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Dissertations / Theses on the topic 'DNA intercalators'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Paradis, Michel 1976. "The design and synthessis of platinum-based DNA intercalators /." Thesis, McGill University, 2000. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=31523.

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Over the past years, considerable attention has focused on the synthesis of small complexes that can bind and react at specific DNA sequences. This understanding of how to target DNA sites with specificity becomes important for nucleotide probing and novel chemotherapeutics.<br>Inert and stable transition-metal complexes are already being used for this purpose. Square planar platinum (II) complexes containing an aromatic heterocyclic ligand can insert and stack between the double helix base pairs. Two known ligands, DPPZ and phi, do intercalate DNA when chelating ruthenium, rhodium, or osmium.

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2

Maehigashi, Tatsuya. "Ultra-high resolution DNA crystallography." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29684.

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Thesis (Ph.D)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.<br>Committee Chair: Williams, Loren; Committee Member: Bottomley, Lawrence; Committee Member: Hud, Nicholas; Committee Member: Oyelere, Adegboyega; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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3

Derrat, Hanan S. "Organic and metal organic cationic DNA intercalators based on DPPZ analogues." Thesis, University of Sheffield, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.574605.

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New metal complex derivatives of tppz containing cationic "diquat" sites have been synthesized and characterized. Their interaction with DNA has also been explored .. Water-soluble organic cationic derivatives of the dppz ligand with a variety of functional groups and number of aromatic rings in the phenazine region have also been synthesised and characterized. These systems were synthesized with the aim of modulating the energy of the internal charge transfer excited state of the parent cation. The interactions of the new organic diquaterary salts of dppz with ON A have been studied. Metal co

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4

Sprague, Robin M. "Molecular modeling of DNA with minor groove binding agents and intercalators." Scholarly Commons, 2000. https://scholarlycommons.pacific.edu/uop_etds/539.

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The molecular modeling of several drugs in complexes with deoxyribonucleic acid (DNA) was undet1aken. Selected bis-lexitropsins, based upon NMR and modeling studies of bis-distamycin A, were modeled with an oligonucleotide d(CGAACA TGTTCG)2 using MidasPlus and AMBER 4.0. Intercalators ethidium, ellipticinc. mitoxantrone, and bisantrene were modeled with an oligonucleotide d(CGCG)~ using SpartanPlus and DOCK 4.0. The binding site was prepared from an x-ray study of this oligonucleotide interacting with ditercalinium, a bis-intercalator. The purpost: of this study was to estimate the conformatio

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5

Deeyaa, Blessing D. "DNA Photocleavage by 9-Aminomethylanthracene Dyes at pH 7.0: Ionic Strength Effects." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/chemistry_theses/39.

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DNA photosensitizers are compounds that are capable of binding in to DNA strands through groove binding, intercalation, or electrostatic interactions. Excitation of these agents by light generates reactive oxygen species which causes extensive photo-oxidative damage to genomic DNA. Physiological concentrations of NaCl and KCl are ~ 150 mM and 260 mM within the cell nucleus where DNA is contained. Unfortunately, the ability of most photosensitizers to bind to double-helical DNA is reduced and photocleavage yields are diminished as concentrations of salt increase. The aim of this project is t

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6

Fagenson, Alexander. "Gold (iii) macrocycles are dna intercalators that inhibit topoisomerase i and ii." Honors in the Major Thesis, University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1536.

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Human Topoisomerase IB (TOP1) and Topoisomerase II? (TOP2?) are essential nuclear enzymes that control DNA topology during DNA replication, gene transcription and cell division. These enzymes carry out their catalytic function by making transient single-strand (type I) or double-strand (type II) breaks in the DNA. In vivo, these complexes are short-lived but can be exploited by anti-cancer drugs to mechanistically kill cancer cells. Two general classes of compounds can kill cancer cells through a topo-targeted mechanism. Interfacial Poisons (IFPs) act at the enzyme-DNA interface to inhibit the

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7

Liu, Tao Lewis Nathan Saul Barton Jacqueline K. "Electrochemical studies of electron transfer in DNA films with covalently tethered intercalators /." Diss., Pasadena, Calif. : California Institute of Technology, 2007. http://resolver.caltech.edu/CaltechETD:etd-08312006-131856.

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8

Rai, Saroj. "Viral inactivation using DNA intercalators and dyes for sterilization of blood products /." The Ohio State University, 1992. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487779120908841.

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9

Sprague, Robin M. "Molecular modeling of DNA with minor groove binding agents and intercalators : a thesis." Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/539.

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The molecular modeling of several drugs in complexes with deoxyribonucleic acid (DNA) was undet1aken. Selected bis-lexitropsins, based upon NMR and modeling studies of bis-distamycin A, were modeled with an oligonucleotide d(CGAACA TGTTCG)2 using MidasPlus and AMBER 4.0. Intercalators ethidium, ellipticinc. mitoxantrone, and bisantrene were modeled with an oligonucleotide d(CGCG)~ using SpartanPlus and DOCK 4.0. The binding site was prepared from an x-ray study of this oligonucleotide interacting with ditercalinium, a bis-intercalator. The purpost: of this study was to estimate the conformatio

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10

Teixeira, Susana Christina Marujo. "Crystallographic studies on a thermophile Xylanase and structural studies on anti-cancer DNA intercalators." Thesis, University of Reading, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501318.

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This thesis describes structural studies on a Xylanase and on DNA intercalators with anticancer properties. The first chapter introduces the molecules under study while in the second chapter the methodology is described. The third chapter describes an anisotropic refinement of the structure of Thermoascus aurantiacus Xylanase I. This glycosyl hydrolase has been studied for it has promising practical applications and its specificity and mechanism of action are not yet fully understood. The important factors lie in structural details, some of which were revealed by the model refined to 1.14A res

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11

Hart, Jonathan Ross Rees Douglas C. Barton Jacqueline K. "Synthesis and applications of bulky rhodium(III) intercalators for the recognition of DNA mismatches /." Diss., Pasadena, Calif. : Caltech, 2006. http://resolver.caltech.edu/CaltechETD:etd-06092006-062410.

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12

Saeed, Hiwa. "Biophysical studies on dinuclear DNA metallo-intercalators containing the ruthenium (II) tris(1-pyrazolyl)methane unit." Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/14401/.

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13

Draganov, Alexander B. "Novel Rhein Analogues as Potential Anicancer Agents and a Novel Metal Free Synthesis of 6H-ISOINDOLO[2,1-A]INDOL-6-ONE." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/chemistry_theses/40.

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The first section of this work describes the synthesis of a library of novel rhein analogues that are potential anticancer agents. The design of these compounds takes advantage of the ability for rhein to intercalate into DNA and as the incorporation of an alkylating agent, which serves to covalently modify DNA. In three cell lines, these compounds showed potent cytotoxicity with IC50 in the low to mid-μM range. The second project was focused on the development of an efficient synthesis of 6H-Isoindolo[2,1-α]indol-6-one (24), a core structure for a number of biologically active compounds. The

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14

Sardesai, Niranjan Y. Barton Jacqueline K. Bercaw John E. "Rhodium intercalators as novel peptide delivery systems to the major groove of DNA : towards the design of artificial repressors /." Diss., Pasadena, Calif. : California Institute of Technology, 1995. http://resolver.caltech.edu/CaltechETD:etd-10222007-132632.

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15

Atsumi, Michiko Daniel Chantal Takano Keiko. "Quantum chemical studies from semi-empirical calculations on large aromatic hydrocarbon networks via density functional theory on Ru(II) intercalators in DNA, to highly correlated methods on silver halides /." Strasbourg : Université Louis Pasteur, 2006. http://eprints-scd-ulp.u-strasbg.fr:8080/634/01/MichikoATSUMI_0eeaod02i66.pdf.

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Thèse de doctorat : Chimie quantique : Strasbourg 1 : 2006. Thèse de doctorat : Chimie quantique : Tokyo - Japon : 2006.<br>Thèse soutenue sur un ensemble de travaux. Thèse soutenue en co-tutelle. Titre provenant de l'écran-titre. Bibliogr. p. 116-125.

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16

Atsumi, Michiko. "Quantum chemical studies : From semi-empirical calculations on large aromatic hydrocarbon networks via density functional theory on Ru(II) intercalators in DNA, to highly correlated methods on silver halides." Université Louis Pasteur (Strasbourg) (1971-2008), 2006. https://publication-theses.unistra.fr/public/theses_doctorat/2006/ATSUMI_Michiko_2006.pdf.

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17

Peek, Mary Elizabeth. "Crystal structures of DNA*bis-intercalator complexes." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/27122.

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18

Schäfer, Sven. "Darstellung, DNA-Wechselwirkungen und Zytotoxizität organometallischer Intercalatoren." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=984504567.

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19

Cabeza, de Vaca López Israel. "Mapping biophysics through enhanced Monte Carlo techniques." Doctoral thesis, Universitat Politècnica de Catalunya, 2015. http://hdl.handle.net/10803/334172.

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This thesis is focused on the study of molecular interactions at the atomistic detail and is divided into one introductory chapter and four chapters referencing different problems and methodological approaches. All of them are focused on the development and improvement of computational Monte Carlo algorithms to study, in an efficient manner, the behavior of these systems at a classical molecular mechanics level. The four biophysical problems studied in this thesis are: induced fit docking between protein-ligand and between DNA-ligand to understand the binding mechanism, protein stretching resp

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20

Rangarajan, Subhashree Friedman Simon H. "Design, synthesis and evaluation of new intercalator analogs targeting human telomerase." Diss., UMK access, 2006.

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Thesis (Ph. D.)--School of Pharmacy and Dept. of Chemistry. University of Missouri--Kansas City, 2006.<br>"A dissertation in pharmaceutical science and chemistry." Advisor: Simon H. Friedman. Typescript. Vita. Description based on contents viewed Nov. 9, 2007; title from "catalog record" of the print edition. Includes bibliographical references (leaves 292-317). Online version of the print edition.

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21

Horowitz, Eric D. "Intercalator-mediated assembly of nucleic acids." Diss., Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/33937.

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The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the sponta

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22

Lisgarten, J. N., M. Coll, J. Portugal, Colin W. Wright, and J. Aymami. "The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites." Nature, 2001. http://hdl.handle.net/10454/4045.

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no<br>Cryptolepine, a naturally occurring indoloquinoline alkaloid used as an antimalarial drug in Central and Western Africa, has been found to bind to DNA in a formerly unknown intercalation mode. Evidence from competition dialysis assays demonstrates that cryptolepine is able to bind CG-rich sequences containing nonalternating CC sites. Here we show that cryptolepine interacts with the CC sites of the DNA fragment d(CCTAGG)2 in a base-stacking intercalation mode.

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23

Fields, Earl John. "DNA Photocleavage by Acridine and Phenazine-Based Chromophores." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/chemistry_theses/6.

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Photodynamic therapy (PDT) is a promising approach used in the treatment of cancer, age related macular degeneration, psoriasis, and other diseases. Our research is focused on the discovery of new photonucleases for use in PDT. This study evaluates the photo-induced DNA cleaving abilities of a series of acridine and phenazine-based chromophores. The extended, aromatic ring systems of these compounds are expected to intercalate between adjoining base pairs in the DNA double-helix. Once irradiated, strand breakage, or nicking of plasmid DNA is achieved at micromolar concentrations of compound (p

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24

Komarov, Dmitry Yurievich. "OXIDATION OF NUCLEIC ACIDS: CHEMISTRY OF PURINE QUINONES AND DEVELOPMENT OF NOVEL PHOTOOXIDIZING AGENTS." Bowling Green State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1285956212.

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25

Leaym, Xiaoxuan. "Synthesis and applications of novel resorcin[4]arene cavitands." Diss., Manhattan, Kan. : Kansas State University, 2008. http://hdl.handle.net/2097/745.

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26

Boone, Edna Karen. "Radical cation propagation through bulged and mis-paired DNA : "A purine:purine staggered walk" (Part I). Part II, bulged DNA cleavage via a "Classic intercalator": a surprising role for siglet-excited ethidium bromide in the selective cleavage of a G-bulge containing duplex. Part III, synthesis and photochemical behavior of peptide nucleic acid trimers containning [sic] benzamidonaphthalimide." Diss., Georgia Institute of Technology, 2001. http://hdl.handle.net/1853/30733.

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27

Fechter, Eric James. "Design of Sequence-Specific DNA Intercalators." Thesis, 2005. https://thesis.library.caltech.edu/2456/2/02Intro.pdf.

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Small molecules that bind specific DNA sequences may have powerful therapeutic applications by influencing the mechanisms of abnormal gene expression. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) specifically bind the minor groove of DNA and have been shown to inhibit many protein-DNA complexes. However, some major groove-binding proteins can co-occupy the same DNA sequences as polyamides. Presented here are polyamide-intercalator conjugates that specifically bind target regions of DNA and deliver a non-specific intercalator to an adjacent site. The studies detail int

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28

Shen, Yo-Yu, and 沈祐宇. "The effects of 5-methylcytosine on the DNA acting efficacy of DNA intercalators." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/80040889100906649652.

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碩士<br>國立中興大學<br>生命科學系所<br>103<br>The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. DNA methylation plays an important role in normal organismal development and in cellular differentiation in higher organisms. Intercalation is a important binding mode employed by DNA-binding drugs, The effects of DNA methylation on the DNA-acting activities of DNA intercalator have remained unclear. Herein, using actinomycin D and daunorubicin as a model, we have attempted to

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29

Liu, Tao. "Electrochemical studies of electron transfer in DNA films with covalently tethered intercalators." Thesis, 2007. https://thesis.library.caltech.edu/3300/1/Thesis.pdf.

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The base stack within double-helical DNA provides an efficient pathway for charge transport. This DNA-mediated charge transport chemistry has been shown to be exquisitely sensitive to minor perturbations in DNA structure and base stacking both in solution and on surfaces. As a result, electrochemical studies on DNA-modified electrodes may provide a novel approach to the development of sensitive, but inexpensive DNA sensing devices. Using intercalated, covalently bound daunomycin as a redox probe, we have examined ground state charge transport in DNA films on gold electrodes. DNA-mediated elect

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30

Elmuccio, Michael L. "Progress towards visualizing the controlled assembly of gold nanoparticles on DNA." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-05-2925.

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Our laboratory has used the 1,4,5,8 Naphthalenetetracarboxylic diimine (NDI) unit to develop threading polyintercalators that bind DNA with the NDI units intercalated in between GpG steps and two different peptide linkers, which connect the NDI units, situated in either the major or minor grooves. The first generation bisintercalators, G₃K and [beta]Ala₃K, were shown to bind two different sequences of DNA, where the peptide linkers reside in the major and minor grooves respectively. These binding modules were then combined to generate threading polyintercalators that bound different DNA sequen

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31

Hart, Jonathan Ross. "Synthesis and Applications of Bulky Rhodium(III) Intercalators for the Recognition of DNA Mismatches." Thesis, 2006. https://thesis.library.caltech.edu/2528/1/thesis3.pdf.

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<p>The recognition of DNA base mismatches is of considerable interest for both the diagnosis and treatment of mismatch repair-deficient cancers. Two new mismatch recognition complexes have been synthesized. The first, [Rh(bpy)2(phzi)]3+ (phzi=benzo[a]phenazine-5,6-quinone diimine), recognizes DNA mismatches with high specificity and affinity, 1 x 107 Mm-1, two orders of magnitude stronger than [Rh(bpy)2(chrysi)]3+ (chrysi=chrysene-5,6-quinone diimine), the parent complex that binds single thermodynamically-destabilized base-mismatch sites in duplex DNA. The second, [Rh(bqdi)2(chrysi)]3+, is ab

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32

Sardesai, Niranjan Y. "Rhodium intercalators as novel peptide delivery systems to the major groove of DNA : towards the design of artificial repressors." Thesis, 1995. https://thesis.library.caltech.edu/4213/1/Sardesai_ny_1995.pdf.

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NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Phenanthrenequinone diimine (phi) complexes of rhodium(III) bearing tethered peptides have been designed to serve as metallointercalating anchors to deliver peptide side chain functionalities for DNA recognition in the major groove. Metal-peptide complexes containing 11-15 amino acid residues were prepared using two complementary synthetic strategies: by direct coupling of a pendant carboxylate on the coordinatively saturated rhodium complex, [...] (phen'=5-amidoglutaryl-1, 10-p

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33

Nekvinda, Jan. "Karboranové strukturní bloky v medicinální chemii." Doctoral thesis, 2018. http://www.nusl.cz/ntk/nusl-451065.

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This work deals with carborane and metallacarborane clusters, in terms of their fundamental chemistry and complexation with cyclodextrins, and in the context of emerging pharmacophores applicable in medicinal chemistry. Arguably, the most important part of this work is the preparation of cobalt bis(dicarbollide) sulfamide derivatives. The sulfamido group is attached to the metallacarborane carbon vertex by an alkyl chain that may be modified in its length. This was accomplished by, firstly, the abstraction of the acidic hydrogen, located on the {CH}-vertex from the metallacarborane, by reactio

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34

Holman, Garen Gilman. "Binding studies of a sequence specific threading NDI intercalator." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-08-3863.

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A series of studies from our lab have investigated the threading polyintercalator approach to sequence specific DNA binding using a 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit connected by flexible peptide linkers. Herein is a report of the sequence specificity, as well as a detailed kinetic analysis, of a threading NDI tetraintercalator. DNase I footprinting using two ~500 base pair DNA fragments containing one designed binding site for the tetraintercalator confirmed highly sequence specific binding. Kinetic analyses include 1H NMR, gel mobility-shift assays, and s

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35

Schäfer, Sven [Verfasser]. "Darstellung, DNA-Wechselwirkungen und Zytotoxizität organometallischer Intercalatoren / vorgelegt von Sven Schäfer." 2007. http://d-nb.info/984504567/34.

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36

Ferreira, Cláudia Sofia Rodrigues. "Development of PNA-DNA Field-Effect Transistor-based biosensors." Master's thesis, 2017. http://hdl.handle.net/10362/30801.

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The high demand for devices with higher sensitivity as well cost-efficiency has put tremendous pressure on the biosensors field. The numerous advantages of Field effect transistors (FETs) such as small size, fast response, label free response, and possibility of on-chip integration of biosensor arrays with a future prospect of low-cost mass production, make their development highly desirable. An elec-trochemical deoxyribonucleic acid (DNA) biosensor using a synthesized ferrocene-based DNA interca-lator as a redox marker was investigated. A peptide nucleic acid (PNA) was employed as a capture p

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37

Arambula, Jonathan. "A stacked intercalator approach to selectively target mismatches within CTG and CUG trinucleotide repeats : aromatic stacking of naphthoyl modified cytosines within PNA DNA duplexes /." 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3363126.

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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008.<br>Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3507. Adviser: Steven C. Zimmerman. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

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38

Werz, Emma. "Darstellung und Verwendung von Nucleolipiden zur Lipophilisierung von Nucleinsäuren sowie deren Wechselwirkung und Duplex-Bildung an horizontalen Lipid-Bilayers und Phasengrenzen zur Entwicklung einer neuartigen RNA/DNA-Analytik." Doctoral thesis, 2016. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2016021714241.

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Ziel der vorgestellten Arbeit war die Synthese von Nucleolipiden zur Lipophilisierung von Oligonucleotiden sowie deren Untersuchung im Hinblick auf ihre Wechselwirkung und Duplex-Bildung an horizontalen Lipidmembranen und verschiedenen Phasengrenzen zur Entwicklung eines neuartigen Bio-Chips für die RNA/DNA-Analyse. Mit der Synthese N(3)-prenylierter und 2’,3’-O-ketalisierter Pyrimidinbasen Uridin und Methyluridin wurden Nucleolipid-Bausteine dargestellt, die auch als terminale Kopfgruppen eines Oligonucleotid-Dodecamers den lipophilen Charakter dieser Oligonucleotid-Sequenz erhöhten. Für den

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