Functional poly(phosphoester)s : the olefin metathesis route

Diese Dissertation zeigt zum ersten Mal den Ansatz gesättigte und ungesättigte Poly(Phosphorester) herzustellen, deren Polymergerüst und Seitenketten durch präzises Anbring-en von funktionellen und/oder solubilisierenden Gruppen modifiziert werden können. Durch Kombinieren der Vorteile der Olefinmetathese mit der Vielseitigkeit der Phos-phorchemie, eröffnet dieser variable Ansatz den Zugang zu einer neuen Klasse ungesättigter Poly-phosphate. Die zu Grunde liegende Idee ist das maßgeschneiderte Anpassen der Architektur und der Mikrostruktur dieser Polymere. Lineare, verzweigte, markierte und telechele Poly(Phosphorester) können in großem Maßstab mit hohen Funktionalisierungsgrad hergestellt werden.rnEiner der größten Vorteile dieses Ansatzes ist es, das Polymerrückrat modifizieren zu können, was weder bei der Ringöffnungs- noch bei klassischen Polymerisationen möglich ist, bei denen nur eine limitierte Anzahl an Monomeren existieren.rnDie Eigenschaften des Phosphors werden in neue Polymerarchitekturen übertragen, was von Nutzen für flammenhemmenden Materialen und Anwendung bei Gewebetherapeutika ist. Diese Doktorarbeit führt auch einzigartige Poly(Phosphorester) ein, welche im Feld der Op-toelektronik als Sauerstofffänger eingesetzten werden können. Die beschriebenen Synthese-vorschriften können einfach in größeren Maßstab durchgeführt werden und sind vielversprechend für industrielle Anwendungen, da ungesättigte Polyester einen sehr wichtigen Markt repräsentieren.

Expanding the scope of poly(ethylene glycol)s for bioconjugation to squaric acid-mediated PEGylation and pH-sensitivity

Poly(ethylene glycol) (PEG) is used in a broad range of applications due to its unique combination of properties and is approved use in formulations for body-care products, edibles and medicine. This thesis aims at the synthesis and characterization of novel heterofunctional PEG structures and the establishment of diethyl squarate as a suitable linker for the covalent attachment to proteins. Chapter 1 is an introduction on the properties and applications of PEG as well as the fascinating chemistry of squaric acid derivatives. In Chapter 1.1, the synthesis and properties of PEG are described, and the versatile applications of PEG derivatives in everyday products are emphasized with a focus on PEG-based pharmaceuticals and nonionic surfactants. This chapter is written in German, as it was published in the German Journal Chemie in unserer Zeit. Chapter 1.2 deals with PEGs major drawbacks, its non-biodegradability, which impedes parenteral administration of PEG conjugates with polyethers exceeding the renal excretion limit, although these would improve blood circulation times and passive tumor targeting. This section gives a comprehensive overview of the cleavable groups that have been implemented in the polyether backbone to tackle this issue as well as the synthetic strategies employed to accomplish this task. Chapter 1.3 briefly summarizes the chemical properties of alkyl squarates and the advantages in protein conjugation chemistry that can be taken from its use as a coupling agent. In Chapter 2, the application of diethyl squarate as a coupling agent in the PEGylation of proteins is illustrated. Chapter 2.1 describes the straightforward synthesis and characterization of squaric acid ethyl ester amido PEGs with terminal hydroxyl functions or methoxy groups. The reactivity and selectivity of theses activated PEGs are explored in kinetic studies on the reactions with different lysine and other amino acid derivatives, followed by 1H NMR spectroscopy. Further, the efficient attachment of the novel PEGs to a model protein, i.e., bovine serum albumin (BSA), demonstrates the usefulness of the new linker for the PEGylation with heterofunctional PEGs. In Chapter 2.3 initial studies on the biocompatibility of polyether/BSA conjugates synthesized by the squaric acid mediated PEGylation are presented. No cytotoxic effects on human umbilical vein endothelial cells exposed to various concentrations of the conjugates were observed in a WST-1 assay. A cell adhesion molecule - enzyme immunosorbent assay did not reveal the expression of E-selectin or ICAM-1, cell adhesion molecules involved in inflammation processes. The focus of Chapter 3 lies on the syntheses of novel heterofunctional PEG structures which are suitable candidates for the squaric acid mediated PEGylation and exhibit superior features compared to established PEGs applied in bioconjugation. Chapter 3.1 describes the synthetic route to well-defined, linear heterobifunctional PEGs carrying a single acid-sensitive moiety either at the initiation site or at a tunable position in the polyether backbone. A universal concept for the implementation of acetal moieties into initiators for the anionic ring-opening polymerization (AROP) of epoxides is presented and proven to grant access to the degradable PEG structures aimed at. The hydrolysis of the heterofunctional PEG with the acetal moiety at the initiating site is followed by 1H NMR spectroscopy in deuterium oxide at different pH. In an exploratory study, the same polymer is attached to BSA via the squarate acid coupling and subsequently cleaved from the conjugate under acidic conditions. Furthermore, the concept for the generation of acetal-modified AROP initiators is demonstrated to be suitable for cholesterol, and the respective amphiphilic cholesteryl-PEG is cleaved at lowered pH. In Chapter 3.2, the straightforward synthesis of α-amino ω2-dihydroxyl star-shaped three-arm PEGs is described. To assure a symmetric length of the hydroxyl-terminated PEG arms, a novel AROP initiator is presented, who’s primary and secondary hydroxyl groups are separated by an acetal moiety. Upon polymerization of ethylene oxide for these functionalities and subsequent cleavage of the acid-labile unit no difference in the degree of polymerization is seen for both polyether fragments.

Dotierte Nanographenstreifen mit definierten Randstrukturen

Die in der vorliegenden Dissertation entwickelten organochemischen Protokolle und Konzepte erweitern die Bottom-Up-Synthese von atompräzisen Nanographenstreifen (GNR) um zwei fundamentale Bereiche. Zum einen die Dotierung der halbleitenden GNR mit Schwefel oder Stickstoffatomen und zum anderen ein Protokoll für eine lösungsbasierte Synthese von stickstoffdotierten Zickzack-Streifen.rnDie Dotierung von GNR beinhaltet die Synthese von monomeren Bausteinen bei denen, im Gegensatz zu ihren reinen Kohlenstoffhomologen, definierte Positionen am Rand mit zwei oder vier Stickstoff- beziehungsweise zwei Schwefelatomen ersetzt wurden. Die Synthese atompräziser GNR konnte mit verschiedenen experimentellen Methoden analysiert und anschaulich über STM visualisiert werden. Neben einer n-Dotierung gelang so auch erstmals eine Bottom-Up-Synthese von schwefeldotierten GNR. Eine mögliche Anwendung in der Nanoelektronik aufbauend auf dotierten GNR wurde bestätigt, indem durch Co-Polymerisation von stickstoffhaltigen mit reinen Kohlenstoffmonomeren Heteroschnittstellen zwischen dotierten und undotierten Bereichen hergestellt werden konnten. Solche Heteroschnittstellen sind fundamentale Grundlage von Dioden und damit Basis einer Vielzahl elektronischer Elemente wie Solarzellen oder Leuchtdioden.rnWährend für halbleitende GNR mit einer Armlehnen-Form ein breites Spektrum an organischen Syntheseprotokollen zur Verfügung stand, existierte zu Beginn dieser Arbeit keines für GNR mit Zickzack-Struktur. Innerhalb dieser Arbeit konnte eine Bottom-Up-Synthese zur Erschließung stickstoffdotierter GNR mit Zickzack-Randstruktur erarbeitet werden. Durch die Verwendung eines (2-Hydroxymethyl)phenylboronsäureesters werden Hydroxymethylsubsituenten entlang eines Polyphenylenrückgrats eingebaut, die nach Kondensation mit dem Stickstoffatom eine Zickzack-Kante ergeben. Innerhalb der synthetisierten Zielstrukturen kann das 9a-Azaphenalen als letztes, bislang nicht erschlossenes Isomer der Azaphenalene, als wiederkehrende Struktur, gefunden werden. Die Reaktivität der Zickzackkante konnte zudem zum Aufbau einer Vielzahl bislang unzugänglicher, polycyclischer Heteroaromaten über 1,3-dipolare Addition dieses polycyclischen Azomethin Ylides (PAMY) genutzt werden.rn

Magnetische Multischalenpartikel für den Transport von siRNA

Die vorliegende Arbeit befasst sich mit der Entwicklung eines nichtviralen, effizienten Transfektionsmittels mit einer Kern-Schale-Struktur in der Größenordnung bis 100 nm. Dafür werden magnetische, negativ geladene Eisenoxid-Nanopartikel mittels Thermolyse mit einem Durchmesser von 17 nm synthetisiert und in Wasser überführt. Diese Nanopartikel bilden den Kern des Erbgut-Trägers und werden mittels Layer-by-Layer –Verfahren (LbL) mit geladenen Polymeren, den bioabbaubaren Makromolekülen Poly-L-Lysin und Heparin, beschichtet. Dafür wird zunächst eine geeignete Apparatur aufgebaut. Diese wird zur Herstellung von Kern-Schale-Strukturen mit fünf Polyelektrolytschichten verwendet und liefert Partikel mit einem hydrodynamischen Durchmesser von 58 nm, die bei Abwesenheit von niedermolekularem Salz aggregatfrei sind. Das System wird gegen Salz stabilisiert, indem die letzte Poly-L-Lysin-Schicht mit Polyethylenglycol modifiziert wird. Die so entstandenen Multischalenpartikel zeigen weder im PBS-Puffer noch in humanem Serum Aggregation. Mittels winkelabhängiger dynamischer Lichtstreuung wird die Aggregatbildung kontrolliert, während ζ-Potential-Messungen die Kontrolle der Oberflächenladung erlauben.rnDa siRNA auf Grund ihres negativ geladenen Phosphat-Rückgrats ebenfalls ein Polyelektrolyt ist, wird sie aggregatfrei auf die positiv geladenen PLL-Nanopartikel aufgetragen. Die eingesetzte siRNA ist farbstoffmarkiert, um eine Detektion in vitro zu ermöglichen. Jedoch sind die entstandenen Komplexe mittels Fluoreszenzkorrelations-spektroskopie (FCS) nicht nachweisbar. Auch die Fluoreszenzmarkierung der PEGylierten Außenschale mittels kupferfreier Click-Chemie ist in der FCS nicht sichtbar, sodass eine Fluoreszenzauslöschung der Farbstoffe in den Multischalenpartikeln vermutet wird.rn

Modellkomplexe zur Sauerstoffaktivierung auf Basis des 1,3,4-Thiadiazols

Das Ziel der vorliegenden Arbeit waren die Synthese und Untersuchung von Modellverbindungen zur Sauerstoffaktivierung auf der Basis neuer Ligandensysteme des 1,3,4-Thiadiazols unter Ausarbeitung einer Synthesestrategie zur Derivatisierung der heteroaromatischen 1,3,4-Thiadiazol-Liganden, deren Koordinationsverhalten in Abhängigkeit ihres 2,5-Substitutionsmusters untersucht wurde, sowie die fortführende Bearbeitung bereits bekannter Ligandensysteme zur Erzeugung von homo- und heterovalenten Übergangsmetallkomplexverbindungen.rnDie unter der Verwendung der modifizierten Liganden TPDE, H1TPDP und H1BPMP resultierenden dinuklearen Komplexverbindungen zeigen unterschiedlich starke antiferromagnetische Wechselwirkungen in Abhängigkeit der vorhandenen Brückenliganden. In der Verbindung [Fe6O2(OH)(L´)2(OOCMe3)9(OEt)2] trat eine Fragmentierung des Liganden H1TPDP auf. Das cisoide Ligandensubstitutionsmuster der entstandenen sechskernigen Verbindung ist verantwortlich für die interessanten magnetischen Eigenschaften des Komplexes. rnNeue Perspektiven zur Erzeugung von Modellverbindungen zur Sauerstoffaktivierung wurden mit dem Mono-Chelatliganden H1ETHP und den Bis-Chelatliganden HL2H, H2L2H und H2BATP aufgezeigt. Die Umsetzung von H1ETHP mit verschiedenen Übergangsmetallsalzen resultierte für die Metalle Cr(III), Fe(III), Co(III) und Ni(II) in mononuklearen Verbindungen des Typs [M(ETHP)2]X (X = ClO4, FeCl4, OMe, Cl, Br) sowie in zwei tetranuklearen Verbindungen mit Mn(II) und Cu(II). [Mn4(ETHP)6] besitzt ein propellerförmiges, planares [Mn4O6]2+-System mit einen Spingrundzustand von S = 5. In allen Verbindungen von H1ETHP konnte eine mono-κN-Koordination des 1,3,4-Thiadiazol-Rückgrates über eines seiner beiden endozyklischen Stickstoffdonoratome beobachtet werden. rnAus Umsetzungen der Bis-Chelatliganden wurden fast ausschließlich polynukleare Übergangsmetallkomplexe erhalten. Insbesondere der Ligand H2L2H zeigt eine ausgeprägte Tendenz zur Ausbildung trinuklearer, linearer Komplexe, welche auf Grund ihrer ungeraden Anzahl von Übergangsmetallionen einen Spingrundzustand S ≠ 0 aufweisen.rn Die mit dem Liganden HL2H erhaltenen Verbindungen unterstreichen die hohe Flexibilität dieser Systeme hinsichtlich der Erzeugung polynuklearer und heterovalenter Komplexverbindungen. So konnten in Abhängigkeit vom verwendeten Übergangsmetallsalz trinukleare, pentanukleare, aber auch hepta- und oktanukleare Verbindungen synthetisiert werden. Insbesondere die Komplexe des Mangans und des Cobalts zeigen ein heterovalentes [MnIIMnIII4]- bzw. [CoII2CoIII3]-Motiv, was sich in Spingrundzuständen von S ≠ 0 äußert. Der diamagnetische, achtkernige Fe8-Cluster besitzt eine pseudo C3-symmetrische Anordnung der Metall-Zentren, während für die heptanukleare Cu7-Kette durch ihre stark unterschiedlichen Kupfer-Koordinationsgeometrien interessante magnetische Austauschwechselwirkungen beobachtet werden konnten. Der dreikernige µ3-oxo-verbrückte Komplex des Liganden H2BATP zeigt als interessante strukturelle Eigenschaft ein ein µ3-Verbrückungsmuster des eingesetzten Sulfat-Anions. rnIn allen Komplexen der Bis-Chelatliganden HL2H, H2L2H und H2BATP konnte ein µ2-κN,κN-Koordiantionsmodus des 1,3,4-Thiadiazols und somit eine Abhängigkeit der Verbrückung vom Ligandensubstitutionsmuster beobachtet werden.rn

Field-free control of magnetism in nanostructured materials probed with high resolution X-ray microscopy

Magnetic memories are a backbone of today's digital data storage technology, where the digital information is stored as the magnetic configuration of nanostructured ferromagnetic bits. Currently, the writing of the digital information on the magnetic memory is carried out with the help of magnetic fields. This approach, while viable, is not optimal due to its intrinsically high energy consumption and relatively poor scalability. For this reason, the research for different mechanisms that can be used to manipulate the magnetic configuration of a material is of interest. In this thesis, the control of the magnetization of different nanostructured materials with field-free mechanisms is investigated. The magnetic configuration of these nanostructured materials was imaged directly with high resolution x-ray magnetic microscopy. rnFirst of all, the control of the magnetic configuration of nanostructured ferromagnetic Heusler compounds by fabricating nanostructures with different geometries was analyzed. Here, it was observed that the magnetic configuration of the nanostructured elements is given by the competition of magneto-crystalline and shape anisotropy. By fabricating elements with different geometries, we could alter the point where these two effects equilibrate, allowing for the possibility to tailor the magnetic configuration of these nanostructured elements to the required necessities.rnThen, the control of the magnetic configuration of Ni nanostructures fabricated on top of a piezoelectric material with the magneto-elastic effect (i.e. by applying a piezoelectric strain to the Ni nanostructures) was investigated. Here, the magneto-elastic coupling effect gives rise to an additional anisotropy contribution, proportional to the strain applied to the magnetic material. For this system, a reproducible and reversible control of the magnetic configuration of the nanostructured Ni elements with the application of an electric field across the piezoelectric material was achieved.rnFinally, the control of the magnetic configuration of La0.7Sr0.3MnO3 (LSMO) nanostructures with spin-polarized currents was studied. Here, the spin-transfer torque effect was employed to achieve the displacement of magnetic domain walls in the LSMO nanostructures. A high spin-transfer torque efficiency was observed for LSMO at low temperatures, and a Joule-heating induced hopping of the magnetic domain walls was observed at room temperatures, allowing for the analysis of the energetics of the domain walls in LSMO.rnThe results presented in this thesis give thus an overview on the different field-free approaches that can be used to manipulate and tailor the magnetization configuration of a nanostructured material to the various technological requirements, opening up novel interesting possibilities for these materials.

Synthesis in millireactor system and stability of intermediates for the functionalization of imidazole

This Master thesis presents the results obtained in the curricular traineeship, carried out within the laboratories of the Department of Chemistry of the University of Bergen, during the Erasmus period, and within the Department of Industrial Chemistry of the University of Bologna. The project followed in Bergen concerned the synthesis of key intermediates used for the functionalization of the backbone of imidazole, using N,N'- diiodo-5,5-dimethylhydantoin (“DIH”) as an iodinating agent, and employing an innovative kind of chemical reactor: the “Multijet Oscillating Disc Millireactor” (MJOD Reactor). Afterwards, the work performed in Bologna consisted in verifying the stability in solution of the above mentioned N,N'-diiodo-5,5-dimethylhydantoin utilising spectrophotometric techniques and High Performance Liquid Chromatography analyses (HPLC).

Lipid remodelling of glycosylphosphatidylinositol (GPI) glycoconjugates in procyclic-form trypanosomes: biosynthesis and processing of GPIs revisited

The African trypanosome, Trypanosoma brucei, has been used as a model to study the biosynthesis of GPI (glycosylphosphatidylinositol) anchors. In mammalian (bloodstream)-form parasites, diacyl-type GPI precursors are remodelled in their lipid moieties before attachment to variant surface glycoproteins. In contrast, the GPI precursors of insect (procyclic)-form parasites, consisting of lyso-(acyl)PI (inositol-acylated acyl-lyso-phosphatidylinositol) species, remain unaltered before protein attachment. By using a combination of metabolic labelling, cell-free assays and complementary MS analyses, we show in the present study that GPI-anchored glycoconjugates in T. congolense procyclic forms initially receive tri-acylated GPI precursors, which are subsequently de-acylated either at the glycerol backbone or on the inositol ring. Chemical and enzymatic treatments of [3H]myristate-labelled lipids in combination with ESI-MS/MS (electrospray ionization-tandem MS) and MALDI-QIT-TOF-MS3 (matrix-assisted laser-desorption ionization-quadrupole ion trap-time-of-flight MS) analyses indicate that the structure of the lipid moieties of steady-state GPI lipids from T. congolense procyclic forms consist of a mixture of lyso-(acyl)PI, diacyl-PI and diacyl-(acyl)PI species. Interestingly, some of these species are myristoylated at the sn-2 position. To our knowledge, this is the first demonstration of lipid remodelling at the level of protein- or polysaccharide-linked GPI anchors in procyclic-form trypanosomes.

Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

Hierarchical Approach for Survivable Network Design

A central design challenge facing network planners is how to select a cost-effective network configuration that can provide uninterrupted service despite edge failures. In this paper, we study the Survivable Network Design (SND) problem, a core model underlying the design of such resilient networks that incorporates complex cost and connectivity trade-offs. Given an undirected graph with specified edge costs and (integer) connectivity requirements between pairs of nodes, the SND problem seeks the minimum cost set of edges that interconnects each node pair with at least as many edge-disjoint paths as the connectivity requirement of the nodes. We develop a hierarchical approach for solving the problem that integrates ideas from decomposition, tabu search, randomization, and optimization. The approach decomposes the SND problem into two subproblems, Backbone design and Access design, and uses an iterative multi-stage method for solving the SND problem in a hierarchical fashion. Since both subproblems are NP-hard, we develop effective optimization-based tabu search strategies that balance intensification and diversification to identify near-optimal solutions. To initiate this method, we develop two heuristic procedures that can yield good starting points. We test the combined approach on large-scale SND instances, and empirically assess the quality of the solutions vis-à-vis optimal values or lower bounds. On average, our hierarchical solution approach generates solutions within 2.7% of optimality even for very large problems (that cannot be solved using exact methods), and our results demonstrate that the performance of the method is robust for a variety of problems with different size and connectivity characteristics.

Conformationally Controlled Electron Delocalization in n-Type Rods: Synthesis, Structure, and Optical, Electrochemical, and Spectroelectrochemical Properties of Dicyanocyclophanes

A series of dicyanobiphenyl-cyclophanes 1-6 with various pi-backbone conformations and characteristic n-type semiconductor properties is presented. Their synthesis, optical, structural, electrochemical, spectroelectrochemical, and packing properties are investigated. The X-ray crystal structures of all n-type rods allow the systematic correlation of structural features with physical properties. In addition, the results are supported by quantum mechanical calculations based on density functional theory. A two-step reduction process is observed for all n-type rods, in which the first step is reversible. The potential gap between the reduction processes depends linearly on the cos(2) value of the torsion angle phi between the pi-systems. Similarly, optical absorption spectroscopy shows that the vertical excitation energy of the conjugation band correlates with the cos(2) value of the torsion angle phi. These correlations demonstrate that the fixed intramolecular torsion angle phi is the dominant factor determining the extent of electron delocalization in these model compounds, and that the angle phi measured in the solid-state structure is a good proxy for the molecular conformation in solution. Spectroelectrochemical investigations demonstrate that conformational rigidity is maintained even in the radical anion form. In particular, the absorption bands corresponding to the SOMO-LUMO+i transitions are shifted bathochromically, whereas the absorption bands corresponding to the HOMO-SOMO transition are shifted hypsochromically with increasing torsion angle phi.

Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy DeltaH. Arranging the tc-residues in a continuous fashion rescues T(m) and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in T(m) when paired to complementary DNA and leads to substantial increases in T(m) when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy.

Synthesis, base pairing properties and trans-lesion synthesis by reverse transcriptases of oligoribonucleotides containing the oxidatively damaged base 5-hydroxycytidine

The synthesis of a caged RNA phosphoramidite building block containing the oxidatively damaged base 5-hydroxycytidine (5-HOrC) has been accomplished. To determine the effect of this highly mutagenic lesion on complementary base recognition and coding properties, this building block was incorporated into a 12-mer oligoribonucleotide for Tm and CD measurements and a 31-mer template strand for primer extension experiments with HIV-, AMV- and MMLV-reverse transcriptase (RT). In UV-melting experiments, we find an unusual biphasic transition with two distinct Tm's when 5-HOrC is paired against a DNA or RNA complement with the base guanine in opposing position. The higher Tm closely matches that of a C-G base pair while the lower is close to that of a C-A mismatch. In single nucleotide extension reactions, we find substantial misincorporation of dAMP and to a lesser extent dTMP, with dAMP almost equaling that of the parent dGMP in the case of HIV-RT. A working hypothesis for the biphasic melting transition does not invoke tautomeric variability of 5-HOrC but rather local structural perturbations of the base pair at low temperature induced by interactions of the 5-HO group with the phosphate backbone. The properties of this RNA damage is discussed in the context of its putative biological function.

Glycoprotein D of bovine herpesvirus 5 (BoHV-5) confers an extended host range to BoHV-1 but does not contribute to invasion of the brain

Bovine herpesvirus 1 (BoHV-1) and BoHV-5 are closely related pathogens of cattle, but only BoHV-5 is considered a neuropathogen. We engineered intertypic gD exchange mutants with BoHV-1 and BoHV-5 backbones in order to address their in vitro and in vivo host ranges, with particular interest in invasion of the brain. The new viruses replicated in cell culture with similar dynamics and to titers comparable to those of their wild-type parents. However, gD of BoHV-5 (gD5) was able to interact with a surprisingly broad range of nectins. In vivo, gD5 provided a virulent phenotype to BoHV-1 in AR129 mice, featuring a high incidence of neurological symptoms and early onset of disease. However, only virus with the BoHV-5 backbone, independent of the gD type, was detected in the brain by immunohistology. Thus, gD of BoHV-5 confers an extended cellular host range to BoHV-1 and may be considered a virulence factor but does not contribute to the invasion of the brain.

A Computational Analysis of the Collision-Induced Dissociation Mechanisms of the Dipeptide Glycine-Serine Under Mass Spectrometry

Collision-induced dissociation (CID) of peptides using tandem mass spectrometry (MS) has been used to determine the identity of peptides and other large biological molecules. Mass spectrometry (MS) is a useful tool for determining the identity of molecules based on their interaction with electromagnetic fields. If coupled with another method like infrared (IR) vibrational spectroscopy, MS can provide structural information, but in its own right, MS can only provide the mass-to-charge (m/z) ratio of the fragments produced, which may not be enough information to determine the mechanism of the collision-induced dissociation (CID) of the molecule. In this case, theoretical calculations provide a useful companion for MS data and yield clues about the energetics of the dissociation. In this study, negative ion electrospray tandem MS was used to study the CID of the deprotonated dipeptide glycine-serine (Gly-Ser). Though negative ion MS is not as popular a choice as positive ion MS, studies by Bowie et al. show that it yields unique clues about molecular structure which complement positive ion spectroscopy, such as characteristic fragmentations like the loss of formaldehyde from the serine residue.2 The increase in the collision energy in the mass spectrometer alters the flexibility of the dipeptide backbone, enabling isomerizations (reactions not resulting in a fragment loss) and dissociations to take place. The mechanism of the CID of Gly-Ser was studied using two computational methods, B3LYP/6-311+G* and M06-2X/6-311++G**. The main pathway for molecular dissociation was analyzed in 5 conformers in an attempt to verify the initial mechanism proposed by Dr. James Swan after examination of the MS data. The results suggest that the loss of formaldehyde from serine, which Bowie et al. indicates is a characteristic of the presence of serine in a protein residue, is an endothermic reaction that is made possible by the conversion of the translational energy of the ion into internal energy as the ion collides with the inert collision gas. It has also been determined that the M06-2X functional¿s improved description of medium and long-range correlation makes it more effective than the B3LYP functional at finding elusive transition states. M06-2X also more accurately predicts the energy of those transition states than does B3LYP. A second CID mechanism, which passes through intermediates with the same m/z ratio as the main pathway for molecular dissociation, but different structures, including a diketopiperazine intermediate, was also studied. This pathway for molecular dissociation was analyzed with 3 conformers and the M06-2X functional, due to its previously determined effectiveness. The results suggest that the latter pathway, which meets the same intermediate masses as the first mechanism, is lower in overall energy and therefore a more likely pathway of dissociation than the first mechanism.