Дисертації з теми "DNA crystals"
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Zhang, Diana. "Modifying DNA Crystals for Nanotechnological Applications." Thesis, University of Maryland, College Park, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10745112.
Повний текст джерелаDNA’s programmable nature and ability to self-assemble provides a powerful tool for the construction of complex nanostructures. The initial goal of the field was to use DNA to construct a continuous 3D DNA periodic lattice or crystal. The ultimate aim of the lattice structure would be to act as scaffold for the strategic placement of guest molecules such as macromolecules for structure determination using X-ray. Since that initial vision, the incorporation of guest molecules in DNA nanostructures has expanded to other applications such as cellular imaging, light-harvesting and drug delivery. However, there are several limitations to utilizing DNA crystals for these types of applications. They require relatively high cation concentrations to crystallize and often have low thermal stability. Additionally, crystals generally take on only one shape, or morphology, which can limit their uses in applications.
Our laboratory studies a 13-mer DNA oligonucleotide that self-assembles into crystals upon the addition of magnesium. I demonstrated that by treating these DNA crystals with a chemical crosslinker and depositing polydopamine on the crystal surface, we increased the overall durability of the crystals. Additionally, we modulated the morphology of the crystal without changing the underlying framework by designing crystal habit modifiers based on the known crystal structure and were able to predictably control the morphology of the overall crystal. This enhanced durability has allowed us to begin testing new applications for DNA crystals. I have explored the incorporation of doxorubicin into the stabilized DNA crystals as a potential form of a new drug delivery device. Together, this work significantly advanced several key areas necessary to diversify the capability of DNA crystals for nanotechnological applications.
You, Seungyong. "The dynamics of DNA electrophoresis in lyotropic polymer liquid crystals." Tallahassee, Florida : Florida State University, 2009. http://etd.lib.fsu.edu/theses/available/etd-11132009-092618/.
Повний текст джерелаAdvisor: David H. Van Winkle, Florida State University, College of Arts and Sciences, Dept. of Physics. Title and description from dissertation home page (viewed on May 10, 2010). Document formatted into pages; contains xvi, 137 pages. Includes bibliographical references.
Cristofaro, Silvia. "Simulating the aggregation of DNA oligonucleotides." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/19187/.
Повний текст джерелаZhou, Yiying. "EPR, ENDOR and DFT Studies on X-Irradiated Single Crystals of L-Lysine Monohydrochloride Monohydrate and L-Arginine Monohydrocloride Monohydrate." unrestricted, 2009. http://etd.gsu.edu/theses/available/etd-07152009-203728/.
Повний текст джерелаTitle from file title page. William H. Nelson, committee chair; Vadym Apalkov, Stuart A. Allison, Douglas Gies, Gary Hastings, committee members. Description based on contents viewed Nov. 5, 2009. Includes bibliographical references.
Hoxha, Kreshnik. "DNA bases in crystal engineering." Thesis, University of Hull, 2014. http://hydra.hull.ac.uk/resources/hull:11660.
Повний текст джерелаPeek, Mary Elizabeth. "Crystal structures of DNA*bis-intercalator complexes." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/27122.
Повний текст джерелаXu, Wenjing. "Crystal structure of paired domain--DNA complex." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32666.
Повний текст джерелаTodd, Alan Kenneth. "Single crystal X ray diffraction studies of DNA and DNA drug complexes." Thesis, University of Reading, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270250.
Повний текст джерелаDesogus, Gianluigi. "Structural studies of lysyl-tRNA synthetases and DNA primases." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369258.
Повний текст джерелаKerzic, Melissa Corinne. "A 1.3Å crystal structure analysis of the sequence [d(CGCGAATTCGCG)]₂ containing cesium ions." Thesis, Georgia Institute of Technology, 2001. http://hdl.handle.net/1853/30083.
Повний текст джерелаLockshin, Curtis Alan 1960. "Determinants of crystal packing by nucleic acid polymers : examples of Z-DNA and cytosine-tetraplex crystal structures." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/50374.
Повний текст джерелаGorman, Michael Anthony. "Crystal structure of the human DNA repair enzyme AP endonuclease 1." Thesis, Open University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242493.
Повний текст джерелаTakahara, Patricia Michele. "Crystal structure of the anticancer drug cisplatin bound to duplex DNA." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/41369.
Повний текст джерелаChen, Zhucheng. "Mechanism of homologous recombination : from crystal structures of RecA-single stranded DNA and RecA-double stranded DNA filaments /." Access full-text from WCMC, 2009. http://proquest.umi.com/pqdweb?did=1619205721&sid=8&Fmt=2&clientId=8424&RQT=309&VName=PQD.
Повний текст джерелаZhang, Jinjin. "Structural Studies of Escherichia coli RecE Exonuclease." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1254972783.
Повний текст джерелаMeade, Shawn O. "Development of a DNA multiplexing system utilizing encoded porous silica photonic crystal particles." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3306682.
Повний текст джерелаTitle from first page of PDF file (viewed June 12, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
Cai, Li. "From cytosine-tetraplexes to adenine-clusters : three crystal structures of DNA telomeric sequences." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/43349.
Повний текст джерелаCarmel, Andrew Barry. "Crystal structure of BstDEAD, a novel DEAD-box protein from Bacillus stearothermophilus /." view abstract or download file of text, 2003. http://wwwlib.umi.com/cr/uoregon/fullcit?p3095239.
Повний текст джерелаTypescript. Includes vita and abstract. Includes bibliographical references (leaves 101-114). Also available for download via the World Wide Web; free to University of Oregon users.
Arndt, Joseph W. "Characterization and structural determination of metalloenzymes DNA polymerase beta, carboxypeptidase, and acetyl coenzyme-A decarbonylase/synthase /." Columbus, OH : Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1061312369.
Повний текст джерелаTitle from first page of PDF file. Document formatted into pages; contains xxii, 172 p. : ill., some col. Includes abstract and vita. Advisor: Michael K. Chan, Dept. of Chemistry. Includes bibliographical references (p. 165-172).
Ganai, Rais Ahmad. "Structural and biochemical basis for the high fidelity and processivity of DNA polymerase ε". Doctoral thesis, Umeå universitet, Institutionen för medicinsk kemi och biofysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-97689.
Повний текст джерелаZhao, Shengliang. "Supramolecular Ru II, Pt II Complexes Bridged by 2,3,5,6-tetrakis(2-pyridyl)pyrazine (tppz)." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77321.
Повний текст джерелаPh. D.
Sung, Baeckkyoung. "Condensation of DNA by spermine in the bulk and in the bacteriophage capsid : a cryo-electron microscopy study." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00725394.
Повний текст джерелаRodrigues, Raquel Oliveira. "Development and optimization of a biological protocol for DNA detection of escherichia coli O157:H7 by quartz crystal microbalance with dissipation (QCM-D)." Master's thesis, Instituto Politécnico de Bragança, Escola Superior de Tecnologia e Gestão, 2012. http://hdl.handle.net/10198/8015.
Повний текст джерелаShi, Chongxu [Verfasser], and Hans-Joachim [Akademischer Betreuer] Anders. "Extracellular DNA contributes to cholesterol crystal embolism-induced clot formation, acute kidney injury, and tissue infarction / Chongxu Shi ; Betreuer: Hans-Joachim Anders." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2021. http://d-nb.info/1233600680/34.
Повний текст джерелаSukackaitė, Rasa. "Restrikcijos endonukleazės BpuJI struktūriniai ir funkciniai tyrimai." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2009. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2009~D_20091215_091822-02694.
Повний текст джерелаType II restriction endonucleases recognize specific DNA sequences and cleave DNA at fixed positions within or close to this sequence. BpuJI recognizes the 5’-CCCGT sequence, but in contrast to other enzymes its cleavage site is very variable. This study shows that BpuJI is a dimer in solution and consists of two separate domains. The N-domain binds to the target sequence as a monomer, while the C-domain is responsible for nuclease activity and dimerization. The nuclease activity is repressed in the apo-enzyme and becomes activated upon specific DNA binding by the N-domains. The activated C-domain cleaves DNA near the target site. In addition, it possesses an end-directed nuclease activity and preferentially cuts ~3 nt from the 3’ terminus. This leads to a very complicated pattern of DNA cleavage. Bioinformatics and mutational analysis revealed that the BpuJI C-domain harbours a PD (D/E)XK active site and is structurally related to archaeal Holliday junction resolvases. The crystal structure of the BpuJI N-domain bound to cognate DNA was solved at 1.3 Å resolution. It revealed two winged-helix subdomains, D1 and D2. The recognition of the target sequence is achieved the amino acid residues located on both the HTH motifs and an N-terminal arm. The BpuJI DNA recognition domain is most similar to the nicking endonuclease Nt.BspD6I. The modelling suggests that Nt.BspD6I could share the specificity-determining regions with BpuJI.
Sukackaitė, Rasa. "Structural and functional studies of the restriction endonuclease BpuJI." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2009. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2009~D_20091215_091842-18511.
Повний текст джерелаII tipo restrikcijos endonukleazės atpažįsta specifines DNR sekas ir kerpa DNR šiose sekose arba šalia jų. BpuJI, atpažįstanti 5’-CCCGT seką, skiriasi nuo kitų fermentų tuo, kad jos kirpimo vieta yra labai variabili. Čia parodoma, kad BpuJI yra dimeras, sudarytas iš dviejų monomerų, kurie turi po du atskirus domenus. BpuJI N domenas atpažįsta taikinį kaip monomeras, o C-domenas pasižymi nukleaziniu aktyvumu ir dimerizuojasi. Apo-fermento nukleazinis aktyvumas yra nuslopintas. N-domenams atpažinus taikinį, aktyvuojamas C-domenas, kuris perkerpa DNR šalia taikinio. Be to, aktyvuotas C-domenas yra nespecifinė nukleazė, linkusi nukirpti ~3 nt nuo buko dvigrandės DNR galo. Taigi, BpuJI DNR karpymo pobūdis yra labai sudėtingas. Bioinformatinė analizė ir kryptinga mutagenezė parodė, kad BpuJI C-domenas turi PD-(D/E)XK struktūrinę sanklodą ir yra panašus į archėjų Holidėjaus jungtis karpančias nukleazes. Išsprendus 1,3 Å skiriamosios gebos BpuJI N-domeno/DNR komplekso erdvinė struktūrą, paaiškėjo, kad šį domeną sudaro du „sparnuotą“ spiralė-linkis-spiralė motyvą turintys subdomenai. BpuJI taikinį atpažįsta aminorūgštys, esančios N-rankoje ir abiejų spiralė-linkis-spiralė motyvų atpažinimo spiralėse. BpuJI N-domenas yra labiausiai panašus į Nt.BspD6I nukleazę, kerpančią vieną DNR grandinę. Nt.BspD6I/DNR komplekso struktūros modelis rodo, kad Nt.BspD6I ir BpuJI taikinį atpažįstantys struktūriniai elementai yra panašūs.
Saurabh, Suman. "Nature of Inter-biomolecular interaction and its consequences : protein, DNA and their Complexes." Thesis, Tours, 2017. http://www.theses.fr/2017TOUR4052/document.
Повний текст джерелаThe biological world is full of mysteries. The understanding of many extremely complex biological processes is greatly improved by the combination of approaches borrowed from different disciplines such as chemistry and more recently physics. Physics uses experimental tools such as optical tweezers and optical and electron microscopes to explore the microscopic mechanisms taking place in the cell. Knowledge of the nature of the interactions between biomolecules and the possibility of translating these interactions into equations allowed physics to construct models that are simple, but contain the ingredients sufficient to describe a specific mechanism. The numerical simulation of such models improves our understanding of the relationship between relevant molecular-scale mechanisms and experimental observations of biological phenomena. The structural organization of biomolecular complexes is a process that involves various scales of length and time
Jayatilaka, Nayana Kumudini. "X-Irradiation of DNA Components in the Solid State: Experimental and Computational Studies of Stabilized Radicals in Guanine Derivatives." unrestricted, 2006. http://etd.gsu.edu/theses/available/etd-04072006-112029/.
Повний текст джерелаTitle from title screen. William H. Nelson, committee chair; Thomas L. Netzel , A.G. Unil Perera, Brian D. Thoms, Gary Hastings, committee members. Electronic text (243 p. : ill. (some col.)) : digital, PDF file. Description based on contents viewed Aug. 16, 2007. Includes bibliographical references.
Fernández, Pérez Francisco. "Cloning, expression, purification and crystallisation of the human ets-1/usf1/dna complex & crystal structure of thermotoga maritima histidinol-phosphate aminotransferase (ec 2.6.1.9)." Doctoral thesis, Universitat Autònoma de Barcelona, 2002. http://hdl.handle.net/10803/3508.
Повний текст джерелаEn este trabajo, emprendimos la elucidación estructural del mecanismo de autoinhibición de Ets-1. Comenzamos con la clonación, expresión y purificación de Ets-1 y las proteínas compañeras USF1 y MafB. A medida que íbamos enfrentando nuevos desafíos, diseñamos métodos y aproximaciones que facilitaran la producción eficaz de proteínas de unión a DNA para biología estructural. Uno de los conceptos fundamentales que ha reaparecido en el presente estudio es la necesidad de proporcionar a cada proteína un entorno lo mas parecido posible al que disfrutan en su contexto biológico. Por ejemplo, la estabilización de Ets-1 no fue posible hasta que se añadió el complejo USF1/DNA , que semeja las condiciones fisiológicas en las que USF1, unido a DNA, recluta Ets-1 sobre su sitio de unión.
Hemos producido con éxito un conjunto de complejos ternarios Ets-1/USF1/DNA para los cuales hemos buscado condiciones de cristalización. Hemos obtenido cristales, que hemos probado contienen Ets-1, USF1 y DNA. El refinamiento (optimización) de esas condiciones de cristalización preliminares debería conducir en definitiva a la obtención de cristales de suficiente calidad para difracción. Estos cristales ofrecen la posibilidad de profundizar nuestro conocimiento en un mecanismo de regulación que tiene una importancia capital en enfermedades como el síndrome de inmunodeficiencia adquirida o muchos tipos de leucemias.
Ets-1 and USF1 are transcription factors involved in many key processes in development and differentiation. Defects in their regulation have been associated with pathological disorders and viral infections. Furthermore, Ets-1 is a paradigm of a regulation mechanism in transcriptional control whereupon its DNA-binding activity and, thereby, its transactivation properties, are constitutively silenced (autoinhibition). Derepression of Ets-1 can be achieved by protein-protein interactions, which unmask Ets-1's DNA binding domain and lead to the formation of a high affinity ternary complex onto DNA between Ets-1, the partner protein and the combined site for both transcription factors.
In this work, we undertook the structural elucidation of the autoinhibitory mechanism of Ets-1. We started off by cloning, expressing and purifying Ets-1 and the partner proteins USF1 and MafB. As new challenges were met in this part of the project, we devised methods and approaches directed towards the efficient production of DNA-binding proteins for structural biology. A key concept turn out to be the necessity to provide proteins with an environment closest to their biological contexts in order to stabilise them. For example, Ets-1 stabilisation could not be attained until a pre-formed USF1/DNA complex was added to it, resembling the in vivo situation, where USF1, bound to their composite binding site, recruits Ets-1 onto DNA.
We successfully produced a number of Ets-1/USF1/DNA ternary complexes and have partially screened the vast space of crystallisation conditions. Crystals have been obtained, and they have been proved to contain both protein partners plus DNA. Refinement of these preliminary crystallisation conditions will ultimately render crystals of sufficient quality for diffraction experiments. We are excited about the possibilities open up by these crystal for deeper insight into a not well understood regulatory mechanism, but which underlies such important diseases as the human immunodeficiency syndrome and many different types of leukaemia.
Verhaven, Alexandra. "Fluorescent detection of DNA single nucleotide polymorphism by electric field assisted hybridization/melting of surface-immobilized oligonucleotides." Doctoral thesis, Universite Libre de Bruxelles, 2020. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/314944.
Повний текст джерелаDeoxyribonucleic acid (DNA) self-assembled monolayers (SAMs) immobilized on gold electrodes are the basis of many electrochemical biosensors. Control of the interfacial behavior of DNA by means of an electric field is of interest for sensing applications such as the detection of single nucleotide polymorphisms (SNPs). Moreover, the in situ characterization of immobilized DNA monolayers at a molecular level is important for the fabrication of robust, reliable and sensitive sensors.The thesis aims at studying the discrimination between DNA strands containing SNPs on the basis of electric-field assisted hybridization/denaturation of DNA. In situ electrochemical fluorescence microscopy is used as a detection methodology and characterization tool for DNA interfaces. For this purpose, fluorescently labeled DNA sequences are immobilized at gold electrodes as thiol SAMs.First, the SAMs under investigation were composed of perfect match or SNP-containing target sequences. The relationship between the applied potential and the denaturation of DNA duplexes was investigated. Electrochemical melting was observed at -0.25 V vs. Ag
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Swan, Michael Kenneth. "The pursuit of crystal structures in four systems : the complex of ribosomal protein S4 withmRNA, π initiator protein in complex with DNA and PGI from two archaea." Thesis, University of Sussex, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399820.
Повний текст джерелаXu, Guozhou. "Crystal structures of the Fanconi anemia proteins : structure of the interstrand cross-linking repair protein Fanconi anemia protein I (FANCI); structure of the human FANCF C-terminal domain; reconstitution and crystallilzation of the sub-complexes in the Fanconi anemia core complex /." Access full-text from WCMC, 2009. http://proquest.umi.com/pqdweb?did=1692100351&sid=1&Fmt=2&clientId=8424&RQT=309&VName=PQD.
Повний текст джерелаTanh, Jeazet Harold Brice. "Metallo-supramolecular Architectures based on Multifunctional N-Donor Ligands." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-39665.
Повний текст джерелаAlexopoulos, Eftichia. "Crystallographic and modeling studies of intermolecular interactions of biological interest." Doctoral thesis, [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972659137.
Повний текст джерелаValle, Orero Jessica. "Dynamics and thermal behaviour of films of oriented DNA fibres investigated using neutron scattering and calorimetry techniques." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2012. http://tel.archives-ouvertes.fr/tel-00734670.
Повний текст джерелаSpecht, Marion. "Comportement mécanique de films minces de chalcogénures sous irradiation de photons." Thesis, Rennes 1, 2017. http://www.theses.fr/2017REN1S087/document.
Повний текст джерелаThis work aims to understand photoinduced phenomena in chalcogenide glasses. These phenomena are known for years but yet not fully understood. Studying thin films, deposited by co-sputtering here, adds an other difficulty : the light-matter interaction takes place in a small amount of matter and it is inevitable to deal with the substrate. To study these photoinduced effects, it was necessary to adapt some already existing methods such as pump-probe spectroscopy which measures ultrafast electronic dynamics (less than a nanosecond), piezoelectric quartz sensors which gives density and mechanical modulus of the materials deposited on. Preliminary tests were run to investigate optical transmission resonance and are promising. A DMA machine (Dynamical Mechanical Analysis) was especially designed in the laboratory to study the behaviour of fibers and films. All these experimental setups allow to study photoinduced phenomena at various timescale and to better understand them
Leite, Wellington Claiton. "Caracterização Funcional e Determinação da Estrutura Tridimensional por Cristalografia de Raios X da Proteína RecA de Herbaspirillum seropedicae." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2016. http://tede2.uepg.br/jspui/handle/prefix/863.
Повний текст джерелаCoordenação de Aperfeiçoamento de Pessoal de Nível Superior
The bacterial RecA protein plays a role in the complex system of DNA damage repair. In the presence of ATP, RecA proteins polymerize onto single-strand DNA (ssDNA) as righthanded helical nucleoprotein laments, and catalyze strand exchange reaction between the ssDNA and homologous double-strand DNA (dsDNA) molecules. These activities are supported or stimulated by accessory proteins, as the single-stranded binding protein (SSB).Here, we report a functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA).We report the crystal structure of HsRecA-ADP/ATP complex to 1.7 Å of atomic resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, similarly to homologous RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. The bacterial polymerization motif contains the sequence SV/IMR/KLG which interacts with the core ATPase domain residues DNLLLV/CS. In the inactive RecA, it is a loop - strand interaction, respectively, while in the active RecA it becomes a dyad strand. In both RecA forms, the polymerization motif seems to stabilize the subunitsubunit interface by hydrophobic interactions. The methionine of this motif may play an important role in the stability and formation of a right-handed helical nucleoprotein lament. The ATPase activity and the structure of the nucleoprotein lament of HsRecA and Escherichia coli RecA (EcRecA) were analyzed in the presence and absence of SSB. When SSB was added after RecA+ssDNA, HsRecA and EcRecA showed similar ATPase activity and nucleolament structure. However, when SSB was either not included or it was added before RecA+ssDNA, the HsRecA showed higher ATPase activity and formed longer nucleoprotein laments than EcRecA. Thus, HsRecA protein is more ecient at displacing SSB from ssDNA than EcRecA protein. HsRecA promoted DNA exchange more eficiently: a greater yield of nicked circular products were obtained in a shorter time. Reconstruction of electrostatic potential from the hexameric structure of HsRecAADP/ ATP revealed a high positive charge along the inner side, which is consistent with the fact that ssDNA binds inside the filament. It may explain the enhance capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote eficiently the DNA strand exchange reaction. Keywords: RecA, Crystallography, RecA nucleoprotein filament, ATPase activity, DNA strand exchange, crystal structure, structural analysis.
A proteína RecA bacteriana desempenha um importante papel no complexo sistema de reparo de danos ao DNA. Na presença de ATP, a proteína RecA se auto-polimeriza sobre o DNA simples ta (ssDNA) (do inglês single-strand DNA (ssDNA)) como um lamento de nucleoproteína helicoidal, cataliza a reação de troca de fitas entre as moléculas ssDNA e a ta de DNA dupla fita homóloga (dsDNA) (do inglês double-strand DNA (dsDNA)). Estas atividades são suportadas ou estimuladas por proteínas acessórias, como a proteína ligadora de ssDNA SSB (do inglês single-stranded binding protein (SSB)). Neste trabalho é apresentado a caracterização estrutural e funcional da proteína RecA da bactéria Herbaspirillum seropedicae. A estrutura tridimensional do complexo HsRecA-ADP/ATP foi resolvida numa resolução 1,7 Å. A estrutura monomérica da proteína HsRecA consiste em um pequeno domínio N-terminal, um domínio central contendo um sitío ATPásico e e um grande domínio C-terminal, similar com proteínas RecAs homólogas. Análises estruturais comparativas mostraram que o motivo de polimerização da região N-terminal de proteí- nas da familia RecA que incluem archaea e eucariotos, também está presente na proteína RecA bacteriana. O motivo de polimerização da região N-terminal de bactérias contêm a sequência de resíduos (Serina, Valina ou Isoleucina, Metionina, Arginina ou Lisina, Leucina, Glicina) que interage com a sequência de resíduos do core ATPásico (Aspartato, Asparagina, Leucina, Leucina, Leucina, Valina, Cisteína, Serina). Na proteína RecA inativa esta interação é do tipo loop - strand, respectivamente, enquanto na proteína RecA ativa essa interação se torna uma dupla -strand. Em ambas formas da RecA, o motivo de polimerização parece estabilizar a interface subunidade-subunidade por interações hidrofóbicas. No motivo N-terminal a presença de uma Metionina altamente conservada talvez desempenha um importante papel na estabilidade e formação do lamento de nucleoproteína. A atividade ATPásica e a estrutura do lamento de nucleoproteína da proteína HsRecA e da Escherichia coli RecA (EcRecA) foram analisadas na presença e ausência da proteína SSB. Quando a SSB foi adicionada após RecA+ssDNA, as proteínas HsRecA e EcRecA mostraram similar atividade ATPásica e estrutura de nucleo lamento. Entretanto, quando a SSB não estava incluída ou quando adicionada anteriormente a adição RecA+ssDNA, a proteína HsRecA mostrou maior atividade ATPásica e formou maiores lamentos de nucleoproteína que a proteína EcRecA. Ainda, a proteína HsRecA é mais eficiente em deslocar a SSB do ssDNA que a proteína EcRecA. A proteína HsRecA também promove a reação de troca de fitas mais eficientemente: uma maior quantidade de produtos duplex substrato convertido em duplex circular foram obtidos em um curto intervalo de tempo. A reconstrução do potencial eletrostático da estrutura hexamérica da proteína HsRecA revelou uma maior densidade de cargas positivas no seu interior, que é consistente com o fato que o ssDNA ligar-se internamente ao filamento hexamérico. Isto talvez possa explicar capacidade melhorada da proteína HsRecA ligar-se ao ssDNA, formando um continuo filamento de nucleoproteína, deslocando a SSB e ainda promovendo de forma eficiente a reação de trocas de fitas.
Reinhardt, Nora Maria Elisabeth. "Modification chimique de surface de nanoparticules de silice pour le marquage d'ADN dans des lipoplexes." Thesis, Bordeaux 1, 2013. http://www.theses.fr/2013BOR14820/document.
Повний текст джерелаSilica nanoparticles are ideal platforms for the conception of bioimaging tools serving for the elucidation of the mechanisms of gene transfection via lipoplex structures. The purpose of the present study is the development of a chemical surface modification for the generation of quaternary ammonium groups on silica nanoparticles permitting the obtainment of highly positively charged silica colloids which strongly attract DNA by electrostatic interactions. Two modification strategies to generate quaternary ammonium groups on silica are presented a) a direct silanization using quaternary ammonium groups containing silane derivatives and b) a modification of silica nanoparticles via a first modification with an amine group containing silane derivative and a subsequent quaternization of the amine groups via an alkylation with iodomethane. Different physicochemical methods were employed (cosedimentation assays, quartz crystal microbalance with dissipation monitoring measurements, TEM and Cryo-TEM imaging) to analyze interactions between quaternized surfaces, DNA and lipids. A preliminary study was carried out which shows the capacity of the synthesized nanoparticles to label DNA in lipoplexes
Mooers, Blaine H. M. "Controlling DNA packing in crystals." Thesis, 1997. http://hdl.handle.net/1957/34392.
Повний текст джерела(6581093), Zhe Li. "ENGINEERED 3D DNA CRYSTALS: CHARACTERIZATION, STABILIZATION AND APPLICATIONS." Thesis, 2019.
Знайти повний текст джерелаIn this thesis, I started by enhancing the stability of engineered 3D DNA crystals. I developed a highly efficient post-assembly modification approach to stabilize DNA crystals. Enzymatic ligation was performed inside the crystal lattice, which was designed to covalently link the sticky ends at the crystal contacts. After ligation, the crystal became a covalently bonded 3D network of DNA motifs. I investigated the stability of ligated DNA crystals under a wide range of solution conditions. Experimental data revealed that ligated DNA crystals had significantly increased stability. With these highly stabilized DNA crystals, we then demonstrated their applications in biocatalysis and protein encapsulation as examples.
I also established electron microscope imaging characterization methods for engineered 3D DNA crystals. For crystals from large-size DNA motifs, they are difficult to study by X-ray crystallography because of their limited diffraction resolutions to no better than 10 Å. Therefore, a direct imaging method by TEM was set up. DNA crystals were either crushed or controlled to grow into microcrystals for TEM imaging. To validate the imaging results, we compared the TEM images with predicted models of the crystal lattice. With the advance in crystal characterization, DNA crystals of varying pore size between 5~20 nm were designed, assembled, and validated by TEM imaging.
The post-assembly ligation was further developed to prepare a series of new materials derived from engineered 3D DNA crystals, which were inaccessible otherwise. With the directional and spatial control of ligation in DNA crystal, I prepared new DNA-based materials including DNA microtubes, complex-architecture crystals, and an unprecedented reversibly expandable, self-healing DNA crystal. The integration of weak and strong interactions in crystals enabled a lot of new opportunities for DNA crystal engineering.
In the final chapter, I investigated the effect of 5’-phosphorylation on DNA crystallization kinetics. I found that phosphorylation significantly enhanced the crystallization kinetics, possibly by strengthening the sticky-ended cohesion. Therefore, DNA crystals can be obtained at much lower ionic strength after phosphorylation. I also applied the result to controling the morphology of DNA crystals by tuning the crystallization kinetics along different crystallographic axes. Together with previously methods to slow down DNA crystallization, the ability to tune DNA crystallization kinetics in both ways is essential for DNA crystal engineering.
Schulman, Rebecca. "The Self-Replication and Evolution of DNA Crystals." Thesis, 2007. https://thesis.library.caltech.edu/1554/1/thesis.pdf.
Повний текст джерелаTang, Hao 1985. "Applications of self-assembly : liquid crystalline semiconductors and DNA-conjugated microparticles." 2012. http://hdl.handle.net/2152/22061.
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Evans, Constantine Glen. "Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly." Thesis, 2014. https://thesis.library.caltech.edu/8232/8/cge-thesis.pdf.
Повний текст джерелаAlgorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.
In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.
As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.
Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.
Liao, Jum-min, and 廖俊閔. "Investigations of the FRET properties in DNA hybridization systems and the relaxation motions of liquid crystals." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/42319643260662192119.
Повний текст джерела國立中山大學
化學系研究所
101
The molecular dynamic (MD) simulation is useful to investigate the physical properties and structures in microscopic systems. In this thesis, we applied molecular dynamic simulations in two different areas: the DNA hybridization systems and the liquid crystal systems. In part I, MD and quantum mechanics were used to investigate fluorescence resonance energy transfer between coumarin and ethidium in two Mergny’s DNA hybridization systems. The FRET efficiencies were compared with Mergny’s experiments from 273 K to 313 K, and showed good agreement. The simulated orientation factor and isotropically averaged orientation factor were compared, and the results demonstrated that the assumption of isotropic orientations is invalid when FRET probes are close to each other. The first order kinetic assumptions were also used to calculate the transfer efficiencies, and the results show this D-A FRET process approximates the first order kinetic reactions. In part II, MD simulations were used to investigate relaxation motions of nematic liquid crystals 4-cyano-4''-pentylbiphenyl (5CB) and 4''-cyanophenyl 4-heptylbenzoate (7CPB) molecules sandwiched between poly-3-APM polyimide (PI) films. A dynamic equation describing the motions was derived by analyzing the simulation results for small systems. The results calculated by the derived parameters fit the experimental observations with commonly used cell gaps. The derived equation also satisfies the theoretical conclusion from the Erickson-Leslie equation that the relaxation time is proportional to the square of the thickness of the LC cell.
Reddy, U. Venkateswara. "Study of Enantiomeric Discrimination and Enzyme Kinetics using NMR Spectroscopy." Thesis, 2013. http://etd.iisc.ernet.in/2005/3364.
Повний текст джерелаTseng, Ching-Ching, and 曾菁菁. "Develop a quartz crystal microbalance (QCM) DNA-sensor." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/63512512255502582858.
Повний текст джерела大同大學
生物工程研究所
91
Quartz crystal microbalance (QCM) is widely used in the biosensor field due to its high sensitivity, selectivity, and stability. The resonance frequency of QCM is associated with a mass change by some biological specific reaction such as hybridization between the complementary oligonucleotides or immunoreactions between antibody and antigen. In this study, a specific DNA fragment of Vibrio parahaemolyticus was selected as target DNA. A pair of 20-mer primer was designed for amplify the specific DNA fragment by PCR, and a 20- mer oligonucleotide probe was also designed. We combine some surface modify methods to immobilize the oligonucleotide probe on the gold electrode surface of QCM that could use to detect the PCR product of Vibrio parahaemolyticus by the frequency change on account of the hybridization between the complementary oligonucleotide probe and PCR product. Our experiment developed the standard curve of oligonucleotide target concentration and found the optimum situation of oligonucleotide probe immobilization. The least detecting quantity was 86 ng/ml by this method, which was superior than electrophoresis. Concentration of PCR products between 86-468 ng/ml showed a linear relationship. Meanwhile the fabricated DNA-QCM could differentiate Vibrio parahaemolyticus from the other treated bacteria. Storing in glycine/PBS at 4℃, the QCM chips could still remain 89% efficacy, after 5 days.
Meng, Qingchao master of arts in cell and molecular biology. "Approaching the crystal structure of the polymerase γ catalytic complex". Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-08-4330.
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Tsai, Kuang-Lei, and 蔡光磊. "Crystal structure of the DNA-binding domain of Interleukin enhancer binding factor bound to DNA." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/03882710589319077483.
Повний текст джерела國立清華大學
生物資訊與結構生物研究所
93
Interleukin enhancer binding factor (ILF) is a transcription factor that binds to purine-rich regulatory motifs in both the human T-cell leukemia virus long terminal region (HILV-1 LTR) and the interleukin-2 (IL-2) promoter. The DNA-binding domain of ILF (ILF-DBD) belongs to a member of winged helix/forkhead family. Here we report a 2.4 Å crystal structure of two copies of the DBD of ILF bound to 16-bp DNA. Extensive contacts are formed between the recognition helix (H3) and the major groove of DNA through direct and water-mediated hydrogen bonds. ILF-DBD is a new member of the winged helix/forkhead proteins because the presence of a C-terminal α-helix (H4) in place of a typical wing 2 changes the orientation of the C-terminal basic residues (RKRRPR) of H4 to recognize DNA. The structure also shows that wing 1 interacts with minor groove of DNA, and the residues (Lys45) from the H2-H3 loop region make interactions with DNA. Comparison of the ILF-DBD/DNA complex with HNF-3��/DNA complex revealed some differences in DNA recognition at both the “TAAACA” core and the flanking regions of the DNA site. Taken together, these results offer new insights into the modulation of DNA binding specificity within a conserved DNA-binding domain, and provide how highly homologous winged helix/forkhead proteins exhibit differential DNA-binding properties.
Xu, Fei. "Insights into mechanisms of nucleosome remodeling from analysis of crystal structures." 2007. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16798.
Повний текст джерелаLu, Guan-Rui, and 盧冠睿. "Periodic Zigzag Structure Characterizations of High Concentration DNA Liquid Crystal." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/r83z3c.
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