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Jacqueline K Barton - One of the best experts on this subject based on the ideXlab platform.
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effective distance for dna mediated Charge Transport between repair proteins
ACS central science, 2019Co-Authors: Edmund C M Tse, Theodore J Zwang, Sebastian Bedoya, Jacqueline K BartonAbstract:The stacked aromatic base pairs within the DNA double helix facilitate Charge Transport down its length in the absence of lesions, mismatches, and other stacking perturbations. DNA repair proteins containing [4Fe4S] clusters can take advantage of DNA Charge Transport (CT) chemistry to scan the genome for mistakes more efficiently. Here we examine the effective length over which Charge can be Transported along DNA between these repair proteins. We define the effective CT distance as the length of DNA within which two proteins are able to influence their ensemble affinity to the DNA duplex via CT. Endonuclease III, a DNA repair glycosylase containing a [4Fe4S] cluster, was incubated with DNA duplexes of different lengths (1.5–9 kb), and atomic force microscopy was used to quantify the binding of proteins to these duplexes to determine how the relative protein affinity changes with increasing DNA length. A sharp change in binding slope is observed at 3509 base pairs, or about 1.2 μm, that supports the existence of two regimes for protein binding, one within the range for DNA CT, one outside of the range for CT; DNA CT between the redox proteins bound to DNA effectively decreases the ensemble binding affinity of oxidized and reduced proteins to DNA. Utilizing an Endonuclease III mutant Y82A, which is defective in carrying out DNA CT, shows only one regime for protein binding. Decreasing the temperature to 4 °C or including metallointercalators on the duplex, both of which should enhance base stacking and decrease DNA floppiness, leads to extending the effective length for DNA Charge Transport to ∼5300 bp or 1.8 μm. These results thus support DNA Charge Transport between repair proteins over kilobase distances. The results furthermore highlight the ability of DNA repair proteins to search the genome quickly and efficiently using DNA Charge Transport chemistry.
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the 4fe4s cluster of human dna primase functions as a redox switch using dna Charge Transport
Science, 2017Co-Authors: Elizabeth Obrien, Lauren E Salay, Marilyn E. Holt, Walter J. Chazin, Matthew K Thompson, Aaron Ehlinger, Jacqueline K BartonAbstract:DNA Charge Transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this Charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA Charge Transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA Charge Transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.
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long range dna Charge Transport
Journal of Organic Chemistry, 2003Co-Authors: Sarah Delaney, Jacqueline K BartonAbstract:The stack of base pairs within double helical DNA has been shown to mediate Charge Transport reactions. Charge Transport through DNA can result in chemistry at a distance, yielding oxidative DNA damage at a site remote from the bound oxidant. Since DNA Charge Transport chemistry depends on coupling within the stacked base pair array, this chemistry is remarkably sensitive to sequence-dependent DNA structure and dynamics. Here, we discuss different features of DNA Charge Transport chemistry, including applications as well as possible biological consequences and opportunities.
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dna mediated Charge Transport characterization of a dna radical localized at an artificial nucleic acid base
Journal of the American Chemical Society, 2002Co-Authors: Matthias Pascaly, Jacqueline K BartonAbstract:DNA assemblies containing 4-methylindole incorporated as an artificial base provide a chemically well-defined system in which to explore the oxidative Charge Transport process in DNA. Using this artificial base, we have combined transient absorption and EPR spectroscopies as well as biochemical methods to test experimentally current mechanisms for DNA Charge Transport. The 4-methylindole radical cation intermediate has been identified using both EPR and transient absorption spectroscopies in oxidative flash-quench studies using a dipyridophenazine complex of ruthenium as the intercalating oxidant. The 4-methylindole radical cation intermediate is particularly amenable to study given its strong absorptivity at 600 nm and EPR signal measured at 77 K with g = 2.0065. Both transient absorption and EPR spectroscopies show that the 4-methylindole is well incorporated in the duplex; the data also indicate no evidence of guanine radicals, given the low oxidation potential of 4-methylindole relative to the nucleic acid bases. Biochemical studies further support the irreversible oxidation of the indole moiety and allow the determination of yields of irreversible product formation. The construction of these assemblies containing 4-methylindole as an artificial base is also applied in examining long-range Charge Transport mediated by the DNA base pair stack as a function of intervening distance and sequence. The rate of formation of the indole radical cation is ≥107 s-1 for different assemblies with the ruthenium positioned 17−37 A away from the methylindole and with intervening A−T base pairs primarily composing the bridge. In these assemblies, methylindole radical formation at a distance is essentially coincident with quenching of the ruthenium excited state to form the Ru(III) oxidant; Charge Transport is not rate limiting over this distance regime. The measurements here of rates of radical cation formation establish that a model of G-hopping and AT-tunneling is not sufficient to account for DNA Charge Transport. Instead, these data are viewed mechanistically as Charge Transport through the DNA duplex primarily through hopping among well stacked domains of the helix defined by DNA sequence and dynamics.
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variations in dna Charge Transport with nucleotide composition and sequence
Journal of the American Chemical Society, 2000Co-Authors: Tashica T Williams, Duncan T Odom, Jacqueline K BartonAbstract:Long-range oxidative damage to DNA has been demonstrated in experiments using a variety of remotely bound oxidants. However, the mechanism(s) by which Charge is Transported through the base pair stack needs still to be established. Recent theoretical proposals bring together tunneling and hopping mechanisms to describe Charge Transport. On the basis of measurements of damage yield, it has been proposed that Charge Transport occurs by hopping between guanine sites and tunneling through TA steps. In accord with guanine hopping, oxidative damage over long distances was not observed when 5‘-TATATA-3‘ intervened between G sites. Phonon-assisted polaron hopping has been suggested as an alternative mechanism. In this model, the sequence-dependent conformational dynamics of DNA are expected to aid in Charge Transport.
Frederick D Lewis - One of the best experts on this subject based on the ideXlab platform.
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wirelike Charge Transport dynamics for dna lipid complexes in chloroform
Journal of the American Chemical Society, 2014Co-Authors: Ashutosh Kumar Mishra, Ryan M Young, Michael R Wasielewski, Frederick D LewisAbstract:The dynamics of Charge separation and Charge recombination have been determined for lipid complexes of DNA capped hairpins possessing stilbene electron-acceptor and -donor chromophores separated by base-pair domains that vary in length and base sequence in chloroform solution by means of femtosecond time-resolved transient absorption spectroscopy. The results obtained for the DNA–lipid complexes are compared with those previously obtained in our laboratories for the same hairpins in aqueous buffer. The Charge separation and Charge recombination times for the lipid complexes are consistently much shorter than those determined in aqueous solution and are only weakly dependent on the number of base pairs separating the acceptor and donor. The enhanced rate constants for forward and return Charge Transport in DNA–lipid complexes support proposals that solvent gating is responsible, to a significant extent, for the relatively low rates of Charge Transport for DNA in water. Moreover, they suggest that DNA–lipid...
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wirelike Charge Transport dynamics for dna lipid complexes in chloroform
Journal of the American Chemical Society, 2014Co-Authors: Ashutosh Kumar Mishra, Ryan M Young, Michael R Wasielewski, Frederick D LewisAbstract:The dynamics of Charge separation and Charge recombination have been determined for lipid complexes of DNA capped hairpins possessing stilbene electron-acceptor and -donor chromophores separated by base-pair domains that vary in length and base sequence in chloroform solution by means of femtosecond time-resolved transient absorption spectroscopy. The results obtained for the DNA-lipid complexes are compared with those previously obtained in our laboratories for the same hairpins in aqueous buffer. The Charge separation and Charge recombination times for the lipid complexes are consistently much shorter than those determined in aqueous solution and are only weakly dependent on the number of base pairs separating the acceptor and donor. The enhanced rate constants for forward and return Charge Transport in DNA-lipid complexes support proposals that solvent gating is responsible, to a significant extent, for the relatively low rates of Charge Transport for DNA in water. Moreover, they suggest that DNA-lipid complexes may prove useful in the development of DNA-based molecular electronic devices.
Ashutosh Kumar Mishra - One of the best experts on this subject based on the ideXlab platform.
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wirelike Charge Transport dynamics for dna lipid complexes in chloroform
Journal of the American Chemical Society, 2014Co-Authors: Ashutosh Kumar Mishra, Ryan M Young, Michael R Wasielewski, Frederick D LewisAbstract:The dynamics of Charge separation and Charge recombination have been determined for lipid complexes of DNA capped hairpins possessing stilbene electron-acceptor and -donor chromophores separated by base-pair domains that vary in length and base sequence in chloroform solution by means of femtosecond time-resolved transient absorption spectroscopy. The results obtained for the DNA–lipid complexes are compared with those previously obtained in our laboratories for the same hairpins in aqueous buffer. The Charge separation and Charge recombination times for the lipid complexes are consistently much shorter than those determined in aqueous solution and are only weakly dependent on the number of base pairs separating the acceptor and donor. The enhanced rate constants for forward and return Charge Transport in DNA–lipid complexes support proposals that solvent gating is responsible, to a significant extent, for the relatively low rates of Charge Transport for DNA in water. Moreover, they suggest that DNA–lipid...
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wirelike Charge Transport dynamics for dna lipid complexes in chloroform
Journal of the American Chemical Society, 2014Co-Authors: Ashutosh Kumar Mishra, Ryan M Young, Michael R Wasielewski, Frederick D LewisAbstract:The dynamics of Charge separation and Charge recombination have been determined for lipid complexes of DNA capped hairpins possessing stilbene electron-acceptor and -donor chromophores separated by base-pair domains that vary in length and base sequence in chloroform solution by means of femtosecond time-resolved transient absorption spectroscopy. The results obtained for the DNA-lipid complexes are compared with those previously obtained in our laboratories for the same hairpins in aqueous buffer. The Charge separation and Charge recombination times for the lipid complexes are consistently much shorter than those determined in aqueous solution and are only weakly dependent on the number of base pairs separating the acceptor and donor. The enhanced rate constants for forward and return Charge Transport in DNA-lipid complexes support proposals that solvent gating is responsible, to a significant extent, for the relatively low rates of Charge Transport for DNA in water. Moreover, they suggest that DNA-lipid complexes may prove useful in the development of DNA-based molecular electronic devices.
Alessandro Troisi - One of the best experts on this subject based on the ideXlab platform.
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Charge Transport in high mobility molecular semiconductors classical models and new theories
Chemical Society Reviews, 2011Co-Authors: Alessandro TroisiAbstract:The theories developed since the fifties to describe Charge Transport in molecular crystals proved to be inadequate for the most promising classes of high mobility molecular semiconductors identified in the recent years, including for example pentacene and rubrene. After reviewing at an elementary level the classical theories, which still provide the language for the understanding of Charge Transport in these systems, this tutorial review outlines the recent experimental and computational evidence that prompted the development of new theories of Charge Transport in molecular crystals. A critical discussion will illustrate how very rarely it is possible to assume a Charge hopping mechanism for high mobility organic crystals at any temperature. Recent models based on the effect of non-local electron–phonon coupling, dynamic disorder, coexistence of localized and delocalized states are reviewed. Additionally, a few more recent avenues of theoretical investigation, including the study of defect states, are discussed.
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dynamic disorder in molecular semiconductors Charge Transport in two dimensions
Journal of Chemical Physics, 2011Co-Authors: Alessandro TroisiAbstract:A semiclassical model to study Charge Transport in molecular semiconductors is extended from one to an arbitrary number of dimensions. The model is applied to the calculation of the Charge mobility of the holes in the two dimensional plane of rubrene with the largest Charge mobility. The absolute values of the computed mobility tensor, evaluated without adjustable parameters, are in excellent agreement with the experimental results of Podzorov et al. [Phys. Rev. Lett. 95, 226601 (2005)] and have the correct temperature dependence. The localization length and density of states determined by dynamic disorder are analyzed in detail and provide a global description of the Charge Transport process in agreement with the spectroscopic experiments. The effect of correlation in the modeling of dynamic disorder is also investigated.
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Charge Transport in self assembled semiconducting organic layers role of dynamic and static disorder
Journal of Physical Chemistry C, 2010Co-Authors: Thorsten Vehoff, Alessandro Troisi, Yeon Sook Chung, Karen Johnston, Do Y Yoon, Denis AndrienkoAbstract:Partial disorder is an inherent property of self-assembled organic semiconductors that complicates their rational design, because electronic structure, self-assembling properties, and stability all have to be accounted for simultaneously. Therefore, the understanding of Charge Transport mechanisms in these systems is still in its infancy. A theoretical study of Charge Transport in organic semiconductors was performed on self-assembled layers of [1]benzothieno[3,2-b]benzothiophene functionalized with alkyl side chains. Analysis showed that semiclassical dynamics misses static (on time scales of Charge Transport) disorder while the solution of the master equation combined with the high-temperature limit Marcus theory for Charge transfer rates does not take into account molecular dynamic modes relaxing on a time scale of Charge hopping. A comparison between predictions based on a perfectly ordered and a realistic crystal structure reveals the strong influence of static and dynamic disorder. The advantage of ...
Mischa Bonn - One of the best experts on this subject based on the ideXlab platform.
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Charge Transport mechanism in networks of armchair graphene nanoribbons
Scientific Reports, 2020Co-Authors: Nils Richter, Zongping Chen, Alexander Tries, Thorsten Prechtl, Akimitsu Narita, Klaus Mullen, Kamal Asadi, Mischa BonnAbstract:In graphene nanoribbons (GNRs), the lateral confinement of Charge carriers opens a band gap, the key feature that enables novel graphene-based electronics. Despite great progress, reliable and reproducible fabrication of single-ribbon field-effect transistors (FETs) is still a challenge, impeding the understanding of the Charge Transport. Here, we present reproducible fabrication of armchair GNR-FETs based on networks of nanoribbons and analyze the Charge Transport mechanism using nine-atom wide and, in particular, five-atom-wide GNRs with large conductivity. We show formation of reliable Ohmic contacts and a yield of functional FETs close to unity by lamination of GNRs to electrodes. Modeling the Charge Transport in the networks reveals that Transport is governed by inter-ribbon hopping mediated by nuclear tunneling, with a hopping length comparable to the physical GNR length. Overcoming the challenge of low-yield single-ribbon transistors by the networks and identifying the corresponding Charge Transport mechanism is a key step forward for functionalization of GNRs.
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Charge Transport mechanism in networks of armchair graphene nanoribbons
arXiv: Mesoscale and Nanoscale Physics, 2018Co-Authors: Nils Richter, Zongping Chen, Alexander Tries, Thorsten Prechtl, Akimitsu Narita, Klaus Mullen, Kamal Asadi, Mischa BonnAbstract:In graphene nanoribbons (GNRs), the lateral confinement of Charge carriers opens a band gap, the key feature to enable novel graphene-based electronics. Successful synthesis of GNRs has triggered efforts to realize field-effect transistors (FETs) based on single ribbons. Despite great progress, reliable and reproducible fabrication of single-ribbon FETs is still a challenge that impedes applications and the understanding of the Charge Transport. Here, we present reproducible fabrication of armchair GNR-FETs based on a network of nanoribbons and analyze the Charge Transport mechanism using nine-atom wide and, in particular, five-atom-wide GNRs with unprecedented conductivity. We show formation of reliable Ohmic contacts and a yield of functional FETs close to unity by lamination of GNRs on the electrodes. Modeling the Charge carrier Transport in the networks reveals that this process is governed by inter-ribbon hopping mediated by nuclear tunneling, with a hopping length comparable to the physical length of the GNRs. Furthermore, we demonstrate that nuclear tunneling is a general Charge Transport characteristic of the GNR networks by using two different GNRs. Overcoming the challenge of low-yield single-ribbon transistors by the networks and identifying the corresponding Charge Transport mechanism puts GNR-based electronics in a new perspective.