Dysfunctional or over and under expressed enzymes play a crucial role in a variety of diseases. A tool that can identify dis-regulated enzymes in individual patients would be beneficial and would allow personalised treatment. For this purpose, a 10,000 membered ‘spit-and-mix’ PNA-encoded peptide library with a cell penetrating peptide was synthesised and interrogated with K562 cell lysate and intact K562 cells. This allowed the specific enzyme activity pattern for ABL tyrosine kinase from both inside a cell and a lysate to be obtained. Hybridisation of this library with a DNA-microarray resulted in bio-fouling by the cell lysate, thereby preventing analysis of the phosphorylation pattern. To allow extraction and purification of the peptide library from the cell lysates, a His-tag was incorporated into the library, and enabled successful library analysis. In addition to this 10,000 member library, a focused 100 PNA-encoded peptide library was synthesised. The library included peptide sequences known to be phosphorylated by specific tyrosine kinases deregulated in acute lymphoblastic leukaemia (ALL) with a PNA-tag complementary to a DNA microarray. Different ligation methods to conjugate the peptides to PNA-tags were screened – this included amide coupling, copper catalysed azide–alkyne cycloaddition, strain promoted azide–alkyne cycloaddition and Diels–Alder cycloaddition. The inverse electron demand Diels–Alder cycloaddition between a tetrazine and norbornene was chosen as the preferred ligation method, and the reaction conditions optimised. To purify the library from cell lysate, a His-tag was again coupled to each member using the strain promoted azide–alkyne cycloaddition. To test the tetrazine ligation, fluorescence in situ hybridisation (FISH) was used in cells, whereby a fluorophore was ligated onto a tetrazine–conjugated PNA probe. This was hybridised onto an mRNA in fixed cells. Results indicated that the ligation needed further optimisation.

Submitted by Amanda Silva (amanda.osilva2@ufpe.br) on 2015-04-08T12:47:45Z No. of bitstreams: 2 dissertação_Luiza Lima_VERSÃO_FINAL.pdf: 1561576 bytes, checksum: 9c995164c6acc839c29d5365b9fb4cc7 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-04-08T12:47:45Z (GMT). No. of bitstreams: 2 dissertação_Luiza Lima_VERSÃO_FINAL.pdf: 1561576 bytes, checksum: 9c995164c6acc839c29d5365b9fb4cc7 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2012 / CAPES / Este trabalho teve como objetivo o desenvolvimento de um método histoquimiluminescente para avaliação quantitativa da expressão de carboidratos em tumores cutâneos utilizando lectinas conjugadas a éster de acridina (EA). As lectinas Con A, PNA e UEA-I foram conjugadas a EA. A atividade hemaglutinante da lectina-EA foi avaliada e a quimiluminescência quantificada e expressa em Unidades Relativas de Luz (URL). Biópsias de pele normal e de tumores cutâneos (ceratose actínica, ceratoacantoma, carcinoma espinocelular e basocelular) foram incubadas com o conjugado lectina-EA. A emissão de fótons foi quantificada e correlacionada com a marcação de tecidos normais e transformados. Os tumores cutâneos apresentaram uma maior expressão de resíduos de Gal-β(1-3)-GalNAc e uma menor expressão de α-Dglicose/ manose e α-L-fucose, evidenciados pelas diferenças nos valores de URL. O método histoquimiluminescente, utilizando lectinas conjugadas a éster de acridina, permitiu a avaliação quantitativa direta da expressão de carboidratos em neoplasias de pele, combinando a especificidade da interação lectina-carboidrato e a sensibilidade dos ensaios quimiluminescentes, contribuindo para eliminar a subjetividade da avaliação histoquímica convencional de carboidratos.

One of the major challenges in cancer treatment is delivering high enough doses of active substance specifically to cancer cells without accumulation in healthy organs. Pretargeting has emerged as a potential solution, where the delivery of a cancer recognizing (primary) agent and a cancer killing (secondary) agent are separated. Pretargeted cancer therapy utilizing PNA probes has proved to be a promising approach to selectively deliver toxic payloads to cancer cells while minimizing accumulation in healthy organs. The aim of this project was to develop a new set of secondary PNA probes specifically designed for PNA pretargeted delivery of cytotoxic drugs. A HER2-specific Affibody molecule, ZHER2:2891-SR-H6, was recombinantly produced in E. coli before being conjugated to a primary PNA hybridization probe, HP9, through sortase A-mediated ligation, to produce the primary agent, ZHER2:2891-SR-HP9. Circular dichroism (CD) spectroscopy confirmed the stability of the constructs with high melting temperatures of 71.2 and 73.7 °C. Surface plasmon resonance (SPR) analysis demonstrated high binding affinity to HER2, slightly affected by PNA conjugation. Three new secondary PNA hybridization probes were designed, differing mainly in prevalence and position of a hydrophilic PEG molecule. The probes were produced by solid phase peptide synthesis and conjugated to the cytotoxic drug DM1 through maleimide-cysteine coupling. Analytical RP-HPLC evaluation revealed a slightly higher apparent hydrophobicity for the probe with PEG in the main chain. All three secondary probes displayed high affinity to the primary probe with KD values between 498–505 pM. In vitro cytotoxicity studies on HER2-overexpressing cells demonstrated comparable potent cytotoxic activity for pre-incubated primary and secondary probes with IC50 values of 10–14 nM. These results indicate the successful development of three PNA-drug conjugates for pretargeted delivery of cytotoxic drugs.

Snow/ice events are indeed a rare occurrence in the southeast United States. As a result, residents of the Southeast often exemplify a passive attitude towards winter weather and are often unprepared when it strikes. This study analyzed every recorded winter weather event that struck the Southeast (Mississippi, Alabama, Georgia) from the winter season of 1961-'62 through 2000-'01 from both a spatial and temporal standpoint. Through the results of this study, it was evident that Georgia saw the most overall winter weather events and January seemed to be the most productive month overall. This study also analyzed teleconnection (ENSO, PNA, NAO, AO) indices per study period season in order to deduce correlations with active/inactive Southeast winters. Through statistical analyses, correlations were deemed insignificant.

HINTERGRUND: Der selektive Tyrosinkinase-Inhibitor Imatinib inhibiert das Wachstum von bcr/abl positiven Zellen und stellt somit eine neue Therapieoption in der Behandlung der CML dar. Mittlerweile sind verschiedene Mutationen innerhalb der abl Sequenz beschrieben worden, die eine adäquate Imatinibbindung verhindern und zu einer zellulären Resistenz der CML Zellen führen. METHODE: Wir untersuchten 69 Patienten unter Behandlung mit Imatinib im Rahmen von laufenden klinischen Studien. Bei Studieneinschluss waren 37 Patienten in chronischer Phase, 21 Patienten in akzelerierter Phase und 11 Patienten in Blastenkrise. Mittels Real-time PCR wurden bcr/abl, WT1, MDR1 und AGP RNA Traskripte aus peripheren Leukozyten quantifiziert. AGP Proteinlevel wurden turbidimetrisch bestimmt. Ausserdem entwickelten wir eine neue, hochsensitive Technik zur Detektion bekannter Mutationen innerhalb der bcr/abl Domäne, indem wir das DNA-Clamping mittels Peptidnukleinsäure (PNA) mit einem Hybridisationssonden-Assay kombinierten. ERGEBNISSE: 1. Unsere Resultate bestätigen die hämatologische Effizienz von Imatinib in Übereinstimmung mit bereits publizierten Daten. 2. Eine komplette molekulare Remission konnte bei einem Patienten erzielt werden. 3. Wir konnten die bcr/abl Mutationen Thr315Ile, Glu255Lys and Tyr253His mit hoher Sensivität nachweisen. In einem Falle konnte die Gly255Lys Mutation vor der Behandlung detektiert werden. SCHLUSSFOLGERUNG: Bcr/abl und WT1 mRNA stellen in der Behandlung der CML Verlaufs- und Prognosemarker dar. Ein Zusammenhang zwischen MDR1 mRNA bzw. AGP mRNA und einer Resistenzentwicklung gegenüber Imatinib konnte nicht bestätigt werden. Durch den PNA-Clamping Assay konnten präexistente und sich entwickelnde bcr/abl Mutationen mit ungünstiger Prognose sicher und frühzeitig detektiert werden. Diese Tatsache ermöglicht eventuell eine Risikostratifizierung der CML und könnte als Model zum individuellen molekularen Monitoring und zur therapeutischen Strategie in anderen malignen Erkrankungen dienen. / BACKROUND: The selective tyrosine kinase inhibitor imatinib inhibits growth of bcr/abl positive cells and, thus, has become a novel therapeutic option for the treatment of Ph+ leukaemic patients. Various mutations within the abl sequence have been described that prevent adequate imatinib binding to bcr/abl resulting in cellular resistance of CML cells. METHODS: We investigated 69 CML patients under treatment with imatinib as part of an ongoing clinical trial. At recruitment 37 patients were in chronic phase, 21 patients in accelerated phase and 11 patients in blast crisis. Bcr/abl, WT1, MDR1and AGP RNA transcripts were quantified in peripheral leucocytes by real time PCR. AGP protein levels in plasma were measured by turbidimetric analysis. By combining peptide nucleic acid (PNA) based DNA clamping with a fluorescence hybridisation probe assay we developed a new and highly sensitive technique for the detection of known mutations within the bcr/abl kinase domain. RESULTS: 1. Our results demonstrate efficacy of imatinib on the haematological level in accordance with previously published data. 2. Complete molecular remission could be achieved in one patient. 3. We could effectively enhance the detection sensitivity (0,2%) for the BCR/ABL mutations Thr315Ile, Glu255Lys and Tyr253His. In one case the Gly255Lys mutation was detectable before treatment. CONCLUSION: Bcr/abl and WT1 mRNA are predictive marker in the treatment of CML. Our investigation could not confirm any relation between MDR1 mRNA nor AGP mRNA and a resistance to imatinib. By the PNA clamping assay pre-existing and evolving bcr/abl mutations associated with an unfavorable prognosis could be safely detected. This may facilitate risk stratification in CML and may serve as a model for individualized molecular monitoring and therapeutic strategies in other malignant diseases.

Nukleinsäuren und Peptide erlauben es, Kontrolle über molekulare Prozesse auszuüben. In dieser Arbeit werden strukturgebende Elemente wie Coiled-Coil-Peptide oder PNA∙DNA-Strukturen genutzt, um Rezeptoren auf lebenden Zellen zu markieren und in ihrem Verhalten zu modulieren, oder cytosolische Proteine in ihrem Bindungsverhalten zu steuern. Im ersten Konzept wird die Interaktion des Coiled-Coil-Paars K3/E3 genutzt, um eine Transferreaktion, in welcher eine PNA-Sequenz vom K3-Donor auf den E3-Akzeptor übertragen wird, zu induzieren. Durch die Fusion des Akzeptorpeptids mit einem Rezeptor werden kovalente PNA-Rezeptorkonjugate auf der Oberfläche lebender Zellen geschaffen. Die Reaktion zwischen Thiol und Thioester erlaubt dabei einen schnellen Transfer. So wurden Rezeptoren aus der Familie der GPCR sowie der EGFR mit einem PNA-Strang versehen und durch fluoreszente PNA oder DNA selektiv markiert. Zusätzlich wurden verzweigte DNA-Architekturen mit mehreren Fluorophoren genutzt, um die Helligkeit der Markierung quantitativ zu erhöhen. Die PNA-EGFR-Konjugate wurden durch eine zwei Rezeptoren verbrückende Cy3-DNA adressiert und so zeitgleich markiert und dimerisiert. Dadurch wurde die Rezeptoraktivität gesteigert, was über Western Blot-, Immunofluoreszenz- und Fluoreszenzmikroskopieanalyse belegt wurde. In weiteren Ansätzen wurden Coiled-Coil-Systeme genutzt, um i) parallel zwei verschiedene Akzeptorpeptide mit verschiedenen Fluorophoren zu markieren und ii) Coiled-Coil-Peptide schaltbar zu machen. Durch die asymmetrische Verlängerung von K3/E3-Paaren mit Coiled-Coil-Sequenzen kann die Interaktion der Peptide an und aus geschaltet werden. Dies wurde sowohl in einem Fluoreszenzassay als auch in einer direkten Anwendung an der Syk-Kinase demonstriert. Die Liganden der Kinase wurden an den schaltbaren Peptiden angebracht und so die Affinität zur Syk-Kinase kontrolliert. / Nucleic acids and peptides can be used to obtain control over molecular processes within living cells. In this work, structural elements as coiled-coil peptides or PNA∙DNA-structures were used to label and modulate receptor behavior on living cells and to control ligand binding of cytosolic proteins. For the first concept the K3/E3-coiled-coil peptide pair was used to establish a proximity-guided, covalent transfer of a PNA strand from a K3-donor peptide onto the complementary E3-acceptor peptide. By fusion of the acceptor peptide to a receptor, PNA-receptor-conjugates were generated selectively on living cells. The native chemical ligation type of reaction allowed a fast PNA-transfer within minutes. Receptors from the family of GPCRs and the EGFR were tagged with a PNA-sequence and subsequently labeled by the addition of a fluorescent DNA or PNA. By recruiting branched DNA architectures which were decorated with several fluorophores, the total brightness of the labeling was increased quantitatively. A twice complementary Cy3-DNA was used to simultaneously label and dimerize the EGFR. Thereby, an artificially induced increase in receptor activity could be achieved, which was shown in Western Blot and immunofluorescence analysis as well as in fluorescence microscopy. In two other approaches coiled-coil peptides were used to i) label two different acceptor peptides simultaneously with two different dyes and ii) introduce coiled-coil peptides as part of a dynamic switchable system. Using an asymmetric coiled-coil elongation on the K3/E3 pair the interaction of both can be turned on and off. This was demonstrated in a fluorescence assay and applied to the Syk kinase, were Syk ligands were attached to the switchable peptides. Those ligands were changed from a bi- to a monovalent presentation status and thus the affinity of the Syk kinase towards its ligands can be controlled.

Die Vermehrung des Influenza A Virus umfasst, neben anderen wichtigen Schritten, die Transkrption der viralen mRNA und die ribosomale Translation der viralen Proteine. Mit großem Aufwand wurde bereits an der Entwicklung von Methoden zur Untersuchung des zeitlichen Verlaufs der Synthese viraler mRNA während des Vermehrungszyklusses in der Wirtszelle geforscht. In der vorliegenden Arbeit wurden sequenzspezifische FIT-PNA-Sonden, welche einen einzelnen, als künstliche fluoreszente Nukleobase dienenden Interkalator tragen, auf die quantitative RT-PCR sowie die Lebendzellmikroskopie angewandt. Die FIT-PNA-Sonden bieten dabei eine hohe Sensitivität und eine enorme Zielspezifität unter nichtstringenten Hybridisierungsbedingungen. Im Speziellen wurden FIT-PNA Sonden mit Sequenzspezifität zur mRNA der Neuraminidase und des Matrixproteins 1 entworfen und untersucht. Die somit erhaltenen Ergebnisse besitzen eine hohe biologische Relevanz und weisen diese Sonden als vielversprechende Methodik in der Virologie und der Zellbiologie aus. Ihre Anwendung konnte bereits auf das Vesikular Stomatitis Virus ausgeweitet werden. Die Kombination aus biologischer Expertise mit modernen Proteomstudien und detaillierten statistischen Analysen ermöglichte einen systemumfassenden Blick auf die durch eine Infektion bedingten Auswirkungen auf die Wirtszelle. Die Markierung von Aminosäuren mit stabilen Isotopen in Zellkultur wurde hierfür benutzt. Es wurden Proben zu verschiedene Zeitpunkten im Infektionszyklus in die Untersuchungen einbezogen, um zeitaufgelöste Detailstudien der zellulären Proteinbiosynthese und Degradation durchzuführen. / Replication of the influenza A virus involves, amongst other critical steps, the transcription of viral mRNA and ribosomal translation of viral proteins. Significant efforts have been devoted to the development of methods that allow the investigation of viral mRNA progression during the replication cycle inside the host cell. In the present thesis sequence specific FIT-PNA probes which contain a single intercalator serving as artificial fluorescent nucleobase were introduced for quantitative RT-PCR and live cell imaging. FIT-PNAs provide for both high sensitivity and high target specificity at nonstringent hybridisation conditions (where both matched and mismatched probetarget complexes coexist). In particular, FIT-PNAs specific to the neuraminidase and matrix protein 1 were successfully designed and examined. The obtained results are of high biological importance and suggest the FIT-PNA technique as promising tool in the field of virology and cell biology as this approach was readily applied to Vesicular Stomatitis Virus as well. By combining biological expertise with modern high throughput quantitative proteomics and detailed statistical analysis a system wide view of the effects and dynamics of the early H1N1 infection on the cell proteome was generated. Stable isotope labelling of amino acids in cell culture (SILAC) was employed to globally track changes in gene expression at the protein level. Furthermore, samples at various time points post infection enabling a more detailed timeresolved analysis of host cell protein biosynthesis and degradation during the infection cycle were included. As a result the specific expression characteristics of single genes and functional gene subsets in response to viral infection were bioinformatically analysed.

No description available.

Les Acides Peptido-nucléiques (PNA) sont des analogues synthétiques d’oligonucleotides naturels, ils sont constitués d’une répétition d’unités N-(2-aminoethyl)-glycine reliées par une liaison peptidique. Leur stabilité chimique et biologique en font une alternative intéressante pour les assemblages supramoléculaires ayant une application biologique tels que l’encodage de chimiothèques combinatoires de petites molécules et des réactions engendrées par hybridation. Ce travail de thèse avait pour objectif la synthèse d’acides peptido-nucléiques modifiés dans le but d’améliorer leur hybridation, leurs propriétés physico-chimiques ainsi que la synthèse des chimiothèques combinatoires. / Peptide nucleic acids (PNA) are structural analogs of natural nucleic acids composed of repeating units of N-(2-aminoethyl)-glycine residues linked by peptide bonds. Their chemical and biological stability makes them very suitable for supramolecular assemblies with biological applications such as encoding combinatorial libraries of small molecules and for performing templated reactions. This phD project aimed at the synthesis of modified peptide nucleic acids to enhance their physicochemical and hybridization properties as well as for construction of combinatorial libraries.

Résumé confidentiel / Résumé confidentiel