RNA catalysis is of fundamental importance in many biological functions, such as the peptidyl transferase activity of the ribosome and genetic control by riboswitches, among others. Small ribozymes are a convenient system to increase our understanding about the structure, folding and catalytic mechanism of ribozymes. This dissertation includes analysis of certain aspects of the catalytic mechanism in the hairpin and hammerhead ribozyme. In the hairpin ribozyme, we studied the functional consequences of molecular substitutions at two conserved positions, A9 and A10. These nucleotides are located close to the scissile phosphate but their exact function is unclear since they do not appear to be making any essential interactions with other nucleotides in the catalytic core. G, C, U, 2-aminopurine, 2, 6-diaminopurine, purine, and inosine were substituted at A9 and A10 and their effects on cleavage and ligation rates were analyzed. The effect of the variations on tertiary structure and docking was monitored by hydroxyl radical footprinting and native gel electrophoresis. It was observed that all the variants that exhibited poor docking and/or tertiary structure formation were also ligation challenged whereas they performed normally in the cleavage reaction. We found a unique variant, A10G that cleaved five times faster than A10 but did not exhibit any ligation. Results suggested that ligation required a more kinetically stable core than that needed to carry out cleavage. The hammerhead ribozyme field featured extensive disagreements between the crystal structure of the minimal hammerhead released in the mid 90s and the accumulating biochemical data. Much of the conflict was resolved with the new crystal structure of the extended hammerhead ribozyme. This structure confirmed many of the biochemical findings and brought out some new interactions, notably the G8·C3 base pair. We studied numerous base substitutions to establish the importance of the base pair for cleavage and ligation. Catalysis requires the formation of the base pair but even the fastest base paired variant was 10-fold slower than G8·C3 base pair. Docking and tertiary structure analysis by hydroxyl radical footprinting and native gel electrophoresis emphasized the importance of having a purine at position 8 and a pyrimidine at 3. Catalysis in the unmodified ribozyme was uniquely accompanied by hydrolysis of the 2′, 3′- cyclic phosphate ring present on one of the cleavage products, leading to the generation of non-ligatable products during a ligation assay. We determined the ligation rate-pH profile for unmodified ribozyme that differed from the cleavage rate-pH profile only at high pH.

The hairpin ribozyme is a small catalytic RNA that cleaves a phosphodiester bond. In order for cleavage to occur, the hairpin ribozyme must properly fold into its docked conformation, in which the two loops interact to form the active site. Metal ions and the four-way junction play critical roles in the stabilization of the docked conformation. The work presented in this thesis attempts to investigate the metal-ion dependence of the docking of the four-way junction construct of the hairpin ribozyme. In addition, the activity of the hairpin ribozyme in the presence of Mn2+ was observed. Initially, a four-stranded four-way junction construct of the hairpin ribozyme and a loopless mutant were characterized by native gel electrophoresis and thermal denaturation to verify ribozyme formation. A novel interaction between the sulfur of a phosphorothioate-substituted mononucleotide, such as adenosine thiomonophosphate (AMPS) or adenosine thiotrisphoshate (ATPgS), and Cd2+ has been characterized by UV-vis spectroscopy. A feature at 208 nm was identified to be a result of sulfur-to-Cd2+ transfer. The apparent binding affinities, the apparent extinction coefficients, and the binding ratios were determined for each complex.

This thesis presents Design, Measurement and analysis for size reduction of the Coupled line micro strip Hairpin band pass filters (MHBPF’s). Hairpin filters are an interesting topic for microwave designers. These planar circuits are widely used in wireless transceivers and other microwave projects due to an easy design process. The filter design and analysis described in this paper can be used for wireless transceivers as well as for microwave links. Two techniques have been employed for the size reduction and four different filters have been designed. 1st Technique, Conventional Hairpin configuration uses folding of the normal λ/2 resonators into U shape. 2nd technique exploits the cross coupling of the resonators for further size reduction of the filters.  From 1st to last design, different properties of micro strip and couple lines have been analyzed, observed, and finally exploited to reach to a more compact solution. Agilent ADS have been used for the simulation process of the initial filters. Further on, AWR Microwave office has been used for the EM simulation part of the project and a detailed analysis for the size reduction with respect to the different properties of the materials used. Since insertion loss method is going to be used for the designs, low pass filter prototypes parameters are used for further conversion to band pass. The loaded Q factor and the mix coupling coefficients between resonators have been calculated from standard empirical equations. FR4 substrate is used for manufacturing process. RogersRO3210 has also been used as a substrate for 3-section design in AWR Microwave Office for the illustration of size reduction with respect to substrate properties. The design with FR4 substrate has been manufactured and tested. The results have been analyzed on Vector Network Analyzer and displayed in results sections.

Ce travail s’inscrit dans le cadre de la recherche relative au développement de biosenseurs à ADN électrochimiques. Des aspects fondamentaux, ainsi que des aspects d’application de la détection d’hybridation d’ADN sont envisagés. Dans un premier temps, le comportement interfacial et le processus d’hybridation d’oligonucléotides d’ADN linéaires et ADN hairpin (structure en épingle à cheveux) nonmarqués sont étudiés en formant des monocouches auto-assemblées mixtes de monobrins d’ADN (ssADN) thiolés et d’un hydroxyalcanethiol (4-mercaptobutan-1-ol) par coadsorption spontanée sur des électrodes d’or polycristallin. L’immobilisation de monocouches mixtes ssADN/MCB est caractérisée par voie électrochimique et par spectroscopie des photoélectrons X. Des mesures de chronocoulométrie, en présence de [Ru(NH3)6]3+ (RuHex), permettent de déterminer la quantité d’ADN dans la monocouche mixte formée. Les résultats montrent que l’excès superficiel d’ADN linéaire est plus important que l’excès superficiel d’ADN hairpin sous des conditions de formation identiques. La réaction de reconnaissance moléculaire d’hybridation est détectée par des mesures d’impédance en présence de [Fe(CN)6]3-/4-. L’hybridation se traduit dans le cas de l’ADN linéaire par une augmentation de la résistance au transfert d’électron Rct tandis que dans le cas de l’ADN hairpin, Rct diminue. Ces différences sont dues au plus faible recouvrement et au changement de conformation des molécules d’ADN hairpin lors de l’hybridation. Des mesures de réflectivité de neutrons nous ont permis de mettre en évidence l’augmentation de l’épaisseur du film d’ADN hairpin et de confirmer le changement conformationel ces sondes lors de la reconnaissance moléculaire. Dans la seconde partie, nous présentons une nouvelle méthode électrochimique de détection d’hybridation, basée sur les interactions électrostatiques entre le complexe cationique RuHex et les groupements phosphates de l’ADN. Afin d’améliorer la détection des molécules de PNA (peptide nucleic acid) ont été immobilisées comme sondes de reconnaissance moléculaire. Après hybridation des sondes PNA avec le brin complémentaire, RuHex s’adsorbe sur l’ADN hybridé et un signal de réduction de ces complexes redox, enregistré par voltampérométrie alternative, constitue une signature claire de l’hybridation d’ADN à l’interface modifiée. Les interactions RuHex/PNA-ADN ont été étudiées. La constante d’adsorption de RuHex sur l’électrode modifiée PNA/MCB après hybridation est évaluée à 2,9 (±0,3) 105 M-1 en milieu Tris-HCl 0,01M, selon une isotherme de Langmuir. Les performances analytiques de la méthode de détection (sensibilité, sélectivité et reproductibilité) ont été évaluées et optimisées pour la détection des séquences d’ADN du gène de l’ARNr 23S d’Helicobacter pylori. La méthode de détection électrochimique présentée est assez sélective pour permettre de discriminer les mutations ponctuelles A2143G et A2144C de la séquence de type sauvage. La diminution significative des signaux d’admittance enregistrés en présence des séquences mutées est attribuée à la capacité accrue de discrimination de mutations ponctuelles des molécules PNA. La réponse de détection est linéaire en fonction du logarithme de la concentration de la cible d’ADN sur plus de quatre ordres de grandeur (10-6 M à 10-10 M). La limite de détection de l’oligonucléotide d’ADN complémentaire de 80 pM est très bonne. La méthode a été appliquée avec succès à la détection de fragments PCR complémentaires de 100 et 400 paires de bases, amplifiés à partir de souches SS1 d’H.pylori.

CArG box is a highly conservative DNA motif found in Serum Response Element (SRE), which regulates expression of c-fos gene. In this thesis, short oligodeoxynucleotides containing CArG box were measured using nuclear magnetic resonance spectroscopy to evaluate their ability to preferentially form hairpin over duplex. 1H spectra were measured at temperature range (274-360) K. We acquired thermodynamic parameters of the transition between hairpin and single strand by fitting the temperature- dependent chemical shifts. The hairpin structure of our oligonucleotide samples was confirmed by non- B-DNA patterns in NOESY spectra, absence of concentration dependence of melting, and other pieces of evidence. Thus, occurrence of unusual DNA conformation of CArG box in native DNA, potentially even cruciform is highly possible. This could explain the high affinity between SRE and its transcription factor. Powered by TCPDF (www.tcpdf.org)

Serum response factor (SRF) is a transcription factor which binds to a highly conserved DNA sequence called the CArG box. According to the nucleotide sequence of CArG box it could form a hairpin structure or a cruciform. In this master thesis, the structure of the CArG box in a human gene c-fos was studied by nuclear magnetic resonance. 1 H spectra at temperatures 274{356 K, two-dimensional 1 H{1 H NOESY spectra, and two-dimensional 1 H{13 C HMBC spectra for DNA sequences with lengths of 12, 14 and 16 nucleoti- des were acquired. The thermodynamic parameters of formation of the secondary structure in the samples were determined from the measured temperature depen- dencies. The hairpin formation in the samples was con rmed based on the NOESY spectra and the lack of dependency of the melting temperature on concentration. The observed difference of the secondary structure from B-DNA could serve as a possible explanation of the high a nity of SRF to CArG box. 1

No description available.

Uma das espécies que atualmente vem despertando interesse econômico por seu elevado valor de mercado é o maracuzajeiro doce (Passiflora alata Curtis). Entretanto, a cultura é afetada por diferentes doenças que prejudicam a produtividade e a qualidade dos frutos, sendo a doença causada pelo Cowpea aphid-borne mosaic virus (CABMV) a que mais afeta a cultura do maracujazeiro no Brasil. O presente trabalho teve como objetivo a obtenção de plantas transgênicas de P. alata visando resistência ao CABMV. O processo de transformação genética utilizado foi via Agrobacterium tumefaciens, estirpe EHA105, contendo o cassete de expressão com um fragmento do gene da proteína capsidial do CABMV, numa construção tipo hairpin e o gene de seleção nptII que confere resistência ao antibiótico canamicina. Para os experimentos de transformação genética foram utilizados como explantes segmentos de hipocótilo e segmentos internodais. Após 2 a 3 dias de co-cultivo em meio de cultura MS (MURASHIGE; SKOOG, 1962) contendo acetosseringona (100 mM), os explantes foram transferidos para meio de cultura de seleção e regeneração constituído de sais minerais e vitaminas de MS, suplementado com benzilaminopurina (BAP - 1mg/L) + thidiazuron (TDZ - 0,5 mg/L) + canamicina (100 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L), pH 5,8. Após 4 a 6 semanas de incubação, determinou-se o número de explantes responsivos e as gemas adventícias desenvolvidas foram transferidas para meio de cultura de alongamento MSM + GA3 (1,0 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L). As plantas desenvolvidas foram aclimatizadas e analisadas por PCR, utilizando primers específicos para a detecção do fragmento do gene da proteína capsidial do CABMV e do gene de seleção (nptII). Foram identificadas 47 plantas transgênicas PCR positivas para do gene nptII. Até o momento, a integração do gene nptII foi confirmada por Southern blot em 9 plantas / One species that is currently attracting interest due to its high economic value is the sweet passionflower (Passiflora alata Curtis). However, the culture is affected by different diseases that harm the productivity and fruit quality. The disease caused by Cowpea aphid-borne mosaic virus (CABMV) is the one that more affect the culture of passionflower in Brazil. This work aimed to obtain transgenic plants of P. alata resistant to the CABMV. The genetic transformation process was via Agrobacterium tumefaciens, strain EHA105, containing the expression cassette with a fragment of the coat protein gene of CABMV, in a hairpin construct and the selection gene nptII, which confers resistance to the antibiotic kanamycin. In the experiments of genetic transformation hypocotyl segments and internodal segments were used as explants. After 2-3 days of co-cultivation in MS medium (MURASHIGE; SKOOG, 1962) containing acetosyringone (100 mM), the explants were transferred to the selection and regeneration culture medium consisting of mineral salts and vitamins of MS medium supplemented with benzylaminopurine (BAP - 1 mg/L) + thidiazuron (TDZ - 0.5 mg/L) + kanamycin (100 mg/L) + cefotaxime (500 mg/L) + silver nitrate (4.0 mg /L), pH 5.8. After 4-6 weeks of incubation, it was determined the number of responsive explants. Shoots developed were transferred to elongating culture medium MSM + GA3 (1.0 mg/L) + cefotaxime (500 mg/L) + nitrate silver (4.0 mg/L). The developed plants were acclimatized and analyzed by PCR using specific primers to detect the fragment of CABMV and the selection gene (nptII). It was identified 47 transgenic plants PCR positive for the gene nptII. Until this moment, the integration of the nptII gene was confirmed by Southern blot in 9 plants

A cultura do maracujazeiro é afetada pela virose causada pelo Cowpea aphid-borne mosaic virus (CABMV), provocando a redução da qualidade e produtividade dos frutos e, em alguns casos, pode inviabilizar o cultivo comercial desta espécie. Uma alternativa para o controle de doenças viróticas é o desenvolvimento de plantas resistentes pela transformação genética. O objetivo deste trabalho foi a obtenção de plantas transgênicas de maracujazeiro (Passiflora edulis f. flavicarpa), utilizando 2 construções gênicas contendo a região codificadora do gene da proteína capsidial do CABMV. A construção pCABMV-asCP, que contém um fragmento na orientação antisenso e a construção pCABMV-dsCP, que contém fragmentos senso e antisenso do gene da proteína capsidial, separados por um íntron, uma construção hairpin. Para os experimentos de transformação genética, via Agrobacterium tumefaciens, foram utilizados os explantes de segmentos de hipocótilo e discos de folhas jovens das variedades FB-100, IAC-275 e IAC-277. Após 2 - 3 dias de co-cultivo em meio de cultura MS (MURASHIGE; SKOOG, 1962) contendo acetosseringona (100 mM), os explantes foram transferidos para meio de cultura de seleção e regeneração constituído de sais minerais e vitaminas de MS, suplementado com canamicina (100 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L), pH 5,8 e os reguladores BAP, TDZ e combinação de BAP e TDZ. Após 4 - 6 semanas, as gemas adventícias desenvolvidas foram transferidas para meio de cultura de alongamento MSM + GA3 (1,0 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L). As plantas desenvolvidas foram aclimatizadas e analisadas por PCR, utilizando-se primers específicos para a detecção dos transgenes. Foram identificadas 30 plantas transgênicas PCR positivas para do gene nptII, sendo 11 positivas para o fragmento antisenso da proteína capsidial do CABMV e 2 positivas para o fragmento da construção gênica hairpin. Até o momento, a integração dos transgenes foi confirmada por Southern blot em 4 plantas. Paralelo aos experimentos de transformação genética, foram avaliadas plantas de maracujazeiro das variedades IAC-275 e IAC-277, obtidas em experimentos anteriores, com a construção gênica pCABMV-CP, que contém o gene da proteína capsidial do CABMV. A análise de Southern blot de 14 plantas destes experimentos, confirmou a integração do transgene em 13 plantas, as quais foram propagadas e inoculadas mecanicamente com 3 isolados do CABMV (SP, RJ, CE). A linhagem T16 foi resistente as 3 inoculações, com os 3 isolados testados. Clones desta linhagem foram analisados por RT-PCR, comprovando a transcrição do transgene / The yellow passionfruit is affected by Cowpea aphid-borne mosaic virus (CABMV), which causes a decrease in fruit quality and productivity and in some cases making it unpractical for commercial cultivation of this species. Ann alternative for the control of virus diseases is the development of resistant plants through genetic transformation techniques. The objective of this work was to obtain passion fruit (Passiflora edulis f. flavicarpa) transgenic plants with two different gene constructs derived from the CABMV coat protein coding region. pCABMV-asCP contains the gene fragment in an antisense direction and pCABMV-dsCP contains a sense and antisense coat protein gene fragments, separated by intron, a hairpin construct. The genetic transformation experiments with Agrobacterium tumefaciens, were done in hypocotyl segments and young leaf disks explants from varieties FB-100, IAC-275 and IAC-277. After two to three days in co-culture in MS culture medium (MURASHIGE; SKOOG, 1962) supplemented with acetoseringone (100 mM) the explants were subcultured to medium for selection and regeneration, composed of MS minerals and vitamins, supplemented with kanamycin (100 mg/L), cefotaxime (500 mg/L) and silver nitrate (4.0 mg/L), at pH 5.8, and the growth regulators BAP, TDZ and combination of BAP and TDZ. After four to six weeks, the adventitious buds developed were transferred to an elongating medium composed of MSM salts supplemented with GA3 (1.0 mg/L), cefotaxime (500 mg/L) and silver nitrate (4.0 mg/L). Plants were acclimatized and analyzed by PCR, with specific primers for the transgenes detection. Thirty transgenic plants were identified as PCR positive for the nptII gene, with 11 being positive for the antisense fragment of the CABMV coat protein gene and two positive for the hairpin gene construct fragment. Currently, the transgene integration was confirmed by Southern blot analysis in four plants. Simultaneously to the genetic transformation experiments, passionfruit plants, varieties IAC-275 e IAC-277, obtained from previous experiments with pCABMV-CP, which contains CABMV coat protein gene, were analized. The Southern blot analysis of 14 plants from these experiments confirmed the transgene integration in 13 plants, which were propagated and mecanically inoculated with three CABMV isolates (SP, RJ, CE). Line T16 was resistant to three inoculations with all three isolates tested. Clones from this line were analyzed by RT-PCR which confirmed the transgene transcription

A cultura do maracujazeiro é afetada pela virose causada pelo Cowpea aphid-borne mosaic virus (CABMV), provocando a redução da qualidade e produtividade dos frutos e, em alguns casos, pode inviabilizar o cultivo comercial desta espécie. Uma alternativa para o controle de doenças viróticas é o desenvolvimento de plantas resistentes pela transformação genética. O objetivo deste trabalho foi a obtenção de plantas transgênicas de maracujazeiro (Passiflora edulis f. flavicarpa), utilizando 2 construções gênicas contendo a região codificadora do gene da proteína capsidial do CABMV. A construção pCABMV-asCP, que contém um fragmento na orientação antisenso e a construção pCABMV-dsCP, que contém fragmentos senso e antisenso do gene da proteína capsidial, separados por um íntron, uma construção hairpin. Para os experimentos de transformação genética, via Agrobacterium tumefaciens, foram utilizados os explantes de segmentos de hipocótilo e discos de folhas jovens das variedades FB-100, IAC-275 e IAC-277. Após 2 - 3 dias de co-cultivo em meio de cultura MS (MURASHIGE; SKOOG, 1962) contendo acetosseringona (100 mM), os explantes foram transferidos para meio de cultura de seleção e regeneração constituído de sais minerais e vitaminas de MS, suplementado com canamicina (100 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L), pH 5,8 e os reguladores BAP, TDZ e combinação de BAP e TDZ. Após 4 - 6 semanas, as gemas adventícias desenvolvidas foram transferidas para meio de cultura de alongamento MSM + GA3 (1,0 mg/L) + cefotaxima (500 mg/L) + nitrato de prata (4,0 mg/L). As plantas desenvolvidas foram aclimatizadas e analisadas por PCR, utilizando-se primers específicos para a detecção dos transgenes. Foram identificadas 30 plantas transgênicas PCR positivas para do gene nptII, sendo 11 positivas para o fragmento antisenso da proteína capsidial do CABMV e 2 positivas para o fragmento da construção gênica hairpin. Até o momento, a integração dos transgenes foi confirmada por Southern blot em 4 plantas. Paralelo aos experimentos de transformação genética, foram avaliadas plantas de maracujazeiro das variedades IAC-275 e IAC-277, obtidas em experimentos anteriores, com a construção gênica pCABMV-CP, que contém o gene da proteína capsidial do CABMV. A análise de Southern blot de 14 plantas destes experimentos, confirmou a integração do transgene em 13 plantas, as quais foram propagadas e inoculadas mecanicamente com 3 isolados do CABMV (SP, RJ, CE). A linhagem T16 foi resistente as 3 inoculações, com os 3 isolados testados. Clones desta linhagem foram analisados por RT-PCR, comprovando a transcrição do transgene / The yellow passionfruit is affected by Cowpea aphid-borne mosaic virus (CABMV), which causes a decrease in fruit quality and productivity and in some cases making it unpractical for commercial cultivation of this species. Ann alternative for the control of virus diseases is the development of resistant plants through genetic transformation techniques. The objective of this work was to obtain passion fruit (Passiflora edulis f. flavicarpa) transgenic plants with two different gene constructs derived from the CABMV coat protein coding region. pCABMV-asCP contains the gene fragment in an antisense direction and pCABMV-dsCP contains a sense and antisense coat protein gene fragments, separated by intron, a hairpin construct. The genetic transformation experiments with Agrobacterium tumefaciens, were done in hypocotyl segments and young leaf disks explants from varieties FB-100, IAC-275 and IAC-277. After two to three days in co-culture in MS culture medium (MURASHIGE; SKOOG, 1962) supplemented with acetoseringone (100 mM) the explants were subcultured to medium for selection and regeneration, composed of MS minerals and vitamins, supplemented with kanamycin (100 mg/L), cefotaxime (500 mg/L) and silver nitrate (4.0 mg/L), at pH 5.8, and the growth regulators BAP, TDZ and combination of BAP and TDZ. After four to six weeks, the adventitious buds developed were transferred to an elongating medium composed of MSM salts supplemented with GA3 (1.0 mg/L), cefotaxime (500 mg/L) and silver nitrate (4.0 mg/L). Plants were acclimatized and analyzed by PCR, with specific primers for the transgenes detection. Thirty transgenic plants were identified as PCR positive for the nptII gene, with 11 being positive for the antisense fragment of the CABMV coat protein gene and two positive for the hairpin gene construct fragment. Currently, the transgene integration was confirmed by Southern blot analysis in four plants. Simultaneously to the genetic transformation experiments, passionfruit plants, varieties IAC-275 e IAC-277, obtained from previous experiments with pCABMV-CP, which contains CABMV coat protein gene, were analized. The Southern blot analysis of 14 plants from these experiments confirmed the transgene integration in 13 plants, which were propagated and mecanically inoculated with three CABMV isolates (SP, RJ, CE). Line T16 was resistant to three inoculations with all three isolates tested. Clones from this line were analyzed by RT-PCR which confirmed the transgene transcription