Modified Nucleosides As Dna Sugar Centered Radical Precursors
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Modified Nucleosides As Dna Sugar Centered Radical Precursors
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Author : Antonio Manetto
language : en
Publisher: Cuvillier Verlag
Release Date : 2008
Modified Nucleosides As Dna Sugar Centered Radical Precursors written by Antonio Manetto and has been published by Cuvillier Verlag this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with categories.
I Modified Nucleosides As Dna Sugar Centered Radical Precursors Ii Dna Excess Electron Transfer Studies Iii A New Direct Dna Detection Method Dna Photography
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Author : Antonio Manetto
language : en
Publisher: Cuvillier Verlag
Release Date : 2008-04-21
I Modified Nucleosides As Dna Sugar Centered Radical Precursors Ii Dna Excess Electron Transfer Studies Iii A New Direct Dna Detection Method Dna Photography written by Antonio Manetto and has been published by Cuvillier Verlag this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-04-21 with Science categories.
During cellular metabolism of oxygen to water in the mithocondria, a small fraction of the oxygen is reductively converted into superoxide (O2•-) as a by product. Through complex biochemical processes, superoxide may be converted into various reactive oxygen species (ROS), e.g. hydroxyl radicals (•OH), H2O2, 1O2, etc. These ROS and in particular the highly diffusible •OH are known to cause chemical modifications on DNA through the formation of strand breaks and nucleobase modifications. DNA damage and strand breaks may also be induced through other environmental influences such as ionizing radiation, photooxidation and naturally occurring or synthetic chemical mutagens. Oxidative DNA damage can be produced by the oxidation of the nucleobases or of the sugar units. In the last case carbon centered radicals are formed by direct or indirect hydrogen abstraction. In the first part of this thesis (Chapter 1), the fate of the carbon centered radicals C5’ and pseudo C4’ of the sugar was investigated at the nucleoside level. The syntheses of new thermal or photolabile C5’ and pseudo C4’ radical precursors were achieved to this end and the mechanistic aspects were studied under various conditions. Kinetic data were obtained as well and the access to biological lesions was possible through these studies. In section 1.2.1, the synthesis of a novel perester radical precursor was achieved. The unprecedented selective generation of the pseudo C4’ radical was established as well. The radical was studied in solution under various conditions and the pathways of base releasing and degradation were proved and described. In section 1.2.2 a short and efficient synthetic sequence for the preparation of cyclonucleosides has been disclosed, based on consecutive radical reactions followed by a photochemical desilylation. The C5’ radicals, generated by the addition of a (TMS)3Si• radical to the corresponding 5’ carboxaldehyde, are the key intermediates in these transformations. The rate constant kC of the subsequent cyclisation reaction was estimated for the first time in such systems through a radical clock reaction setup. The value of kC = 7 × 103 s 1 at 25 °C found here is strictly correlated with the C5’ radical repair reaction. In section 1.2.3 a new synthetic route for the preparation of (5’R) tert butyl ketones was disclosed. Photolysis experiments selectively afforded the corresponding C5’ radical. In the presence of a physiological concentration of alkanethiol, the thymidin 5’ yl radical is efficiently reduced. Under these conditions the half life of the thymidin 5’ yl radical was calculated to be t1/2 = 6.6 min. without any cyclisation product being observed. The resulting C5’ radical could be obtained either by Norrish Type I photocleavage or by initial formation of an acyl radical that decarbonylates with a rate constant in the range of 105–106 s–1. The presence of a thiol prevents subsequent reactions such as the intramolecular attack onto the C6–C5 double bond of thymine. When an electron donor injects electrons into a duplex, negative charges move to an acceptor site in DNA. Investigations on how charges move through DNA and studies of how the electron transfer can be accelerated and controlled is an active field of research. In the second part of the thesis (Chapter 2) the study of the excess electron transfer (EET) through the DNA was undertaken. A flavin used as electron donor was alternated with a single electron injector in order to establish diverse EET features. A CPD lesion (T=T dimer) and one of three bromo nucleosides were used as electron acceptors enabling the evaluation of the sequence dependence and the donor/acceptor system influence on the EET. Three series of five flavin containing hairpins were prepared. They contained the flavin electron injector placed in the loop region of the hairpin and one of the three electron acceptors positioned in the stem region at a distance of about 17 Å to the flavin. The nature of the acceptor influences the debromination yield and therefore the EET process analysis. Moreover, the differences shown by the traps indicate that the reduction of the acceptor can indeed be the rate determining step. Thus, in the process of electron migration through DNA, which involves electron injection, migration and capture, the latter step might determine the final efficiency of the whole process. As a result of these studies, a G:C bp between the donor and the acceptor reduces the excess electron transfer efficiency approximately by a factor of two. More important is the unprecedented observation that the position of G:C base pairs between the donor and the acceptor strongly influences the efficiency of the process. Although every G:C bp reduces the EET efficiency by about 50 %, the position of a single G:C bp in proximity to the trap can decrease the efficiency by more than 85 %. To further investigate the EET through DNA, it was chosen to initiate the process by the injection of one single electron per strand using a single electron donor (SED). In section 2.2.2 the use of SED was alternated with the use of the flavin donor in systems containing two electron acceptors in a row. The irradiation at 320 nm of SED containing double strands initiates a cascade of homolysis, charge translocation and deprotonation enabling the final electron injection into the DNA base stack. This process is initiated by a Norrish type I photolysis of the tert butyl α hydroxy ketone of the SED moiety. On the other hand, the results observed upon irradiation of a flavin containing hairpin, provide an astonishing outcome. The chemistry that is triggered by a charge in DNA depends on how the charge was initially injected. In excited state systems, the injected electron feels the efficient charge recombination process, which seems to limit and bias charge propagation. If, however, ground state chemistry is employed to inject the charge, no recombination trap is present. In this case, the charge can move freely. Excess electrons injected by such a system can trigger more than one reaction, establishing a catalytic electron, and they can hop over acceptors if their triggering mechanism is slower than the hopping step. Strong efforts are under way to create DNA based nanoelectronic materials with self organizing properties. The long term goal is that such a novel material may self assemble into complex conductive nano wire networks with computing or diagnostic potential. Recently, a controlled assembly of metallised DNA in which one or more natural base pairs are replaced by nucleosides carrying flat metal complexes was reported. The design and the synthesis of DNA structures containing an internal metal complex between an electron donor and an acceptor opened the access to the study of EET through metal base pairs (metal mediated EET, M MEET). A series of DNA hairpins containing the light dependent flavin electron donor and the fast electron acceptor BrdU were designed. A salen metal complex between the donor and the electron acceptor was introduced via the oligonucleotide solid phase synthesis in order to establish the influence of one metal in the electron transfer process. The hairpins design was aimed at exploring the electron transfer through the salen metal complexes in the context of mixed sequences. The effect of only one metal per DNA was investigated in this proof of concept study, in which only the nature of the metal and the irradiation conditions were systematically changed. In the third part of the thesis (Chapter 3) a new direct DNA detection method was established based on the principle of the black and white photography, called DNA photography, DP. A detection limit lower than 300 attomoles of DNA (10-18 mol) was achieved with a simple setup in a photography dark room. Moreover the detection of 600 femtomoles (10-15mol) of a sequence associated with a gene of Y. pestis, which causes the mortal disease plague, was achieved. In the latter case, molecular beacons (MBs) were used in order to use the FRET principle together with the DP method.
Charged Particle And Photon Interactions With Matter
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Author : A. Mozumder
language : en
Publisher: CRC Press
Release Date : 2003-11-14
Charged Particle And Photon Interactions With Matter written by A. Mozumder and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-11-14 with Science categories.
Charged Particle and Photon Interactions with Matter offers in-depth perspectives on phenomena of ionization and excitation induced by charged particle and photon interactions with matter in vivo and in vitro. This reference probes concepts not only in radiation and photochemistry, but also in radiation physics, radiation biochemistry, and radiatio
Modified Nucleosides
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Author : Piet Herdewijn
language : de
Publisher: John Wiley & Sons
Release Date : 2008-09-08
Modified Nucleosides written by Piet Herdewijn and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-09-08 with Science categories.
Edited by one of the main driving forces behind the field's momentous rise in recent years, this one-stop reference is the first comprehensive resource to integrate recent advances. The first part addresses biochemical aspects and applications, the second and third parts are devoted to compounds with therapeutic potential, with the third part focusing on newly introduced anticancer nucleoside drugs. Essential reading for every scientist working in this area.
Mechanisms Of Dna Damage And Repair
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Author : Michael G. Simic
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-11-21
Mechanisms Of Dna Damage And Repair written by Michael G. Simic and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-21 with Science categories.
This book is based on the papers presented at the conference on "Mecha nisms of DNA Damage and Repair: Implications for Carcinogenesis and Risk Assessment," held at the National Bureau of Standards on June 2-7, 1985, This volume deals with mechanisms of DNA damage and repair at the molecular level; consequences of unrepaired or misrepaired damage, with major emphasis on carcinogenesis; drugs which bind selectively to altered and potentially damaging DNA sequences; and potential utilization of DNA damage as an endpoint for assessing risks of UV light, ionizing radiations, chemicals, drugs, and hazardous agents in foods. Because the induction of mutations by radiation and genotoxic chemicals has been observed to follow one-hit kinetics in some instances, it is generally assumed that any level of exposure to a DNA-damaging agent may increase the risk of genetic disease or cancer in an exposed population. At the same time, however, there is evidence that although the DNA of living cells is continually damaged by natural background radiation, free radicals, and other naturally occurring processes, most of the damage is normally repaired.
Chemical Abstracts
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Author :
language : en
Publisher:
Release Date : 2002
Chemical Abstracts written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002 with Chemistry categories.
Dna And Rna Modification Enzymes
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Author : Henri Grosjean
language : en
Publisher: CRC Press
Release Date : 2009-06-11
Dna And Rna Modification Enzymes written by Henri Grosjean and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-11 with Science categories.
This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008). They ended by a short ‘conclusion and future prospect’ section and an exhaustive list of 35 to up to 257 references (in average 87). Contributors are geneticists, structural enzymologists and molecular biologists working at the forefront of this exciting, fast-moving and diverse field of researches. This book will be a major interest to PhD students and University teachers alike. It will also serve as an invaluable reference tool for new researchers in the field, as well as for specialists of RNA modification enzymes generally not well informed about what is going on in similar processes acting on DNA and vice-versa for specialists of the DNA modification-editing and repair processes usually not much acquainted with what is going on in the RNA maturation field. The book is subdivided into 41 chapters (740 pages). The common links between them are mainly the enzymatic aspects of the different modification-editing and repair machineries: structural, mechanistic, functional and evolutionary aspects. It starts with two general and historical overview of the discovery of modified nucleosides in DNA and RNA and corresponding modification-editing enzymes. Then follows eleven chapters on DNA modification and editing (mechanistic and functional aspects). Two additional chapters cover problems related to DNA/RNA repair and base editing by C-to-U deaminases, followed by three chapters on RNA editing by C-to-U and A-to-I type of deamination. Discussions about interplay between DNA and RNA modifications and the emergence of DNA are covered in two independent chapters, followed by twenty chapters on different but complementary aspects of RNA modification enzymes and their cellular implications. The last chapter concerns the description of the present state-of-the art for incorporating modified nucleosides by in vitro chemical synthesis. At the end of the book, six appendicies give useful details on modified nucleosides, modification-editing enzymes and nucleosides analogs. This information is usually difficult to obtain from current scientific literature.
Nucleic Acids Abstracts
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Author :
language : en
Publisher:
Release Date : 1996
Nucleic Acids Abstracts written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996 with Nucleic acids categories.
Deutsche Nationalbibliographie Und Bibliographie Der Im Ausland Erschienenen Deutschsprachigen Ver Ffentlichungen
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Author :
language : de
Publisher:
Release Date : 2009
Deutsche Nationalbibliographie Und Bibliographie Der Im Ausland Erschienenen Deutschsprachigen Ver Ffentlichungen written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with Dissertations, Academic categories.
Oxidative Damage To Nucleic Acids
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Author : Mark D. Evans
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-06-11
Oxidative Damage To Nucleic Acids written by Mark D. Evans and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-06-11 with Science categories.
This book provides up-to-date coverage of selected topics in nucleic acid oxidation. The topics have been selected to cover everything from basic chemical mechanisms, repair of damage and the biological and pathological meaning of DNA oxidation. The chapters are authored by leading, research active, international experts in the respective topics.