 2013; 3:10.1142/S1793984413400072. [PMID: 24294307 PMCID: PMC3842156 DOI: 10.1142/s1793984413400072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report an integrated nanochannel/nanoelectrode sensor for the detection of DNA using alternating currents. We find that DNA can be detected using platinum as the metal for the detecting electrodes, with a signal to noise ratio exceeding 10. We argue that the signal is at least in part electrochemical in nature, thus holds the promise to yield a sequence-dependent signal. However, we also find that for large voltages, DNA attaches irreversibly to the driving electrodes.
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Affiliation(s)
- BRET H. DAVIS
- Department of Physics, North Carolina State University Campus Box 8202, Raleigh, NC 27695, USA
| | - JUNHAN PAN
- Department of Physics, North Carolina State University Campus Box 8202, Raleigh, NC 27695, USA
| | - CHIH-KUAN TUNG
- Department of Physics, Princeton University, Jadwin Hall Washington Road, Princeton, NJ 08544-0708, USA
| | - ROBERT H. AUSTIN
- Department of Physics, Princeton University, Jadwin Hall Washington Road, Princeton, NJ 08544-0708, USA
| | - ROBERT RIEHN
- Department of Physics, North Carolina State University Campus Box 8202, Raleigh, NC 27695, USA
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64
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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65
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Schill M, Koslowski T. Sensing organic molecules by charge transfer through aptamer-target complexes: theory and simulation. J Phys Chem B 2013; 117:475-83. [PMID: 23227783 DOI: 10.1021/jp308042n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aptamers, i.e., short sequences of RNA and single-stranded DNA, are capable of specificilly binding objects ranging from small molecules over proteins to entire cells. Here, we focus on the structure, stability, dynamics, and electronic properties of oligonucleotides that interact with aromatic or heterocyclic targets. Large-scale molecular dynamics simulations indicate that aromatic rings such as dyes, metabolites, or alkaloides form stable adducts with their oligonucleotide host molecules at least on the simulation time scale. From molecular dynamics snapshots, the energy parameters relevant to Marcus' theory of charge transfer are computed using a modified Su-Schrieffer-Heeger Hamiltonian, permitting an estimate of the charge transfer rates. In many cases, aptamer binding seriously influences the charge transfer kinetics and the charge carrier mobility within the complex, with conductivities up to the nanoampere range for a single complex. We discuss the conductivity properties with reference to potential applications as biosensors.
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Affiliation(s)
- Maria Schill
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
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66
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Xia J, Ou YP, Wu D, Jin GJ, Yin J, Yu GA, Liu SH. Dithia[3.3]paracyclophane-bridged bimetallic ruthenium acetylide complexes: synthesis, structures and influence of transannular π–π interactions on their electronic properties. Dalton Trans 2013; 42:14212-22. [DOI: 10.1039/c3dt51756j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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67
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Fakhari F, Chen YYK, Rokita SE. Enhancing excess electron transport in DNA. Chem Commun (Camb) 2013; 49:7073-5. [DOI: 10.1039/c3cc43887b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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68
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Williams BR, Dalton SR, Skiba M, Kim SE, Shatz A, Carroll PJ, Burgmayer SJN. Pteridine Cleavage Facilitates DNA Photocleavage by Ru(II) Polypyridyl Compounds. Inorg Chem 2012; 51:12669-81. [DOI: 10.1021/ic301219z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benjamin R. Williams
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | - Shannon R. Dalton
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | - Meredith Skiba
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | - Sung Eun Kim
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | - Allison Shatz
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | - Patrick J. Carroll
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
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69
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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.
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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
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70
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Torres-Vega A, Pliego-Rivero BF, Otero-Ojeda GA, Gómez-Oliván LM, Vieyra-Reyes P. Limbic system pathologies associated with deficiencies and excesses of the trace elements iron, zinc, copper, and selenium. Nutr Rev 2012. [PMID: 23206282 DOI: 10.1111/j.1753-4887.2012.00521.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Deficiencies of nutrients such as amino acids, vitamins, lipids, and trace elements during gestation and early infanthood have strong deleterious effects on the development of the limbic system; these effects may be irreversible, even when adequate supplementation is provided at later developmental stages. Recent advances in the neurochemistry of biometals are increasingly establishing the roles of the trace elements iron, copper, zinc, and selenium in a variety of cell functions and are providing insight into the repercussions of deficiencies and excesses of these elements on the development of the central nervous system, especially the limbic system. The limbic system comprises diverse areas with high metabolic demands and differential storage of iron, copper, zinc, and selenium. This review summarizes available evidence suggesting the involvement of these trace elements in pathological disorders of the limbic system.
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Affiliation(s)
- Adriana Torres-Vega
- Neurofisiología de la Conducta, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, Mexico
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71
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Sontz PA, Muren NB, Barton JK. DNA charge transport for sensing and signaling. Acc Chem Res 2012; 45:1792-800. [PMID: 22861008 DOI: 10.1021/ar3001298] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA duplex is an exquisite macromolecular array that stores genetic information to encode proteins and regulate pathways. Its unique structure also imparts chemical function that allows it also to mediate charge transport (CT). We have utilized diverse platforms to probe DNA CT, using spectroscopic, electrochemical, and even genetic methods. These studies have established powerful features of DNA CT chemistry. DNA CT can occur over long molecular distances as long as the bases are well stacked. The perturbations in base stacking that arise with single base mismatches, DNA lesions, and the binding of some proteins that kink the DNA all inhibit DNA CT. Significantly, single molecule studies of DNA CT show that ground state CT can occur over 34 nm if the duplex is well stacked; one single base mismatch inhibits CT. The DNA duplex is an effective sensor for the integrity of the base pair stack. Moreover, the efficiency of DNA CT is what one would expect for a stack of graphite sheets: equivalent to the stack of DNA base pairs and independent of the sugar-phosphate backbone. Since DNA CT offers a means to carry out redox chemistry from a distance, we have considered how this chemistry might be used for long range biological signaling. We have taken advantage of our chemical probes and platforms to characterize DNA CT in the context of the cell. CT can occur over long distances, perhaps funneling damage to particular sites and insulating others from oxidative stress. Significantly, transcription factors that activate the genome to respond to oxidative stress can also be activated from a distance through DNA CT. Numerous proteins maintain the integrity of the genome and an increasing number of them contain [4Fe-4S] clusters that do not appear to carry out either structural or enzymatic roles. Using electrochemical methods, we find that DNA binding shifts the redox potentials of the clusters, activating them towards oxidation at physiological potentials. We have proposed a model that describes how repair proteins may utilize DNA CT to efficiently search the genome for lesions. Importantly, many of these proteins occur in low copy numbers within the cell, and thus a processive mechanism does not provide a sufficient explanation of how they find and repair lesions before the cell divides. Using atomic force microscopy and genetic assays, we show that repair proteins proficient at DNA CT can relocalize in the vicinity of DNA lesions and can cooperate in finding lesions within the cell. Conversely, proteins defective in DNA CT cannot relocalize in the vicinity of lesions and do not assist other proteins involved in repair within the cell. Moreover such genetic defects are associated with disease in human protein analogues. As we continue to unravel this chemistry and discover more proteins with redox cofactors involved in genome maintenance, we are learning more regarding opportunities for long range signaling and sensing, and more examples of DNA CT chemistry that may provide critical functions within the cell.
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Affiliation(s)
- Pamela A. Sontz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Natalie B. Muren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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72
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Garo F, Häner R. Influence of a GC Base Pair on Excitation Energy Transfer in DNA-Assembled Phenanthrene π-Stacks. Bioconjug Chem 2012; 23:2105-13. [DOI: 10.1021/bc300302v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Garo
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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73
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Wenge U, Wengel J, Wagenknecht HA. Photoinduced reductive electron transfer in LNA:DNA hybrids: a compromise between conformation and base stacking. Angew Chem Int Ed Engl 2012; 51:10026-9. [PMID: 22945791 DOI: 10.1002/anie.201204901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Ulrike Wenge
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe, Germany
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74
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Wenge U, Wengel J, Wagenknecht HA. Photoinduzierter reduktiver Elektronentransfer in LNA:DNA-Hybriden: Kompromiss aus Konformation und Basenstapelung. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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75
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Xia JL, Man WY, Zhu X, Zhang C, Jin GJ, Schauer PA, Fox MA, Yin J, Yu GA, Low PJ, Liu SH. Synthesis and Characterization of Dithia[3.3]paracyclophane-Bridged Binuclear Ruthenium Vinyl and Alkynyl Complexes. Organometallics 2012. [DOI: 10.1021/om300338j] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jian-Long Xia
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Wing Y. Man
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Xinxun Zhu
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Chan Zhang
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Guo-Jun Jin
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Phil A. Schauer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Mark A. Fox
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jun Yin
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Guang-Ao Yu
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
| | - Paul J. Low
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Sheng Hua Liu
- Key Laboratory
of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s
Republic of China
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76
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Butchosa C, Simon S, Blancafort L, Voityuk A. MS-CASPT2 Study of Hole Transfer in Guanine–Indole Complexes Using the Generalized Mulliken–Hush Method: Effective Two-State Treatment. J Phys Chem B 2012; 116:7815-20. [DOI: 10.1021/jp303675h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Butchosa
- Institut de Química Computacional,
Departament de Química, Universitat de Girona, Campus de Montilivi, Girona, 17071 Spain
| | - S. Simon
- Institut de Química Computacional,
Departament de Química, Universitat de Girona, Campus de Montilivi, Girona, 17071 Spain
| | - L. Blancafort
- Institut de Química Computacional,
Departament de Química, Universitat de Girona, Campus de Montilivi, Girona, 17071 Spain
| | - A. Voityuk
- Institut de Química Computacional,
Departament de Química, Universitat de Girona, Campus de Montilivi, Girona, 17071 Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Spain
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77
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Clark DW, Phang T, Edwards MG, Geraci MW, Gillespie MN. Promoter G-quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia-induced transcription. Free Radic Biol Med 2012; 53:51-9. [PMID: 22583700 PMCID: PMC3377816 DOI: 10.1016/j.freeradbiomed.2012.04.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/29/2012] [Accepted: 04/18/2012] [Indexed: 01/17/2023]
Abstract
The G-quadruplex, a non-B DNA motif that forms in certain G-rich sequences, is often located near transcription start sites in growth regulatory genes. Multiple lines of evidence show that reactive oxygen species generated as second messengers during physiologic signaling target specific DNA sequences for oxidative base modifications. Because guanine repeats are uniquely sensitive to oxidative damage, and G4 sequences are known "hot spots" for genetic mutation and DNA translocation, we hypothesized that G4 sequences are targeted for oxidative base modifications in hypoxic signaling. Approximately 25% of hypoxia-regulated genes in pulmonary artery endothelial cells harbored G4 sequences within their promoters. Chromatin immunoprecipitation showed that common base oxidation product 8-oxoguanine was selectively introduced into G4s, in promoters of hypoxia up-, down-, and nonregulated genes. Additionally, base excision DNA repair (BER) enzymes were recruited, and transient strand breaks formed in these sequences. Transcription factor Sp1, constitutively bound to G4 sequences in normoxia, was evicted as 8-oxoguanine accumulated during hypoxic exposure. Blocking hypoxia-induced oxidant production prevented both base modifications and decreased Sp1 binding. These findings suggest that oxidant stress in hypoxia causes oxidative base modifications, recruitment of BER enzymes, and transient strand breaks in G4 promoter sequences potentially altering G4 integrity and function.
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Affiliation(s)
- David W. Clark
- Department of Pharmacology and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Tzu Phang
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, University of Colorado Denver, CO, 80045, USA
| | - Michael G. Edwards
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, University of Colorado Denver, CO, 80045, USA
| | - Mark W. Geraci
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, University of Colorado Denver, CO, 80045, USA
| | - Mark N. Gillespie
- Department of Pharmacology and Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
- To whom correspondence should be addressed. Tel: (251) 460-6497; Fax: (251) 460-6798;
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78
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Abstract
Electrocatalysis offers a means of electrochemical signal amplification, yet in DNA-based sensors, electrocatalysis has required high-density DNA films and strict assembly and passivation conditions. Here, we describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low-density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low-density DNA films. Electrocatalysis with methylene blue that is covalently tethered to the DNA by a flexible alkyl chain linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of a single cytosine-adenine (CA) mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: It is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.
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79
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JACS Perspectives. J Am Chem Soc 2012. [DOI: 10.1021/ja305068k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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80
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Investigation of DNA damage treated with perfluorooctane sulfonate (PFOS) on ZrO2/DDAB active nano-order film. Biosens Bioelectron 2012; 35:180-185. [DOI: 10.1016/j.bios.2012.02.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/08/2012] [Accepted: 02/20/2012] [Indexed: 11/22/2022]
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81
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Pheeney CG, Barton JK. DNA electrochemistry with tethered methylene blue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7063-70. [PMID: 22512327 PMCID: PMC3398613 DOI: 10.1021/la300566x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Methylene blue (MB'), covalently attached to DNA through a flexible C(12) alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB' is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 ± 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB'-DNA is found to be least 3-fold larger than that of Nile blue (NB)-DNA, indicating that MB' is even more strongly coupled to the π-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB' on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB' at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions.
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Affiliation(s)
- Catrina G Pheeney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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82
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Lessner FH, Jennings ME, Hirata A, Duin EC, Lessner DJ. Subunit D of RNA polymerase from Methanosarcina acetivorans contains two oxygen-labile [4Fe-4S] clusters: implications for oxidant-dependent regulation of transcription. J Biol Chem 2012; 287:18510-23. [PMID: 22457356 DOI: 10.1074/jbc.m111.331199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subunit D of multisubunit RNA polymerase from many species of archaea is predicted to bind one to two iron-sulfur (Fe-S) clusters, the function of which is unknown. A survey of encoded subunit D in the genomes of sequenced archaea revealed six distinct groups based on the number of complete or partial [4Fe-4S] cluster motifs within domain 3. Only subunit D from strictly anaerobic archaea, including all members of the Methanosarcinales, are predicted to bind two [4Fe-4S] clusters. We report herein the purification and characterization of Methanosarcina acetivorans subunit D in complex with subunit L. Expression of subunit D and subunit L in Escherichia coli resulted in the purification of a D-L heterodimer with only partial [4Fe-4S] cluster content. Reconstitution in vitro with iron and sulfide revealed that the M. acetivorans D-L heterodimer is capable of binding two redox-active [4Fe-4S] clusters. M. acetivorans subunit D deleted of domain 3 (DΔD3) was still capable of co-purifying with subunit L but was devoid of [4Fe-4S] clusters. Affinity purification of subunit D or subunit DΔD3 from M. acetivorans resulted in the co-purification of endogenous subunit L with each tagged subunit D. Overall, these results suggest that domain 3 of subunit D is required for [4Fe-4S] cluster binding, but the [4Fe-4S] clusters and domain 3 are not required for the formation of the D-L heterodimer. However, exposure of two [4Fe-4S] cluster-containing D-L heterodimer to oxygen resulted in loss of the [4Fe-4S] clusters and subsequent protein aggregation, indicating that the [4Fe-4S] clusters influence the stability of the D-L heterodimer and therefore have the potential to regulate the assembly and/or activity of RNA polymerase in an oxidant-dependent manner.
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Affiliation(s)
- Faith H Lessner
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
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83
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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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84
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Brosh RM. Finding a needle in the haystack: recognition of DNA damage by collaboration between DNA repair proteins able to perform DNA charge transport. Cell Cycle 2012; 11:1055-6. [PMID: 22377696 DOI: 10.4161/cc.11.6.19785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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85
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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86
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Conductivity by Electron Pairs. Chem Phys 2012. [DOI: 10.1201/b11524-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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87
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The interplay of mutations and electronic properties in disease-related genes. Sci Rep 2012; 2:272. [PMID: 22355784 PMCID: PMC3280594 DOI: 10.1038/srep00272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 01/16/2012] [Indexed: 11/13/2022] Open
Abstract
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as p53 by detection of oxidative damage. However, the reproducible measurement and modelling of charge migration through DNA molecules at the nanometer scale remains a challenging and controversial subject even after more than a decade of intense efforts. Here we show, by analysing 162 disease-related genes from a variety of medical databases with a total of almost 20,000 observed pathogenic mutations, a significant difference in the electronic properties of the population of observed mutations compared to the set of all possible mutations. Our results have implications for the role of the electronic properties of DNA in cellular processes, and hint at the possibility of prediction, early diagnosis and detection of mutation hotspots.
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88
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Gollub C, Avdoshenko S, Gutierrez R, Berlin Y, Cuniberti G. Charge Migration in Organic Materials: Can Propagating Charges Affect the Key Physical Quantities Controlling Their Motion? Isr J Chem 2012. [DOI: 10.1002/ijch.201100092] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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89
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Wu Y, Brosh RM. DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster. Nucleic Acids Res 2012; 40:4247-60. [PMID: 22287629 PMCID: PMC3378879 DOI: 10.1093/nar/gks039] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Conserved Iron-Sulfur (Fe-S) clusters are found in a growing family of metalloproteins that are implicated in prokaryotic and eukaryotic DNA replication and repair. Among these are DNA helicase and helicase-nuclease enzymes that preserve chromosomal stability and are genetically linked to diseases characterized by DNA repair defects and/or a poor response to replication stress. Insight to the structural and functional importance of the conserved Fe-S domain in DNA helicases has been gleaned from structural studies of the purified proteins and characterization of Fe-S cluster site-directed mutants. In this review, we will provide a current perspective of what is known about the Fe-S cluster helicases, with an emphasis on how the conserved redox active domain may facilitate mechanistic aspects of helicase function. We will discuss testable models for how the conserved Fe-S cluster might operate in helicase and helicase-nuclease enzymes to conduct their specialized functions that help to preserve the integrity of the genome.
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Affiliation(s)
- Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada.
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90
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DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A 2012; 109:1856-61. [PMID: 22308447 DOI: 10.1073/pnas.1120063109] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. We have proposed a model where repair proteins containing redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in finding lesions. In this model, the population of sites to search is reduced by a localization of protein in the vicinity of lesions. Here, we examine this model using single-molecule atomic force microscopy (AFM). XPD, a 5'-3' helicase involved in nucleotide excision repair, contains a [4Fe-4S] cluster and exhibits a DNA-bound redox potential that is physiologically relevant. In AFM studies, we observe the redistribution of XPD onto kilobase DNA strands containing a single base mismatch, which is not a specific substrate for XPD but, like a lesion, inhibits CT. We further provide evidence for DNA-mediated signaling between XPD and Endonuclease III (EndoIII), a base excision repair glycosylase that also contains a [4Fe-4S] cluster. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto the mismatched strand. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between different repair proteins in their search for damage in the genome.
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91
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Lo FC, Lee JF, Liaw WF, Hsu IJ, Tsai YF, Chan SI, Yu SSF. The Metal Core Structures in the Recombinant Escherichia coli Transcriptional Factor SoxR. Chemistry 2012; 18:2565-77. [DOI: 10.1002/chem.201100838] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 09/14/2011] [Indexed: 11/10/2022]
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92
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Sjakste N, Bielskiene K, Bagdoniene L, Labeikyte D, Gutcaits A, Vassetzky Y, Sjakste T. Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes. Gene 2012; 492:54-64. [PMID: 22001404 DOI: 10.1016/j.gene.2011.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/08/2011] [Accepted: 09/22/2011] [Indexed: 01/05/2023]
Affiliation(s)
- N Sjakste
- Faculty of Medicine, University of Latvia, Šarlotes 1a, LV1001, Riga, Latvia
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93
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Lande ADL, Babcock NS, Řezáč J, Lévy B, Sanders BC, Salahub DR. Quantum effects in biological electron transfer. Phys Chem Chem Phys 2012; 14:5902-18. [DOI: 10.1039/c2cp21823b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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94
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White MF, Dillingham MS. Iron-sulphur clusters in nucleic acid processing enzymes. Curr Opin Struct Biol 2011; 22:94-100. [PMID: 22169085 DOI: 10.1016/j.sbi.2011.11.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 12/25/2022]
Abstract
Several unexpected reports of iron-sulphur clusters in nucleic acid binding proteins have recently appeared in the literature. Once thought to be relatively rare in these systems, iron-sulphur clusters are now known to be essential components of diverse nucleic acid processing machinery including glycosylases, primases, helicases, nucleases, transcription factors, RNA polymerases and RNA methyltransferases. In many cases, the function of the cluster is poorly understood and crystal structures of these iron-sulphur enzymes reveal little in common between them. In this article, we review the recent developments in the field and discuss to what extent there might exist common mechanistic roles for iron-sulphur clusters in nucleic acid enzymes.
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Affiliation(s)
- Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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95
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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.
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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
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96
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Kalosakas G. Charge transport in DNA: dependence of diffusion coefficient on temperature and electron-phonon coupling constant. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:051905. [PMID: 22181442 DOI: 10.1103/physreve.84.051905] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/14/2011] [Indexed: 05/31/2023]
Abstract
The diffusion coefficient is calculated for a charge propagating along a double-stranded DNA, while it interacts with the nonlinear fluctuational openings of base pairs. The latter structural dynamics of DNA is described by the Peyrard-Bishop-Dauxois model [T. Dauxois, M. Peyrard, and A. R. Bishop, Phys Rev. E 47 R44 (1993)], which represents essential anharmonicities of base-pair stretchings. The dependence of the diffusion coefficient on the temperature and the electron-phonon coupling constant is presented. The diffusion coefficient decreases when either the temperature or the electron-phonon coupling increases. Analytical expressions are provided that describe the temperature dependence of the diffusion coefficient. The variation of the parameters of these expressions with the electron-phonon coupling constant is also discussed. These results quantitatively demonstrate how DNA structural nonlinear dynamics affects macroscopic charge transport properties.
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97
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98
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Bonin J, Robert M. Photoinduced Proton-Coupled Electron Transfers in Biorelevant Phenolic Systems. Photochem Photobiol 2011; 87:1190-203. [DOI: 10.1111/j.1751-1097.2011.00996.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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99
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Zhang X, Zhao Z, Mei H, Qiao Y, Liu Q, Luo W, Xia T, Fang X. A fluorescence aptasensor based on DNA charge transport for sensitive protein detection in serum. Analyst 2011; 136:4764-9. [PMID: 21949940 DOI: 10.1039/c1an15265c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescence aptasensor based on DNA charge transport for sensitive protein detection has been developed. A 15nt DNA aptamer against thrombin was used as a model system. The aptamer was integrated into a double strand DNA (dsDNA) that was labeled with a hole injector, naphthalimide (NI), and a fluorophore, Alexa532, at its two ends. After irradiation by UV light, the fluorescence of Alexa532 was bleached due to the oxidization of Alexa532 by the positive charge transported from naphthalimide through the dsDNA. In the presence of thrombin, the binding of thrombin to the aptamer resulted in the unwinding of the dsDNA into ssDNA, which led to the blocking of charge transfer and the strong fluorescence emission of Alexa532. By monitoring the fluorescence signal change, we were able to detect thrombin in homogeneous solutions with high selectivity and high sensitivity down to 1.2 pM. Moreover, as DNA charge transfer is resistant to interferences from biological contexts, the aptasensor can be used directly in undiluted serum with similar sensitivity as that in buffer. This new sensing strategy is expected to promote the exploitation of aptamer-based biosensors for protein assays in complex biological matrixes.
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Affiliation(s)
- Xinyue Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, P.R. China
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100
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Mui TP, Fuss JO, Ishida JP, Tainer JA, Barton JK. ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase. J Am Chem Soc 2011; 133:16378-81. [PMID: 21939244 DOI: 10.1021/ja207222t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using DNA-modified electrodes, we show DNA-mediated signaling by XPD, a helicase that contains a [4Fe-4S] cluster and is critical for nucleotide excision repair and transcription. The DNA-mediated redox signal resembles that of base excision repair proteins, with a DNA-bound redox potential of ~80 mV versus NHE. Significantly, this signal increases with ATP hydrolysis. Moreover, the redox signal is substrate-dependent, reports on the DNA conformational changes associated with enzymatic function, and may reflect a general biological role for DNA charge transport.
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Affiliation(s)
- Timothy P Mui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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