Download or read book DNA mediated Charge Transport in a Biological Context written by Pamela Alisa Sontz and published by . This book was released on 2012 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fundamental Mechanisms and Biological Applications of DNA mediated Charge Transport written by Katherine Emily Augustyn and published by . This book was released on 2007 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA mediated Charge Transfer in Biological Contexts written by Anand Vadehra and published by . This book was released on 2003 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Charge Migration in DNA written by Tapash Chakraborty and published by Springer Science & Business Media. This book was released on 2007-08-15 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: Charge migration through DNA has been the focus of considerable interest in recent years. This book presents contributions from an international team of researchers active in this field. It contains a wide range of topics that includes the mathematical background of the quantum processes involved, the role of charge transfer in DNA radiation damage, a new approach to DNA sequencing, DNA photonics, and many others.
Download or read book Charge Transfer in DNA written by Hans-Achim Wagenknecht and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: The past few years have witnessed intense research in this fascinating field as well as many controversial discussions. Now the time is ripe for a comprehensive book covering not only theoretical aspects, but also such mechanistic topics as principles and mechanisms of photoinduced charge injection, transport and trapping in DNA, sequence-dependent DNA dynamics, spectroscopic investigations of hole transport and much more. From the contents: * Principles and Mechanisms of Photoinduced Charge Injection, Transport and Trapping in DNA * Sequence-Dependent DNA Dynamics: The Regulator of DNA-Mediated Charge Transport * Excess Electron Transfer in DNA Probed with Flavin and Thymine Dimer Modified Oligonucleotides * Dynamics of Photoinitiated Hole and Electron Injection in Duplex DNA * Spectroscopic Investigation of Oxidative Hole Transfer via Adenine Hopping in DNA * Chemical Probing of Reductive Electron Transfer in DNA * Chemical Approach for Modulating Hole Transport in DNA * Spectroscopic Investigation of Charge Transfer in DNA * Spectroscopic Probing of Ultrafast Structural Relaxation and Electron Transfer Dynamics in DNA Edited by Hans-Achim Wagenknecht, and written by renowned international authors, this book provides an excellent overview with high quality contributions, making it a "must-have" for everyone working in the field.
Download or read book Long Range Charge Transfer in DNA I written by Gary B. Schuster and published by Springer Science & Business Media. This book was released on 2004-03-24 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fundamental Aspects of DNA mediated Charge Transport written by Tashica Tréshun Williams and published by . This book was released on 2004 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA mediated Charge Transport for Long range Sensing and Protein Detection written by Natalie Bloom Muren and published by . This book was released on 2013 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Investigations of DNA mediated Protein Oxidation written by Anna Ruth Arnold and published by . This book was released on 2015 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA pi-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt pi-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA pi-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins. Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. 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 CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance. Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)2, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)2 is substituted with poly(dAdT)2, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species. We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate. DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster. While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]3+ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells. In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.
Download or read book Charge Transport in DNA Insights from Simulations written by Wolter, Mario and published by KIT Scientific Publishing. This book was released on 2014-10-16 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Charge transport and charge transfer (CT) capabilities of deoxyribonucleic acid (DNA) are investigated. A QM/MM multi-scale framework is applied to calculate the CT capabilities of DNA under conditions resembling the experimental setup. The simulations are able to explain and predict the outcome of experiments and therefore make suggestions in advance. Based on the findings, suitable DNA sequences can be opted for the design of DNA-based devices as nano-scale electronic elements.
Download or read book DNA mediated Charge Transport Devices for Protein Detection written by Ariel L. Furst and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA mediated Charge Transport Devices for Protein Detection written by Ariel L. Furst and published by . This book was released on 2015 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA mediated Charge Transport in DNA Repair written by Amie Kathleen Boal and published by . This book was released on 2008 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Investigating DNA mediated Charge Transport by Time resolved Spectroscopy written by Eric Daniel Olmon and published by . This book was released on 2012 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: In all organisms, oxidation threatens the integrity of the genome. Numerous studies have suggested that DNA-mediated charge transport (CT) may play an important role in the sequestration, detection, and repair of oxidative damage. To fully understand the mechanism of DNA-mediated CT, it is necessary to characterize transient intermediates that arise during the reaction and to determine the lifetimes of these intermediates. Time-resolved spectroscopy is the most appropriate experimental method for such observations. Each intermediate has a characteristic spectrum. By observing time-dependent changes in the absorption spectrum of the sample, it is therefore possible to determine what species are present at a particular time and how long it exists in solution. Experiments presented here involve the use of time-resolved spectroscopy to better understand the process of DNA-mediated CT.
Download or read book Long Range Charge Transfer in DNA I written by Gary B. Schuster and published by Springer. This book was released on 2004-03-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: T. Douki, J.-L. Ravanat, D. Angelov, J.R. Wagner, J. Cadet: Effects of Duplex Stability on Charge-Transfer Efficiency within DNA .- B. Giese: Hole Injection and Hole Transfer Through DNA. The Hopping Mechanism .- F.D. Lewis, M.R. Wasielewski: Dynamics and Equilibrium for Single Step Hole Transport Processes in Duplex DNA .- M.A. O'Neill, J.K. Barton: DNA-Mediated Charge Transport Chemistry and Biology .- K. Kawai, T. Majima: Hole Transfer in DNA by Monitoring the Transient Absorption of Radical Cations of Organic Molecules Conjugated to DNA .- G.B. Schuster, U. Landman: The Mechanism of Long-Distance Radical Cation Transport in Duplex DNA: Ion-Gated Hopping of Polaron-Like Distortions .- K. Nakatani, I. Saito: The Charge Transport in Duplex DNA Containing Modified Nucletotide Bases .- C. Behrens, M.K. Cichon, F. Grolle, U. Hennecke, T. Carell: Excess Electron Transfer in Defined Donor- Nucleobase and Donor-DNA-Acceptor Systems
Download or read book Electroanalytical Methods Of Biological Materials written by Anna Brajter-toth and published by CRC Press. This book was released on 2002-03-21 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text details contemporary electroanalytical strategies of biomolecules and electrical phenomena in biological systems. It presents developments in sequence-specific DNA detection for more efficient medical diagnosis of genetic and infectious diseases and microbial and viral pathogens.
Download or read book Long Range Charge Transfer in DNA I written by Gary B. Schuster and published by Springer. This book was released on 2004-02-24 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt:
