Dissertations / Theses on the topic 'DNA crystals'
To see the other types of publications on this topic, follow the link: DNA crystals.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'DNA crystals.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Zhang, Diana. "Modifying DNA Crystals for Nanotechnological Applications." Thesis, University of Maryland, College Park, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10745112.
Full textAbstract:
DNA’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.
2
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/.
Full textAbstract:
Thesis (Ph. D.)--Florida State University, 2009.Advisor: 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.
3
Cristofaro, Silvia. "Simulating the aggregation of DNA oligonucleotides." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/19187/.
Full textAbstract:
In this work we have studied, by means of Molecular Dynamics simulations, the process of denaturation and self-assembly of short oligonucleotides. Supramolecular ordering of DNA short strands is a promising field which is constantly enriched with new findings. Examples are provided by micellar and fibrils formations and due to the selectivity of DNA bindings, "intelligent" devices have been developed to perform simple logic operations. It is worth to notice that computer simulations of these DNA nanosystems would complement experiments with detailed insight into processes involved in self-assembly. In order to obtain an accurate description of the interactions involved in the complex structure of DNA we used oxDNA, a coarse-grained model developed by Ouldridge. We simulated the melting transition of 4, 6, and 8 base pair sequences. Sequence and length dependence were analyzed, specifically we compared thermodynamic parameters DeltaH, DeltaS and the melting temperature with literature results. Moreover, we have attempted to reproduce liquid crystal ordering of the ultrashort sequence GCCG at relatively high saline concentration, until now only experimentally observed in Bellini's works. We found that our simple model successfully reproduces the experimental phase sequence (isotropic, nematic, columnar) at T= 5 °C as a function of oligonucleotide concentration, and we fully characterized the microscopic structure of the three phases.
4
Zhou, 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/.
Full textAbstract:
Thesis (Ph. D.)--Georgia State University, 2009.Title 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.
5
Hoxha, Kreshnik. "DNA bases in crystal engineering." Thesis, University of Hull, 2014. http://hydra.hull.ac.uk/resources/hull:11660.
Full textAbstract:
The work described in this thesis focuses on understanding the solid state interactions of organic molecules such as DNA nucleobases using established principles from crystal engineering and the synthon theory. Studying the intermolecular interactions is an indispensable tool to the crystal engineer when it comes to identifying functional groups which generate synthons that govern molecular recognition and self-assembly. Chapter 3 focuses on the growth and design of single crystal materials of DNA bases and their carboxylic acid derivatives with various other molecules. The aim of the chapter was to probe the hydrogen bonding displayed by these systems. The challenges associated with dissolving the nucleobases in organic and aqueous solvents prompted alternative synthetic route to mitigate solubility challenges. Altering the pH of the system was found useful in aiding dissolution. Such synthetic approach has led to the preparation of novel nucleobase salts of bis-guaninium sulphate in three different hydrate forms. The material obtained was a channel hydrate and it was possible to remove water partially and fully while retaining crystallinity. No structural collapse was observed upon full dehydration and the material obtained contained an empty channel hydrate. Co-crystallisation of cytosine with 1,10-phenanthroline is discussed in depth and the results are compared to crystal structure prediction results to rationalise co-crystal formation from an energetic perspective. Calculations on the energy landscape revealed that in the case of cytosine and 1,10-phenanthroline there is a favourable energetic driving force for co-crystallisation. This, however, does not apply to the co-crystallisation of the other DNA bases with 1,10-phenanthroline as these systems did not produce co-crystals and remained as mixtures of precursors. The chapter also describes structural features of thymine acetic acid, melaminium nitrilotriacetate trihydrate and co-crystals of caffeine with 2-nitroterepthalic acid. These structures are closely examined for their hydrogen bonding motifs. Chapter 4 covers a wide range of coordination compounds which relate to hydrogen-bonded networks of DNA nucleobases and their carboxylic acid derivatives. These complex architectures contain both coordination bonds as well as intermolecular interactions in the form of hydrogen bonding and stacking interactions. Metal-dipicolinate complexes treated with adenine and cytosine afforded hydrogen-bonded networks where protonated DNA bases interacted with the ligand via hydrogen bonding. The chapter discusses the role of water molecules in acting as spacers and stabilising crystal structure, especially in cases where there is an imbalance of hydrogen bond donors and acceptors. Orotic acid was heavily used owing to its chelating nature. This part of Chapter 4 focuses on novel crystal structures where orotic acid utilises its hydrogen bonding capability. An extensive discussion is provided on how the level of hydration impacts crystal packing and alters synthon formation. In addition, the chapter also focuses on the structural changes resulting from changing the position of the functional group in the ligands.
6
Peek, Mary Elizabeth. "Crystal structures of DNA*bis-intercalator complexes." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/27122.
Full text
7
Xu, Wenjing. "Crystal structure of paired domain--DNA complex." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32666.
Full text
8
Todd, 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.
Full text
9
Desogus, 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.
Full text
10
Kerzic, 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.
Full text
11
Lockshin, 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.
Full text
12
Gorman, 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.
Full text
13
Takahara, 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.
Full text
14
Chen, 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.
Full text
15
Zhang, Jinjin. "Structural Studies of Escherichia coli RecE Exonuclease." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1254972783.
Full text
16
Meade, 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.
Full textAbstract:
Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed June 12, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
17
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.
Full text
18
Carmel, 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.
Full textAbstract:
Thesis (Ph. D.)--University of Oregon, 2003.Typescript. 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.
19
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.
Full textAbstract:
Thesis (Ph. D.)--Ohio State University, 2003.Title 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).
20
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.
Full textAbstract:
DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε. To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide. B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites. In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.
21
Zhao, 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.
Full textAbstract:
The main theme of this dissertation is the study of two racemic compounds: a bimetallic complex, [(tpy)Ru(tppz)PtCl](PF₆)₃, and a trimetallic complex, [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄, in solution and in the solid state, where tpy is 2,2':6',2''-terpyridine and tppz is 2,3,5,6-tetrakis(2-pyridyl)pyrazine. These two supramolecular assemblies display remarkably different stereochemistry, electrochemistry and photochemistry. The chapters in this document deal with a multidisciplinary project that is fundamental to the design and synthesis of similar entities with potential applications as antitumor agents.
Chapter 1 gives an overview on the metal polyazine supramolecules. More specifically, the section is focused on the tridentate ruthenium and platinum metallic supramolecular assemblies with emphasis on their functionality and the methods used to study such systems.
Chapter 2 describes the design and syntheses of the title complexes and their analogs using a building block strategy. The details of the experimental methods are included in this section.
Chapter 3 presents the identification of the title complexes in solution and in the solid state by means of single crystal crystallography, mass spectrometry including FAB-MS and ESI-MS, and multiple NMR techniques including 1D ¹H-NMR, ¹⁹⁵Pt-NMR and 2D COSY, NOESY and ¹⁹⁵Pt-¹H HMQC, as well as dynamic ¹H-NMR at variable temperatures. The bi- and tri-metallic complexes are crystallized in the chiral space group of C2/c and P21/c as racemic compounds. The interconversion of the three steroisomers, M-M, P-P and M-P of trimetallic complexes are detected in the NMR timescale. The assignments of the atypical NMR resonance of the bi- and tri-metallic complexes are supported with the help of multidimensional NMR techniques and NMR spectroscopy of known systems. The process of assigning the NMR spectra is accomplished step by step with complexities presented by ring current effects. The 1D-fiber, 2D-plate and 3D-flowerlike topography of the trimetallic complex of [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄ was illustrated by SEM.
Chapter 4 demonstrates the electrochemical and photochemical differences between the title complexes and a comparison to known systems. Electrochemically, the RuII,PtII bimetallic and trimetallic complexes display RuII/III oxidations at 1.63 and 1.83 V and ligand-based reduction at -0.16 and -0.03 V versus Ag/AgCl, respectively. Spectroscopically, the Ru(dπ)⟶ tppz(π*) MLCT transitions are red-shifted relative to the monometallic synthons ([(tpy)Ru(tppz)](PF₆)₂, λmaxabs = 472 nm and [Ru(tppz)₂](PF₆)₂, λmaxabs = 478 nm) occurring in the visible region, centered at 530 and 538 nm in CH₃CN for [(tpy)Ru(tppz)PtCl](PF₆)₃ and [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄, respectively, consistent with the bridging coordination of the tppz ligand. [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄ displays an intense emission (Φem = 5.4×10₄) from the Ru(dπ)⟶ tppz(π*) ³MLCT state at RT with λmaxem = 754 nm and lifetime ofτ„ = 80 ns in CH₃CN solution. The trimetallic complex, [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄, exhibits a strong emission property in the solid state with λmaxem = 764 nm, which was also studied by confocal laser induced emission scanning microscopy. By contrast, a barely detectable emission was observed for the bimetallic complex, [(tpy)Ru(tppz)PtCl](PF₆)₃. The redox and luminescence differences between bi- and tri-metallic complexes is the consequence of the nature of these supramolecular assemblies. All together the data suggest strong PtPt interactions in solution providing for assembly of these molecules into dimers or larger assemblies.
Chapter 5 reports the applications of these complexes as bioactive species interacting with DNA. The prelimary data show the title complexes bind to DNA producing larger changes in DNA migration during gel electrophoreses than does the well-established anticancer drug, cisplatin. Preliminary study indicates trimetallic complex [ClPt(tppz)Ru(tppz)PtCl](PF₆)₄ can photochemically condenses DNA. This data could provide a form for development of a new class of photodynamic therapy agents in cancer treatment.
Chapter 6 concludes with summaries of current research and perspective for further work.Ph. D.
22
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.
Full textAbstract:
By using cryo-electron microscopy, we analyzed the morphology and structure of long double-stranded DNA chains condensed upon addition of varying amounts of the tetravalent polycation spermine (polyamine). Experiments have been performed i) with chains diluted in the bulk and ii) with individual chains confined in a virus capsid.Bulk experiments have been done with lambda DNA (48.5 kbp) at low concentration (0.03 mM Ph) and in low salt conditions (10 mM Tris HCl, 1 mM EDTA, pH 7.6). We explored a wide range of spermine concentration, from the onset of precipitation (0.05 mM sp) up to above the resolubilization limit (400 mM sp). Sixteen min after mixing spermine and DNA, samples have been trapped in thin films and vitrified in liquid ethane to keep ionic conditions unchanged, and imaged at low temperature with low doses of electrons (cryoTEM). DNA chains mostly form large aggregates of toroids in which DNA chains are hexagonally packed with interhelical spacings of 2.93, 2.88, and 2.95 nm at 0.05, 1 and 100 mM spermine, respectively, in agreement with previous X-ray data. At higher spermine concentration (200 mM), hexagonal toroids are replaced by cholesteric bundles with a larger interhelical spacing (3.32 nm). We conclude that the shape and the structure of the liquid crystalline sp-DNA condensates are linked to the DNA interhelix spacing and determined by the ionic conditions i.e. by the cohesive energy between DNA strands. Outside of the precipitation domain (400 mM spermine), DNA chains form a soluble network of thin fibers (4-6 nm in diameter) that let us reconsider the state of these DNA chains in excess of spermine. We also designed experiments to visualize condensates formed 6-60 sec after mixing Lambda DNA with 0.05 mM spermine, under identical buffer conditions. Among multiple original shapes (not found after 16 min), the presence of stretched and helical elongated fibers seen only 9sec after addition of spermine let us propose that DNA chains are immediately stretched upon addition of spermine, relax into helical structures and finally form small toroids (containing in some cases less than one Lambda chain) that further grow and aggregate. We also analyzed the dimensions and structural details of the complete collection of toroids, and reveal the existence of geometric constraints that remain to be clarified. Since it was only exceptionally possible to prevent the aggregation of DNA in dilute solution, we used another approach to observe the collapse of single DNA chains. We handled a population of T5 viruses containing a fraction of their initial genome (12-54 kbp long). The Na-DNA chain, initially confined in the small volume of the capsid (80nm in diameter) is collapsed by the addition of spermine. Compared to the first set of experiments, we explored a higher DNA concentration range (0.45 mM Phosphates in the whole sample) and the spermine concentration was varied from 0.05 to 0.5 mM (which corresponds to much lower +/- charge ratios). Experiments are thus performed close to the precipitation line, in the coexistence region, between the region where all chains are in a coil conformation, and the region where all chains are collapsed into toroids. We describe the existence of intermediate states between the coil and the toroidal globule that were not reported yet. In these "hairy toroids", part of the DNA chain is condensed in the toroid and the other part stays uncondensed outside of it. The interhelical spacing was also measured; it is larger in these partly-condensed toroids than in the fully organized toroids formed at higher spermine concentration.These two series of experiments show the interest of cryoEM to analyze the structural polymorphism and local structure of spermine-DNA aggregates. We also demonstrated how the confinement interferes with DNA condensation and the interest to investigate such effects that are important in the biological context.
23
Rodrigues, 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.
Full textAbstract:
Escherichia coli O157:H7 is a foodborne pathogen associated to outbreaks with high mortality. Since the traditional methods for its detection are often time-consuming, there is a need to develop new techniques that allow a rapid, simple, reliable, specific and sensitive detection. The present study aimed to develop a biological protocol for DNA detection of Escherichia coli O157:H7 using a Quartz Crystal Microbalance with Dissipation (QCM-D), to be applied as a genosensor. DNA thiol Probes and the respective DNA Target were selected from the eae gene of E. coli O157:H7. Several parameters (such as, concentration, incubation time and temperature) were studied and optimized, on the steps of DNA thiol Probes immobilization, 6-Mercapto-1-hexanol (MCH) blocking agent deposition and DNA Target hybridization. Both the DNA probe and target oligonucleotides were linked to fluorochromes allowing the use of Epifluorescence microscopy, to verify the mass deposition results obtained by the QCM-D device, in the gold electrode. In this study, the best results regarding immobilization on the gold electrode at 22ºC were obtained using 1.00 μM of DNA probe and 30 minutes of incubation. MCH blocking agent was prepared with 1x TE buffer instead of Milli-Q water, and best results were achieved with 1.00 mM and 30 minutes of incubation. Co-immobilization of DNA thiol probes with MCH did not reveal a significant improvement compared with the separated steps. An increase in the quantity of target DNA detected in the gold electrode was observed when using 1.00 μM target DNA at 30ºC, however the analysis of the Epifluorescence microscope images indicate that this increase is possibly related with non-specific immobilization instead of hybridization efficiency increase. Escherichia coli O157:H7 é um microrganismo patogénico associado a surtos alimentares com elevada mortalidade. Considerando que os métodos tradicionais de deteção são demasiado morosos, torna-se necessário desenvolver novas técnicas que permitam uma rápida, simples, fiável, específica e sensível deteção. O presente trabalho teve como objetivo, o desenvolvimento de um protocolo biológico para a deteção de ADN de Escherichia coli O157:H7 usando uma Microbalança de Cristal de Quartzo com factor de Dissipação (QCM-D), de forma a ser aplicado como um genossensor. As sondas tioladas de ADN e, respetivo ADN complementário, foram selecionadas a partir do gene eae de E. coli O157:H7. Foram estudados e otimizados vários parâmetros (concentração, tempo de incubação e temperatura) nos passos de imobilização de sondas tioladas de ADN, de deposição de 6-Mercapto-1-Hexanol (MCH) e hibridação de ADN complementar. Foram adicionados fluorocromos às sondas tioladas de ADN e ADN complementar, para a verificação dos resultados obtidos em massa a partir da QCM-D por microscopia de epifluorescência. Neste estudo, os melhores resultados relativamente à imobilização das sondas de ADN foram conseguidos com 1.00 μM de concentração e tempo de imobilização de 30 minutos. O agente bloqueador (MCH) foi preparado em tampão 1x TE e os melhores resultados foram alcançados com 1.00 mM e 30 minutos de incubação. A co-imobilização de sondas de ADN com MCH não mostrou melhorias significativas. Usando 1.00 μM de ADN complementar a 30ºC, observou-se um aumento da quantidade de ADN depositado no eléctrodo de ouro, contudo as imagens obtidas por microscopia de epifluorescência mostraram que este aumento pode ser devido a imobilização inespecífica e não por aumento da eficiência de hibridação.
24
Shi, 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.
Full text
25
Sukackaitė, 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.
Full textAbstract:
II 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.Type 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.
26
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.
Full textAbstract:
Type 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.II 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.
27
Saurabh, Suman. "Nature of Inter-biomolecular interaction and its consequences : protein, DNA and their Complexes." Thesis, Tours, 2017. http://www.theses.fr/2017TOUR4052/document.
Full textAbstract:
Le monde biologique est rempli de mystères. La compréhension de nombreux processus biologiques extrêmement complexes est grandement améliorée par la combinaison d’approches empruntées à différentes disciplines telles que la chimie et plus récemment la physique. La physique utilise des outils expérimentaux tels que les pinces optiques et les microscopies optique et électronique pour explorer les mécanismes à l’échelle microscopique se déroulant dans la cellule. La connaissance de la nature des interactions entre biomolécules et la possibilité de traduire ces interactions en équations ont permis à la physique de construire des modèles simples mais contenant les ingrédients suffisants à la description d’un mécanisme spécifique. La simulation numérique de tels modèles permet d’améliorer notre compréhension de la relation entre les mécanismes pertinents à l’échelle moléculaire et les observations expérimentales de phénomènes biologiquesThe 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
28
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/.
Full textAbstract:
Thesis (Ph. D.)--Georgia State University, 2006.Title 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.
29
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.
Full textAbstract:
Ets-1 y USF1 son factores de transcripción implicados en muchos procesos fundamentales del desarrollo y la diferenciación celular. Defectos en su regulación se han asociado con desórdenes patológicos e infecciones virales. Ets-1, en particular, es un paradigma del mecanismo de regulación transcripcional en virtud del cual la capacidad de Ets-1 para unir DNA y, por tanto, de transactivación, están silenciadas constitutivamente (autoinhibición). La desrepresión de Ets-1 se puede lograr por medio de interacciones proteína-proteína, que desenmascaran el dominio de unión a DNA de Ets-1 y conducen a la formación de un complejo ternario de gran afinidad entre Ets-1, una proteína compañera y el sitio de unión combinado para ambos factores de transcripción.En 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.
30
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.
Full textAbstract:
RésuméLes monocouches auto-assemblées d'ADN immobilisées sur électrodes d'or sont à la base de nombreux biocapteurs électrochimiques. Le contrôle du comportement interfacial de l'ADN par le biais d'un champ électrique est intéressant pour la détection de polymorphisme nucléotidique simple (PNS). La caractérisation in situ de monocouches d'ADN à l'échelle moléculaire est importante pour la fabrication de biocapteurs robustes, fiables et sensibles.La thèse porte sur la détection du PNS dans l'ADN par le biais d'hybridation/dénaturation induite par le champ électrique. La microscopie de fluorescence sous conditions électrochimiques est utilisée comme méthodologie de détection et outil de caractérisation de l'interface d'ADN. À cette fin, des séquences d'ADN marquées par des sondes fluorescentes sont immobilisées sur des électrodes d'or sous forme de monocouches auto-assemblées (SAM) thiolées.Premièrement, les SAMs sont composées de séquences cibles présentant ou non une mutation ponctuelle. La relation entre le potentiel appliqué et la dénaturation du double brin est étudiée. La dénaturation électrochimique est observée à -0,25 V vs AgDeoxyribonucleic 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
31
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.
Full text
32
Xu, 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.
Full text
33
Tanh, 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.
Full textAbstract:
Self-assembly processes were used to construct supramolecular architectures based on metal-ligand interactions. The structures formed strongly depend on the used metal ion, the ligand type, the chosen counter ion and solvent as well as on the experimental conditions. The focus of the studies was the design of multifunctional N-donor ligands and the characterization of their complexing and structural properties. This work was divided into three distinct main parts: The bis(2-pyridylimine), the bis(2-hydroxyaryl) imine and the tripodal imine / amine ligand approach.
In the first part a series of bis(2-pyridylimine) derivatives having different linking elements were employed as building blocks for novel supramolecular architectures. Reaction of individual d-block metal salts with these ligands has led to the isolation of coordination polymers, a metallamacrocycle, double-stranded helicates, triple-stranded helicates as well as of circular meso-helicates. The nature of the spacer in the Schiff base ligands, the noncovalent weak interactions, such as hydrogen bond, face-to-face π-π and edge-to-face CH-π interactions, are all important factors influencing the architecture of the final products.
Topological control of the assembly process of the hexanuclear meso-helicates is clearly associated with the bidentate coordination of the sulfate anion which directs the formation of a double- rather than a triple-stranded helicate around the octahedrally coordinated Cu(II). Surprisingly, the variation of the linker function in the ligands, which significantly changes the linking angle of the pyridylimine strands, has only a little influence of the resulting structure. Also the use of a mixture of ligands does not influence the meso-helicate topology; the result is the symmetrically mixed meso-helicate.
The new iron(II) triple helicate [Fe2(L5)3](PF6)4 14 {L5 = bis[4-(2-pyridylmethyleneimino)phenyl]-1,1-cyclohexane} in its chloride form binds strongly to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the helicate. The induced CD spectrum gives some evidence that [Fe2(L5)3]4+ interacts with the DNA in a single binding mode, which is consistent with major groove binding.
The cytotoxicity of the new iron(II) triple helicate 14 was evaluated on human lung cancer A549 cells and compared with that of cisplatin and that of the previously reported iron(II) triple helicate [Fe2(L1)3]4+{L1 = bis[4-(2-pyridylmethyleneimino)phenyl]methane}. The first results show some distinguishing features for 14 obviously caused by the existing structural differences of the complexes.
In the second part of the thesis, novel uranyl complexes of the bis(2-hydroxyaryl) imine ligands have been synthesized and characterized. 1D coordination polymers and mononuclear structures were formed. In all complexes a distorted hexagonal bipyramidal coordination geometry around the uranyl centre is observed. The imine nitrogen atoms of the ligands do not bind to the metal centre but interact strongly with the hydroxy group via H-bonding. DFT calculations made with L8 ( α,α’-Bis(salicylimino)-m-xylene) are in good agreement with the X-ray crystal structure data. Liquid-liquid extraction studies involving selected ligands and Eu(III) or U(VI) indicate remarkably high selectivity for U(VI) over Eu(III) at weak acidic pH conditions. We believe that the study made opens up new possibilities for uranyl ion extraction which could be interesting in view of the treatment of nuclear waste.
In the third part of the thesis, a series of multifunctional tripodal ligands with different N-donor centres were used for U(VI) and lanthanide, Nd(III), Eu(III) and Yb(III), binding and extraction. Reaction of these metal ions with selected tripodal ligands afforded complexes which were characterized by ESI mass spectroscopy. The complex composition was found to be 1:1 in all cases. The extraction behaviour of the tripodal ligands towards Eu(III) and U(VI) was studied both in the absence and presence of octanoic acid as co-ligand using the extraction system Eu(NO3)3 or UO2(NO3)2–buffer–H2O/ ligand–CHCl3. These separation systems show a remarkably high selectivity for U(VI) over Eu(III). It is interesting to note that the addition of the octanoic acid to the extraction system leads to high synergistic effects. A series of Eu(III) extraction experiments were done to clarify the composition of the extracted complexes. The results clearly point to the formation of various species with changing composition.
34
Alexopoulos, 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.
Full text
35
Valle, 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.
Full textAbstract:
The majority of structural studies on DNA have been carried out using fibre diffraction, while studies of its dynamics and thermal behaviour have been mainly performed in solution. When the DNA double helix is heated, it exhibits local separation of the two strands that grow in size with temperature and lead to their complete separation. This work has investigated various aspects of this phenomenon. The experiments reported in this thesis were carried out on films of oriented fibres of DNA prepared with the Wet Spinning Apparatus. Thus, sample preparation and characterisation are essential parts of the research. The structures of two forms of DNA, A and B, have been explored as a function of relative humidity at fixed ionic conditions. A method to eliminate traces of ever-present B-form contamination in A-form samples was established. The high orientation of the DNA molecules within the samples allowed us to investigate dynamical fluctuations and the melting transition of DNA using neutron scattering, which can provide the spatial information crucial to understand a phase transition, probing the static correlation length along the molecule as a function of temperature. The transition has been investigated for A and B-forms in order to understand its dependence on molecular configuration.Furthermore, after the first melting, denatured DNA films show typical glass behaviour. Their thermal relaxation has been explored using calorimetry.Neutron and X-ray inelastic scattering (INS and IXS) were used in the past to measure longitudinal phonons in fibre DNA, and the results shown disagreement. Recent INS measurements supported with phonon simulations have been crucial to understand the different dispersion curves reported to date. Experiments using INS and IXS have been carried out to continue with this investigation. Attempts to observe the transverse fluctuations associated to the thermal denaturing of DNA, never experimentally investigated before, have been made.
36
Specht, Marion. "Comportement mécanique de films minces de chalcogénures sous irradiation de photons." Thesis, Rennes 1, 2017. http://www.theses.fr/2017REN1S087/document.
Full textAbstract:
Ce travail est dédié à la compréhension de phénomènes photoinduits dansles verres de chalcogénure. Ces phénomènes, bien que connus depuis des années,ne sont pas encore bien compris. Travailler sur des couches minces, fabriquées icipar co-pulvérisation cathodique, ajoute une diffculté supplémentaire : il y a peude matière qui interagit avec la lumière et il faut composer avec la présence dusubstrat. Afin d'étudier les phénomènes photoinduits, il a été nécessaire d'adapterdes techniques expérimentales déjà existantes telles que la spectroscopie pompe-sonde, qui permet d'étudier la dynamique électronique ultra-rapide (inférieure à lananoseconde) et les capteurs au quartz piezoélectrique qui permettent de mesurerla masse volumique et les modules mécaniques du matériau déposé à leurs surface.Des essais préliminaires de résonance en transmission ont été également réalisés etsont prometteurs. Une machine de DMA (Dynamical Mechanical Analysis) a étéspécialement conçue au laboratoire afin de réaliser une étude dynamique des verres de chalcogénures sous formes de fibres et de films minces. Toutes ces techniquesexpérimentales permettent d'étudier les effets photoinduits à différentes échelles detemps et de mieux les expliquerThis 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
37
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.
Full textAbstract:
Made available in DSpace on 2017-07-21T19:25:54Z (GMT). No. of bitstreams: 1
Wellington Claiton Leite.pdf: 3789073 bytes, checksum: f4c16b4260fbd54f4eada652038ae5bc (MD5)
Previous issue date: 2016-09-06Coordenação 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.
38
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.
Full textAbstract:
Les nanoparticules de silice sont des plateformes idéales pour la conception d’outils de bioimagerie afin d’étudier les mécanismes de transfert de gènes par des lipoplexes. L’objectif de notre étude est le développement d’une modification chimique de surface permettant d’obtenir des colloïdes de silice chargés positivement susceptible de lier de l’ADN par des interactions électrostatiques. Deux stratégies pour la génération de groupements ammonium quaternaires sur des nanoparticules de silice sont présentées a) une silanisation directe par l’utilisation d’un agent de couplage silanique contenant un groupement ammonium quaternaire et b) un procédé en deux étapes mettant en jeu une modification de surface chimique par des aminosilanes primaires et secondaires suivie d’une alkylation des amines par l’iodomethane. Différentes méthodes physico-chimiques (essais de cosédimentation, des expériences de microbalance à cristal de quartz avec mesure de dissipation et d’imagerie MET et Cryo-MET) ont été utilisées pour mettre en évidence et caractériser les interactions entre les biomolécules et les surfaces quaternisées. Des études préliminaires ont montrées les capacités de marquage de lipoplexes par de telles nanoparticulesSilica 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
39
Mooers, Blaine H. M. "Controlling DNA packing in crystals." Thesis, 1997. http://hdl.handle.net/1957/34392.
Full text
40
(6581093), Zhe Li. "ENGINEERED 3D DNA CRYSTALS: CHARACTERIZATION, STABILIZATION AND APPLICATIONS." Thesis, 2019.
Find full textAbstract:
In recent years, DNA nanotechnology has emerged as one of the most
powerful strategies for bottom-up construction of nanomaterials. Due to
the high programmability of DNA molecules, their self-assembly can be
rationally designed. Engineered 3D DNA crystals, as critical products
from the design of DNA self-assembly, have been proposed as the
structural scaffolds for organizing nano-objects into three-dimensional,
macroscopic devices. However, for such applications, many obstacles
need to be overcome, including the crystal stability, the
characterization methodology, the revision of crystal designs as well as
the modulation of crystallization kinetics. My PhD research focuses on
solving these problems for engineered 3D DNA crystals to pave the way
for their downstream applications.In 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.
41
Schulman, Rebecca. "The Self-Replication and Evolution of DNA Crystals." Thesis, 2007. https://thesis.library.caltech.edu/1554/1/thesis.pdf.
Full textAbstract:
How life began is still a mystery. While various theories suggest that life began in deep sea volcanic vents or that a world where life consisted predominantly of RNA molecules preceded us, there is no hard evidence to give shape to the chain of events that led to cellular life.
Perhaps the fundamental enigma of our origins is how life began to self-replicate in such a way that evolution could produce Earth's "endless forms most beautiful." With the exception of biological organisms, we have no examples of self-replicating, evolving chemical systems, despite an extensive research program with the goal of identifying them.
In this thesis, I construct a chemical system that is capable of the most basic self-replication and evolution. The system uses no enzymes or biological sequences, can support and replicate a combinatorial genome, and is completely autonomous. There are no fundamental obstacles to the replication by this system of much more complex sequences or to open-ended evolution.
The design of the system is inspired by the work of Graham Cairns-Smith, who has proposed that life began with clay. Clays are tiny layered crystals; some clay crystals can contain one of several different patterns of atoms or molecules in each layer. The choice of patterns for the layers could be viewed as a sort of genome: it would be copied as the clay grew, and if the crystal broke, each new piece would inherit its pattern from the old piece and could replicate it in the same manner. If some patterns of layers could grow and reproduce faster than other patterns, crystals with faster-growing patterns would be selected for.
Instead of the atoms or small molecules of which clay consists, I use molecules consisting of 4-6 interwoven, synthetic DNA strands called DNA tiles to construct crystals that replicate and evolve as Cairns-Smith imagined. While the choice of construction material was influenced by ease of use -- in contrast to clay crystals, DNA tile crystals have been previously characterized and are easy to crystallize and image in the laboratory -- the choice was fundamentally made because DNA tile monomers are programmable, allowing us to create novel crystal morphologies rationally.
The crystals I construct, termed "zig-zag ribbons", contain a sequence of information ("a genome") in each row. Growth of the ribbon adds rows, one at time, each of which contain an arrangement of DNA tiles that encode the same information sequence as the previous row. Altering the set of tiles used to assemble ribbons allows us to alter the alphabets for and the permitted lengths of sequences that can be copied.
I describe how to design tile sets that can replicate genomes with different alphabets and the kind of sequence evolution that is in theory possible with some simple tile sets. Altering the tile set can not only change the kinds of sequences that may be replicated, it can also make growth and splitting more robust. I show how to make changes to the crystals' design to prevent errors during growth and splitting and to reduce the rate of spontaneous generation of new crystals.
It has been previously shown that DNA tile crystallization can be used to perform universal computation; I show that in theory crystals that can compute can undergo open-ended evolution as they try to produce more and more complex programs to take advantage of available growth resources. This mechanism is simple enough to potentially observe in the laboratory in the near future. In experiments, I demonstrate a much more basic kind of replication and evolution, in which zig-zag ribbons maintain a preference for a certain width into a second generation.
This work suggests that the concept of a self-replicating chemistry is closely related to the concept of a chemistry that can store information and compute. It is only by clearly understanding how chemistry can perform these latter tasks that we can hope to understand how self-replication and evolution can occur, and by implication, understand how life might have begun.
42
Tang, Hao 1985. "Applications of self-assembly : liquid crystalline semiconductors and DNA-conjugated microparticles." 2012. http://hdl.handle.net/2152/22061.
Full textAbstract:
Self-assembly provides an efficient way to build complex structures with great flexibility in terms of components and properties. This dissertation presents two different forms of self-assembly for technical applications. The first example is the molecular assembly of liquid crystals (LCs). Attaching appropriate side chains on anthracene, oligothiophene, and oligoarenethiophene successfully constructed liquid crystalline organic semiconductors. The phase transitions of the LC semiconductors were analyzed by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The effect of the LC phase change on charge transport was probed by the space-charge limited current (SCLC) method and the field-effect transistor (FET) method. Mobility in the LC phase rose in anthracenyl esters but decreased in oligothiophenes and oligoarenethiophenes. The different electronic behavior of LC semiconductors may be caused by the difference in domain size and/or the difference in response to electric field. The second example of self-assembly in this dissertation is DNA-guided self-assembly of micrometer-sized particles. Patternable bioconjugation polymers were synthesized to allow for lithographic patterning and DNA conjugation. The base pairing of DNA was then used to drive the self-assembly of DNA-conjugated particles. The DNA conjugation chemistry was studied in detail using a fluorescence-based reaction test platform. The conjugated DNA on the polymer surface retained its ability to hybridize with its complement and was efficient in binding microspheres with complementary strands. Highly specific bead-to-bead assembly was analyzed using imaging flow cytometry, and the fractions of self-assembly products were explained on the basis of chemical equilibrium. The process of particle fabrication using photolithography was successfully developed, and the self-assembly of lithographically-patterned particles was demonstrated. We envision that the technologies described in this dissertation will be useful in a variety of fields ranging from microelectronics to biotechnology.text
43
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.
Full textAbstract:
Algorithmic 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.
44
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.
Full textAbstract:
博士國立中山大學
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.
45
Reddy, U. Venkateswara. "Study of Enantiomeric Discrimination and Enzyme Kinetics using NMR Spectroscopy." Thesis, 2013. http://etd.iisc.ernet.in/2005/3364.
Full textAbstract:
Obtaining enantio pure drug molecules is a long standing challenge in asymmetric synthesis implying that the identification of enantiomers and the determination of enantiomeric purity from a racemic mixture are of profound importance. In achieving this target NMR spectroscopy has proven to be an excellent analytical tool. It is well known that normal achiral NMR solvents do not distinguish the spectra of enantiomers. On the other hand, the conversion of substrates to diastereomers using one of the enantiopure chiral auxiliaries, such as, chiral solvating agent, chiral derivatizing agent and chiral lanthanide shift reagent, circumvents this problem. The imposition of diasteomeric interactions circumvents this problem. There is a pool of chiral auxiliaries available in the literature, each of which is specific to molecules of certain functionalities and has its own advantages and limitations. These classical methods have two limitations as they demand the presence of a targeted functional group in the chiral molecule and utilize only chemical shifts to visualize enantiomers. On the other hand in chiral anisotropic medium, due to differential ordering effect, the order-sensitive NMR observables, viz. chemical shift anisotropies (∆σi), dipolar couplings (Dij) and for nuclei with spin >1/2 the quadrupolar couplings (Qi) have enormous power of exhibiting different spectrum for each enantiomer permitting their discrimination. Numerous weakly ordered chiral aligning media have been reported in the literature. Nevertheless there is a scarcity of water compatible medium. Research work presented in this thesis is focused on various aspects, such as, the discovery of new chiral aligning medium for the enantiodiscrimination of water soluble chiral molecules, potential utility of DNA liquid crystal for discrimination of amino acids, on-the-fly monitoring of enzyme kinetics and the preparation of novel composite liquid crystals, hydrogels and thin films. The derived results are discussed in different chapters.
Chapter 1 provides a brief introduction to NMR spectroscopy with special emphasis on the conceptual understanding of the tensorial interaction parameters, such as chemical shifts, scalar and dipolar couplings, quadrupolar couplings, effect of r.f pulses, basic introduction to 2D NMR experiments. Subsequently, a broad overview of the enantiomers, specification of their configurations, chirality without stereogenic carbon, chirality in molecules containing different atoms, are discussed. Following this a brief introduction to liquid crystals and their properties, their classification, their orientation in the magnetic field, order parameter are also discussed. The description on the chiral liquid crystals, the differential ordering effect, employment of the orientation dependent NMR interactions, utility of 2H NMR experiments for the visualization of enantiomers and the measurement of enantiomeric composition has been set out in brief.
Chapter 2: As far as the organo soluble chiral molecules is concerned (in solvents such as, chloroform, dioxane, tetrahydrofuran and dimethylformamide), it has been well established that an ideal choice of chiral liquid crystal for enantiodiscrimination is poly-�-benzyl-L-glutamate (PBLG). Nevertheless, there is a scarcity of weak aligning medium for water soluble chiral molecules. This chapter introduces the chiral liquid crystal derived from the polysaccharide xanthan, which has numerous applications. The detailed discussion on the preparation of polysaccharide xanthan mesophase is given. The appearance of the mesophse is established by detecting the quadrupole split doublet of dissolved water. Subsequently enantiodiscrimination power of this new medium has been investigated on deuterated D/L-Alanine and (R/S)-β-butyrolactone. For such a purpose the selective 2D-SERF (SElective ReFocussing) experiment has been employed. It has been convincingly demonstrated that the medium has wide applicability for the discrimination of enantiomers, enantiotopic directions in prochiral molecules, measurement of enantiomeric excess and the RDCs in medium sized molecules. The new medium is sustainable over a wide range of temperature and concentration of ingredients, the mesophase is reversible, reproducible, easy to prepare besides being cost effective. It is possible to have the controlled tuning of the degree of order for specific application.
Chapter 3: In this chapter the real discriminatory potential of DNA liquid crystalline phase has been explored. It is unambiguously established that; i) the fragmented DNA liquid crystal is able to differentiate between enantiomers of structurally different chiral amino acids; ii) the T1 (2H) values for L/D (alanine) is nearly equal indicating the similar dynamics for both the enantiomers, thus permitting the measurement of ee from the integral areas of the peaks of the contours of 2D spectrum; iii) the enantiotopic discrimination in prochiral compounds has also been successfully explored. Furthermore the analyses of NMR results yielded fruitful information on the analytical potential of DNA chiral liquid crystal, such as, (a) the chiral discrimination is effective on a large range of amino acids with spectral differences ΔΔʋQ‘s and ΔʋQ‘s varying from 80 to 338 Hz, and 50 to 900 Hz respectively; (b) the discrimination phenomenon remain active irrespective of the structure and the electronic nature (polarity) of the fourth substituent around the stereogenic center; (c) compared to an alkyl moiety, the presence of a terminal –OH or –SH group seems to slightly increase both the degree of alignment of the solute and the enantiodiscrimination efficiency compared to alanine; (d) The enantiodiscrimination can be detected easily not only on CD3 and CD groups, but also on CD2 sites exhibiting inequivalent diastereotopic directions; (e) discriminations with rather large differential ordering effect were obtained even for the sites that are situated far away from the asymmetric center; (f) The relative position of quadrupolar doublets from one 2H site to another can be reversed with regard to the absolute configuration (L/D).
Chapter 4: Racemases recognize a chiral substrate such as (L-Alanine) and convert it into its enantiomer, i.e., (D-Alanine) and vice versa. Alanine racemase plays a vital role for certain bacteria, providing D-Alanine for peptidoglycan cell-wall biosynthesis. Elucidating the mechanism of enzymatic racemization is crucial for designing new inhibitors that may be useful as a novel class of antibiotics. This requires techniques to discriminate L-and D-Alanine and follow their concentrations as a function of time, so that one can determine the kinetic parameters and study the effect of inhibitors. In this chapter the utility of DNA liquid crystal media for in situ and real-time monitoring of the interconversion of L-and D-alanine-d3 by alanine racemase from Bacillus stearothermophilus has been demonstrated. The enantiomeric excess has been measured at different time intervals to monitor the enzymatic racemization at different time intervals in pseudo 2D NMR. The study unambiguously ascertains the reliability and robustness of utility of NMR in chiral anisotropic phase for monitoring the enzymatic racemization. The method thus provides new mechanistic insight and a better understanding of enzymatic reactions, in particular for alanine racemase.
Chapter 5: In continuation with the development of weakly ordered liquid crystals, this chapter reports the spontaneous formation of composite graphene oxide (GO)/double stranded DNA (dsDNA) liquid crystals at higher concentrations of ingredients, and hydrogels at lower concentrations of ingredients, the process of which involves simple mixing in an aqueous phase has been demonstrated. The liquid crystalline phases and hydrogels have been characterized using optical polarized microscopy (OPM), scanning electron microscopy (SEM), Raman spectroscopy and 2H NMR spectroscopy. The observation of strong birefringence in the optical polarized microscope gives evidence for the formation of GO/dsDNA liquid crystals. The strong interaction between the dsDNA and GO was confirmed using Raman spectroscopic analysis. Furthermore, GO/dsDNA thin films have also been prepared and characterized using SEM and OPM. The GO/dsDNA thin film was prepared and its liquid crystal nature was established using OPM and 2H NMR. Importantly, the GO/dsDNA hydrogels were formed without any heat treatment to unwind dsDNA molecules and the porosity of hydrogels can be controlled by changing concentration of the dsDNA. This novel multifunctional composite liquid crystals and hydrogels of GO/dsDNA thus opens up new avenues for many applications like security papers, optical devices such as circular polarizers, reflective displays and drug delivery as well as tissue engineering using GO composite hydrogels.
46
Tseng, Ching-Ching, and 曾菁菁. "Develop a quartz crystal microbalance (QCM) DNA-sensor." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/63512512255502582858.
Full textAbstract:
碩士大同大學
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.
47
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.
Full textAbstract:
In this thesis, a 4.7Å crystal structure of the human mitochondria DNA
polymerase γ catalytic complex is reported. Though the DNA substrate-binding site is not
identifiable in the structure, two conformational changes in the enzyme architecture are
described: 1) rotation of the distal monomer of the accessory subunit towards the
catalytic subunit, and 2) shift of the thumb motif of the polymerase domain towards the
active site. Both conformational changes suggest a structure of Pol γ in the DNA-bound
state and in its active site “closed” conformation.text
48
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.
Full textAbstract:
碩士國立清華大學
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.
49
Xu, Fei. "Insights into mechanisms of nucleosome remodeling from analysis of crystal structures." 2007. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16798.
Full text
50
Lu, 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.
Full text