The mdx mouse is widely used as a model for Duchenne Muscular Dystrophy, a fatal X-linked disease caused by a deficiency of the sub-sarcolemmal protein, dystrophin. This dissertation reports characterisation of the features of dystrophy in the mdx mouse, including parameters such as electrophysiological and contractile properties of dystrophic cardiac tissue, quantitative evaluation of kyphosis throughout the mdx lifespan, and contractile properties of respiratory and paraspinal muscles. Following these characterisation studies, the efficacy of antisense oligonucleotides (AOs) to induce alternative mRNA splicing in mdx skeletal muscles (diaphragm and paraspinal muscles) was evaluated. The left atria of younger (<6 weeks) and older (>15 months) mdx mice showed consistently lower basal forces and responsiveness to increased calcium, while action potential duration was significantly shorter in young mice (3 weeks) and older mice (9 and 12 months) (P<0.05). Cardiac fibrosis increased with age in mdx atria and ventricles and was elevated in young (6-8 weeks) and old (15 months) mdx compared to control mice (P<0.01). This study provided insights into DMD cardiomyopathy, and suggested that very young or old mdx mice provide the most useful models. Mdx mice show thoracolumbar kyphosis like boys with Duchenne Muscular Dystrophy. A novel radiographic index, the Kyphotic Index (KI), was developed and showed that mdx mice are significantly more kyphotic from 9 months of age, an effect maintained until 17 months (P<0.05). At 17 months, the paraspinal and respiratory muscles (latissimus dorsi, diaphragm and intercostal muscles) are significantly weaker and more fibrotic (P<0.05). Administration of AOs at four sites within the diaphragm at 4 and 5 months of age significantly increased twitch and tetanic forces compared to sham treated mdx (P<0.05). However, no difference in collagen was evident and dystrophin was not detected, possibly due to the low concentration of AO utilised. This study suggested that AOs can provide functional improvement in treated skeletal muscles. Monthly injections with AOs into the paraspinal muscles from 2 months to 18 months of age alleviated kyphosis, without significantly altering twitch and tetanic forces of latissimus dorsi, diaphragm and intercostal muscles. There was evidence of less fibrosis in diaphragm and latissimus dorsi muscles (P<0.05) and reduced central nucleation of the latissimus dorsi and intercostal muscles (P<0.05). Again, dystrophin was not detected by immunoblot. These studies indicate that very young and old mdx mice display previously uncharacterised dystrophic features, and are useful models for testing new therapies such as AOs. Low doses of AOs were shown to be safe and efficacious for long-term use, however there remains a need for testing higher concentrations and improved delivery strategies.

Thesis (Ph.D.)--McMaster University, 2006. / Supervisor: Yingfy Li. Includes bibliographical references (leaves 151-167).

<p>Different prosthetic groups containing a trialkylstannyl- and an electrophilic group have been synthesised and labelled with the accelerator produced ⁷⁶Br (T_1/2=16 h) through oxidative bromination. The labelled prosthetic groups were conjugated to amino-containing macromolecules such as proteins and 5´-modified oligonucleotides.</p><p><i>N</i>-Succinimidyl 4-[⁷⁶Br]bromobenzoate <b>14 </b>was synthesised in 65 % radio-chemical yield and was conjugated to 5´-hexylamino-modified phosphodiester and phosphorothioate oligonucleotides in 12-19 % isolated radiochemical yield. The stability of the ⁷⁶Br-oligonucleotide-conjugates <i>in vivo</i> in rats was investigated. No degradation from the 5´-end, resulting in labelled, low molecular weight compounds was detected. Compound <b>14</b> has also been used for labelling of different proteins in 23-61% radiochemical yield.</p><p><i>N</i>-Succinimidyl-5-[⁷⁶Br]bromo-3-pyridinecarboxylate <b>17</b> and methyl-4-[⁷⁶Br]bromo-benzimidate <b>15 </b>were synthesised from the corresponding trimethylstannyl-compound in 25% and 40 % yield respectively. Compounds <b>14 </b>and <b>17</b> were conjugated to ε-Boc-octreotide in 55 and 50% isolated radiochemical yield respectively after microwave heating. Compound <b>15</b> did not react with octreotide under the conditions investigated. The two ⁷⁶Br-labelled octreotide derivatives showed different lipophilicity and different binding-properties to tissue from meningiomas.</p><p>Hyaluronic acid, a polysaccharide, was modified with tyramine and labelled by oxidative bromination using ⁷⁶Br in 10% radiochemical yield.</p><p>The generator produced ⁶⁸Ga (T_1/2=68 min) was used to label octreotide and oligonucleotides modified with the metal chelating group 1,4,7,10-tetraazacyclo-dodecane-1,4,7,10-tetraacetic acid (DOTA). ⁶⁸Ga-DOTA-octreotide was isolated in 65% radiochemical yield and a phosphorothioated ⁶⁸Ga-DOTA-oligonucleotide was isolated in 35% radio-chemical yield after 30 min synthesis time.</p><p>Compound<b> 14 </b>was reacted with 3-aminomethylbenzylamine to give compound <b>18</b>. The specific radioactivity<b> </b>of<b> 18 </b>was determined to be 36 GBq/µmol by measuring the ratio between the mass-peaks for the ⁷⁶Br and ⁷⁹Br-compounds using packed-capillary LC-MS.</p>

Different prosthetic groups containing a trialkylstannyl- and an electrophilic group have been synthesised and labelled with the accelerator produced 76Br (T1/2=16 h) through oxidative bromination. The labelled prosthetic groups were conjugated to amino-containing macromolecules such as proteins and 5´-modified oligonucleotides. N-Succinimidyl 4-[76Br]bromobenzoate <b>14 </b>was synthesised in 65 % radio-chemical yield and was conjugated to 5´-hexylamino-modified phosphodiester and phosphorothioate oligonucleotides in 12-19 % isolated radiochemical yield. The stability of the 76Br-oligonucleotide-conjugates in vivo in rats was investigated. No degradation from the 5´-end, resulting in labelled, low molecular weight compounds was detected. Compound <b>14</b> has also been used for labelling of different proteins in 23-61% radiochemical yield. N-Succinimidyl-5-[76Br]bromo-3-pyridinecarboxylate <b>17</b> and methyl-4-[76Br]bromo-benzimidate <b>15 </b>were synthesised from the corresponding trimethylstannyl-compound in 25% and 40 % yield respectively. Compounds <b>14 </b>and <b>17</b> were conjugated to ε-Boc-octreotide in 55 and 50% isolated radiochemical yield respectively after microwave heating. Compound <b>15</b> did not react with octreotide under the conditions investigated. The two 76Br-labelled octreotide derivatives showed different lipophilicity and different binding-properties to tissue from meningiomas. Hyaluronic acid, a polysaccharide, was modified with tyramine and labelled by oxidative bromination using 76Br in 10% radiochemical yield. The generator produced 68Ga (T1/2=68 min) was used to label octreotide and oligonucleotides modified with the metal chelating group 1,4,7,10-tetraazacyclo-dodecane-1,4,7,10-tetraacetic acid (DOTA). 68Ga-DOTA-octreotide was isolated in 65% radiochemical yield and a phosphorothioated 68Ga-DOTA-oligonucleotide was isolated in 35% radio-chemical yield after 30 min synthesis time. Compound<b> 14 </b>was reacted with 3-aminomethylbenzylamine to give compound <b>18</b>. The specific radioactivity<b> </b>of<b> 18 </b>was determined to be 36 GBq/µmol by measuring the ratio between the mass-peaks for the 76Br and 79Br-compounds using packed-capillary LC-MS.

Our previous studies have demonstrated that RNA can serve as a template for double-strand break (DSB) repair in the yeast Saccharomyces cerevisiae using synthetic RNA-containing oligonucleotides (oligos). Following this initial work, we show that the RNA tract of RNA-containing oligos can be copied into DNA to transfer a genetic change at the chromosomal level also in the bacterium Escherichia coli and in human cells. Exploiting the use of oligos containing ribonucleoside monophosphates (rNMPs), we developed a molecular approach to generate RNA/DNA hybrids of chosen sequence and structure at the chromosomal level in both yeast and E. coli cells. Such technique allows us to study how rNMPs present in the DNA genome of cells are tolerated by cells, what factors recognize and target rNMPs in DNA and to what extent the embedded rNMPs may alter genome integrity. Here we proved that mispaired rNMPs embedded into genomic DNA, if not removed, serve as templates for DNA synthesis during chromosomal replication and produce a genetic change. We discovered that mispaired rNMPs that are embedded in genomic DNA are not only targeted by ribonucleases H (RNases H) but also by the mismatch repair (MMR) system both in yeast and in E. coli. Our data reveal novel substrates for the MMR system, and also uncover an unpredicted competition between RNase H and MMR for the RNA/DNA mispairs.

Oligonucleotides are short fragments of DNA (10-100nt) which are of great interest because their applications in molecular biology, biomedicine and nanotechnology. As a result of their ability to base pairing, oligonucleotides can be used as primers, hybridization probes in biosensors, agents for controlling gene expression, structural material in nanotechnology or as substrates for a variety of biochemical and biophysical studies. Chemical modification of oligonucleotides as well as conjugation to different functional molecules allows for modulation of both therapeutical and biotechnological properties. This thesis is focused in the nucleic acid chemistry field and the main objective is the synthesis of modified oligonucleotides for obtaining structures with therapeutical and/or biotechnological interest. Oligonucleotides capable to form structures other than the canonical DNA double helix have received considerable attention in the last years. The ability of triplex forming oligonucleotides (TFOs) to bind specifically to certain duplex DNA regions provides a strategy for site-directed modification of genomic DNA. Besides, G-quadruplexes are four-stranded DNA structures stabilized by stacking of guanine tetrads which have been found in telomeres and some promoters and play a role in regulation of transcription and translation. In addition, they are also interesting for nanotechnological devices. In this context, the first part of the research work was addressed to synthesize parallel stranded oligonucleotide clamps carrying LNA (locked nucleic acid) residues and study the stability of the triplex formed with DNA and RNA target sequences. Secondly, a novel strategy to obtain parallel clamps using the non-templated chemical ligation of two oligonucleotides by 5’-5’ linkages was developed. For this purpose, several protocols for introduce azido and alkyne moieties in the 5’-end of different sequences were developed so that the modified DNA strands could form a parallel hairpin after their chemical ligation by click chemistry. Thirdly, a system composed of four DNA strands whose 5’ ends are covalently attached was designed to form a monomolecular parallel G-quadruplex, which was used to study the effects of some nucleobase modifications in quadruplex structure. Finally, oligonucleotide conjugates carrying Cu(II) complexes were synthesized to construct arrays of electrochemical oscillators for nanotechnology applications.

The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the spontaneous generation of an RNA World (e.g., strand-cyclization, heterogeneous backbones, non-selective ligation of activated nucleotides). The Molecular Midwife hypothesis, proposed by Hud and Anet in 2000, provides a possible solution to several problems associated with the assembly of the first nucleic acids. In this hypothesis, nucleic acid base pairs are assembled by small, planar molecules that resemble molecules which are known today to intercalate the base pairs of nucleic acid duplexes. Thus, the validity and merits of the Molecular Midwife hypothesis can be, to some extent, explored by studying the effects of intercalation on the non-covalent assembly of nucleic acids. In this thesis, I explore the role of the sugar-phosphate backbone in dictating the structure and thermodynamics of nucleic acid intercalation by using 2′,5′-linked RNA intercalation as a model system of non-natural nucleic acid intercalation. The solution structure of an intercalator-bound 2′,5′ RNA duplex reveals structural and thermodynamic aspects of intercalation that provide insight into the origin of the nearest-neighbor exclusion principle, a principle that is uniformly obeyed upon the intercalation of natural (i.e. 3′,5′-linked) RNA and DNA. I also demonstrate the ability of intercalator-mediated assembly to circumvent the strand-cyclization problem, a problem that otherwise greatly limits the polymerization of short oligonucleotides into long polymers. Together, the data presented in this thesis illustrate the important role that the nucleic acid backbone plays in governing the thermodynamics of intercalation, and provide support for the proposed role of intercalator-mediated assembly in the prebiotic formation of nucleic acids.

The discovery of RNA interference and the increasing understanding of disease genetics have created a new class of potential therapeutics based on oligonucleotides. This therapeutic class includes antisense molecules, small interfering RNA (siRNA), and microRNA modulators such as antagomirs (antisense directed against microRNA) and microRNA mimics, all of which function by altering gene expression at the translational level. While these molecules have the promise of treating a host of diseases from neurological disorders to cancer, a major hurdle is their inability to enter cells on their own, where they may render therapeutic effect. Nanotechnology is the engineering of materials at the nanometer scale and has gained significant interest for nucleic acid delivery due to its biologically relevant length-scale and amenability to multifunctionality. While a number of nanoparticle vehicles have shown promise for oligonucleotide delivery, there remains a lack of understanding of how nanoparticle coating and size affect these delivery processes. This dissertation seeks to elucidate some of these factors by evaluating oligonucleotide delivery efficiencies of a panel of iron oxide nanoparticles with varying cationic coatings and sizes. A panel of uniformly-sized nanoparticles was prepared with surface coatings comprised of various amine groups representing high and low pKas. A separate panel of nanoparticles with sizes of 40, 80, 150, and 200 nm but with the same cationic coating was also prepared. Results indicated that both nanoparticle surface coating and nanoparticle hydrodynamic size affect transfection efficiency. Specific particle coatings and sizes were identified that gave superior performance. The intracellular fate of iron oxide nanoparticles was also tracked by electron microscopy and suggests that they function via the proton sponge effect. The research presented in this dissertation may aid in the rational design of improved nanoparticle delivery vectors for nucleic acid-based therapy.

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Strukturaufklärung gehört zu den wichtigsten Gebieten der Grundlagenforschung, da sie direkte Einblicke in biologische Systeme und ihre Mechanismen liefert. Der NMR Spektroskopie kommt dabei eine besondere Bedeutung zu, denn sie ermöglicht Forschung unter physiologischen Bedingungen. Dementsprechend ist die Entwicklung neuer Techniken zur Verbesserung dieser Methode weiterhin ein zentrales Forschungsgebiet. Paramagnetische Markierung von Biomolekülen ermöglicht die Bestimmung von NMR Parametern, wie z.B. residuale dipolare Restkopplungen (RDCs) oder Pseudokontaktverschiebungen (PCSs), die für die Strukturaufklärung wertvolle Winkel- und Abstandsinformationen über das Zielmolekül beinhalten. In diesem Zusammenhang wurden Lanthanoidionen-koordinierende Tags entwickelt und erfolgreich an Proteinen angebracht. Durch die paramagnetischen Eigenschaften der Lanthanoidionen wird eine partielle Ausrichtung des Zielmoleküls im Magnetfeld des NMR Spektrometers induziert und somit das Messen residualer dipolarer Kopplungen ermöglicht. Zusätzlich werden die NMR Signale durch eine Dipol-Dipol-Wechselwirkung zwischen dem Lanthanoidion und den Kernen verschoben (PCS). In der konventionellen NMR Spektroskopie werden diese Effekte, aufgrund der Brownschen Molekularbewegung und dem Fehlen eines Metallions, nicht beobachtet. In der Fachliteratur ist ein Transfer dieser Methode auf Oligonukleotide nicht bekannt, obwohl DNA und RNA zu den wichtigsten Biomolekülen überhaupt zählen. In dieser Arbeit wurde mit Hilfe des kürzlich entwickelten Cys-Ph-TAHA Tags ein Protokoll zur Bestimmung von paramagnetischen Effekten in der DNA entwickelt. Dafür wurde eine modifizierte Nukleobase synthetisiert, die eine passende Bindungsstelle für den Tag aufweist. Mit der neu entwickelten Methode wurden zwei paramagnetische und eine diamagnetische Referenzprobe hergestellt. Mittels hochauflösender NMR Spektroskopie konnten paramagnetisch-induzierte PCSs und RDCs gemessen werden. Die Auswertung zeigte eine hohe Qualität der gemessenen PCSs in beiden paramagnetischen Proben. Die RDCs wiesen einen signifikanten Fehler auf. Die in der NMR Spektroskopie übliche Isotopenmarkierung (13C/15N) ist bei im DNA-Synthesizer hergestellten Oligonukleotiden auf Grund der teuren Ausgangsmaterialien nicht möglich, sodass die hergestellten NMR Proben eine natürliche Isotopenhäufigkeit aufwiesen. In den NMR Spektren zur Bestimmung der RDCs ist damit das Verhältnis von Signal-zu-Rausch relativ niedrig, was zusammen mit der paramagnetischen Relaxationsverstärkung zu einem größeren Messfehler führt. Dennoch konnten die erhaltenen paramagnetischen Daten mit einem Ensemblemodell beschrieben werden. In der vorliegenden Arbeit wurde die Methode der paramagnetischen Markierung erfolgreich auf die Stoffklasse der Oligonukleotide übertragen. Dabei wurde ein reproduzierbares Protokoll entwickelt, mit dem eine Bindungsstelle in einen DNA Strang eingebaut und das Zielmolekül anschließend mit dem Cys-Ph-TAHA Tag markiert wurde. Die erfolgreiche Anwendung der Methode konnte durch die erhaltenen paramagnetischen Messwerte von hoher Qualität verifiziert werden.