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Photo-Activatable Oligonucleotides for Protein Modification and Surface Immobilization

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Photo-Activatable Oligonucleotides for Protein Modification and Surface Immobilization Photo-Activatable Oligonucleotides for Protein Modification and Surface Immobilization Zur Erlangung des akademischen Grades eines DOKTORS DER NATURWISSENSCHAFTEN (Dr. rer. nat.) von der KIT-Fakultät für Chemie und Biowissenschaften des Karlsruher Instituts für Technologie (KIT) genehmigte DISSERTATION von Dipl.-Chem. Antonina Francevna Kerbs aus Almaty, Kasachstan KIT-Dekan: Prof. Dr. Willem Klopper Referent: Priv. Doz. Dr. Ljiljana Fruk Korreferent: Prof. Dr. Christopher Barner-Kowollik Tag der mündlichen Prüfung: 21.10.2016 This document is licensed under the Creative Commons Attribution – Share Alike 3.0 DE License (CC BY-SA 3.0 DE): http://creativecommons.org/licenses/by-sa/3.0/de/ Ich erkläre hiermit wahrheitsgemäß, dass die vorliegende Doktorarbeit im Rahmen der Betreuung durch Priv. Doz. Dr. Ljiljana Fruk selbständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel verwendet sowie alle wörtlich oder inhaltlich übernommenen Stellen als solche kenntlich gemacht wurden. Des Weiteren erkläre ich, dass ich mich derzeit in keinem laufenden Promotionsverfahren befinde, keine vorausgegangenen Promotionsversuche unternommen habe sowie die Satzung zur Sicherung guter wissenschaftlicher Praxis beachtet habe. Zusätzlich erkläre ich, dass die elektronische Version der Arbeit mit der schriftlichen übereinstimmt und dass die Primärdaten gemäß Abs. A (6) der Regeln zur Sicherung guter wissenschaftlicher Praxis des KIT beim Institut für Biologische Grenzflächen 1 zur Archivierung abgegeben wurden. Karlsruhe, den 03.11.2016 Antonina Kerbs Die vorliegende Arbeit wurde von Oktober 2012 bis Juni 2016 unter der Anleitung von Priv. Doz. Dr. Ljiljana Fruk am Karlsruher Institut für Technologie − Universitäts- und Großforschungsbereich angefertigt. Für meine Familie Abstract The ability to synthesize and modify short DNA sequences has helped to advance numerous research fields such as genomics, molecular biology, molecular engineering and nanobiotechnology. DNA has ceased to be used only as a genetic code carrier, but became also an important structural and functional element for the assembly of nanostructures, in design of the antisense therapeutics and for development of the microarray and biosensors technology. Various strategies with different extent of success have been used to introduce number of functional groups to DNA and in such way, enable both the further biomolecular studies and the surface immobilization. Within this thesis, covalent coupling strategies, namely light-induced Diels-Alder cycloaddition and nitrile imine-mediated tetrazole-ene cycloaddition (NITEC) were employed for attachment of DNA to different molecules and surfaces in a temporally and spatially controlled manner. The functionalization of DNA with photo-activatable groups; 2,5- dimethylbenzophenone derivative (PE1), 2-methoxy-6-methylbenzaldehyde derivative (PE2) for Diels-Alder cycloaddition, and tetrazole derivative (Tz) for NITEC was achieved utilizing phosphoramidite, H-phosphonate and amide coupling methodologies. In order to determine the suitability of the light-induced reactions for further DNA modification, detailed kinetic studies using functionalized DNAs were performed, indicating that photoenol containing DNA (PE2- DNA) is the most efficient reacting agent for further applications in protein conjugation and surface structuring. This was additionally confirmed by successful light-induced conjugation of PE2-DNA to horseradish peroxidase (HRP), which resulted in HRP-DNA conjugate with preserved inherent functions of both the DNA and protein. Finally, light-induced immobilization of DNA onto glass surface was performed in order to establish mild, simple and easily controllable route to DNA surface structuring. To achieve that, two different strategies, which differ in the level of resolution and versatility of the achieved pattern, were employed for DNA patterning: one based on the use of the shadow mask and the other on Direct Laser Writing (DLW). DLW enabled design of the DNA line pattern with resolution of 600 nm, surpassing other commercially available strategies and also allowing for fast and simple structuring of multiple DNA sequences and subsequent immobilization of complementary DNA and DNA-protein conjugates for future protein array applications. This was the first demonstration of the use of light-induced chemistry and direct laser writing for precise patterning of DNA sequences on the surface, paving the way for advanced applications in design of biomolecular arrays and new functional materials. Zusammenfassung Die Fähigkeit kurze DNA Sequenzen zu synthetisieren und zu modifizieren, hat entscheidende Weiterentwicklungen in Forschungsbereichen wie der Genomik, Molekularbiologie, Molekulartechnik und Nanobiotechnologie ermöglicht. Die DNA ist nicht mehr nur ein Träger der Erbinformation, sondern ist zu einem wichtigen struktur- und funktionsgebenden Element für die Nanostrukturierung, die Entwicklung der Antisense-Therapeutika und DNA Chip-Technologie sowie der Biosensorik geworden. Diverse Strategien wurden mit unterschiedlichem Erfolg zur Einführung zahlreicher funktioneller Gruppen verwendet, um weitere biomolekulare Studien und Oberflächenimmobilisierung zu ermöglichen. Im Rahmen dieser Arbeit wurden kovalente Kupplungsstrategien wie die lichtinduzierte Diels-Alder Cycloaddition und die lichtinduzierte Nitrilimin-vermittelte Tetrazol-En Cycloaddition (NITEC) verwendet, um DNA zeitlich und räumlich kontrolliert an verschiedene Moleküle und Oberflächen anzubinden. Die DNA-Funktionalisierung mit lichtaktivierbaren Molekülen wie den 2,5-Dimethylbenzophenon- (PE1) und 2-Methoxy-6-methylbenzaldehyd- (PE2) Derivaten für die Diels-Alder-Reaktion und dem Tetrazol-Derivat (Tz) für die NITEC wurde mittels Phosphoramidit- und H-Phosphonat-Methoden sowie der Amidkupplung realisiert. Um die Eignung der lichtinduzierten Reaktionen für die weitere DNA-Modifikation zu überprüfen, wurden detaillierte kinetische Untersuchungen von Reaktionen funktionalisierter DNA durchgeführt und es konnte festgestellt werden, dass PE2-modifizierte DNA den effizientesten Reaktionspartner für weitere Anwendungen wie die Proteinkonjugation oder die Oberflächenstrukturierung darstellt. Dies wurde zusätzlich durch erfolgreiche lichtinduzierte Konjugation von PE2-DNA mit der Meerrettichperoxidase (HRP) bestätigt. Die natürlichen Funktionen der DNA und des Enzyms blieben in dem gebildeten HRP-DNA-Konjugat erhalten. Im letzten Teil der Arbeit wurde die lichtinduzierte Immobilisierung von DNA auf Silizium- und Glasoberflächen durchgeführt, um somit eine milde, einfache und leicht- kontrollierbare Route zur DNA-Oberflächenstrukturierung zu etablieren. Hierzu wurden zwei verschiedene Strategien verfolgt, die zum einen auf dem Einsatz einer Schattenmaske, zum anderen auf dem Direkten Laserschreiben (DLW) basieren. Die beiden Methoden unterscheiden sich hinsichtlich des Auflösungsvermögens und der Vielseitigkeit der erreichbaren Muster. Mittels DLW konnte ein Linienmuster mit einer Auflösung von 600 nm geschrieben werden, was andere kommerziell erhältliche Strategien übertrifft. Somit konnte eine schnelle und einfache Strukturierung der Oberfläche mit mehreren DNA-Sequenzen sowie die anschließende Immobilisierung der komplementären DNA und von Protein-DNA Konjugaten erreicht werden, was in der Zukunft in der Protein-Chip-Technologie Anwendung finden könnte. Zum ersten Mal wurde die Anwendung der lichtinduzierten Diels-Alder Reaktion in Verbindung mit direktem Laserschreiben für eine präzise Strukturierung von DNA-Sequenzen auf der Oberfläche demonstriert und somit der Weg für weitere Anwendungen im Bereich der Entwicklung biomolekularer Chips und neuer funktionaler Materialien geebnet. Publications Arising from this Thesis Clickable Tyrosine Binding Bifunctional Linkers for Preparation of DNA-Protein Conjugates D. Bauer, I. Ahmed, A. Vigovskaya, Lj. Fruk, Bioconjugate Chem. 2013, 1094-1101. A Self-Reporting Tetrazole-Based Linker for the Biofunctionalization of Gold Nanorods L. Stolzer, A. Vigovskaya, C. Barner-Kowollik, L. Fruk, Chem. Eur. J. 2015, 21, 14309- 14313. Photo-Induced Chemistry for the Design of Oligonucleotide Conjugates and Surfaces A. Vigovskaya, D. Abt, I. Ahmed, C. M. Niemeyer, C. Barner-Kowollik, L. Fruk, J. Mater. Chem. B 2016, 4, 442-449. DNA Surface Structuring using Direct Laser Writing and Light-Induced Cycloadditions A. Kerbs, P. Mueller, M. Kaupp, I. Ahmed, A. S. Quick, D. Abt, M. Wegener, C. M. Niemeyer, C. Barner-Kowollik, L. Fruk, in preparation. Contents 1 Introduction ........................................................................................................................ 1 1.1 DNA Synthesis and Modification ................................................................................ 1 1.2 Oligonucleotide Synthesis ........................................................................................... 4 1.2.1 Phosphoramidite (phosphite triester) Method ...................................................... 4 1.2.2 H-phosphonate Method for Oligonucleotide Synthesis ....................................... 7 1.2.3 Phosphate Triester Method for Oligonucleotide Synthesis .................................. 9 1.3 Modification of Oligonucleotides with Various Functional Moieties ....................... 10 1.3.1 Oligonucleotide Modification on the Solid Support .......................................... 10 1.3.2 In-solution Modification of Oligonucleotides ...................................................
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