Análise das condições de acessibilidade no ensino superior: estudo com pós-graduandos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Lipophilicity as a determinant of binding of procaine analogs to rat alpha(3)beta(4) nicotinic acetylcholine receptor

Nicotinic acetylcholine receptors (nAChRs) have been studied in detail with regard to their interaction with therapeutic and drug addiction-related compounds. Using a structureactivity approach, we have examined the relationship among the molecular features of a set of eight para-R-substituted N,N-[(dimethylamino)ethyl] benzoate hydrochlorides, structurally related to procaine and their affinity for the a3 beta 4 nAChR heterologously expressed in KXa3 beta 4R2 cells. Affinity values (log[1/IC50]) of these compounds for the a3 beta 4 nAChR were determined by their competition with [3H]TCP binding. Log(1/IC50) values were analyzed considering different hydrophobic and electronic parameters and those related to molar refractivity. These have been experimentally determined or were taken from published literature. In accordance with literature observations, the generated cross-validated quantitative structureactivity relationship (QSAR) equations indicated a significant contribution of hydrophobic term to binding affinity of procaine analogs to the receptor and predicted affinity values for several local anesthetics (LAs) sets taken from the literature. The predicted values by using the QSAR model correlated well with the published values both for neuronal and for electroplaque nAChRs. Our work also reveals the general structure features of LAs that are important for interaction with nAChRs as well as the structural modifications that could be made to enhance binding affinity. (c) 2012 Wiley Periodicals, Inc.

Stereoselective Catalytic Processes for the Synthesis of Polycyclic Aromatic Compounds

In this PhD-thesis, two methodologies for enantioselective intramolecular ring closing reaction on indole cores are presented. The first methodology represents a highly stereoselective alkylation of the indole N1-nitrogen, leading to 3,4-dihydro-pyrazinoindol-1-ones – a structural class which is known for its activity on the CNS and therefore of high pharmacological interest concerning related diseases. In this approach, N-benzyl cinchona-alkaloids were used for the efficient catalysis of intramolecular aza-Michael reactions. Furthermore, computational studies in collaboration with the research group Prof. Andrea Bottoni (Department of Chemistry “G. Ciamician”, Bologna) were accomplished in order to get insight into the key interactions between catalyst and substrate, leading to enantiomeric excesses up to 91%. The results of the calculations on a model system are in accordance with the experimental results and demonstrate the high sensibility of the system towards structural modifications. The second project deals with a metal catalyzed, intramolecular Friedel-Crafts (FC)-reaction on indolyl substrates, carrying a side chain which on its behalf is furnished with an allylic alcohol unit. Allylic alcohols are part of the structural class of “π-activated alcohols” – alcohols, which are more easily activated due to the proximity to a π-unit (allyl-, propargyl-, benzyl-). The enantioselective intramolecular cyclization event is catalyzed efficiently by employment of a chiral Au(I)-catalyst, leading to 1-vinyl- or 4-vinyl-tetrahydrocarbazoles (THCs) under the formation of water as byproduct. This striking and novel process concerning the direct activation of alcohols in catalytic FC-reactions was subsequently extended to similar precursors, leading to functionalized tetrahydro-β-carbolines. These two methodologies represent highly efficient approaches towards the synthesis of scaffolds, which are of enormous pharmaceutical interest and amplify the spectra of enantioselective catalytic functionalisations of indoles.

Thiophene- Based Materials for Photovoltaic Applications

Thiophene oligomers (OTs) and polymers (PTs) are currently attracting remarkable attention as organic materials showing semiconducting, fluorescent, nonlinear optical and liquid crystalline properties. All these properties can be fine-tuned through minor structural modifications. As a consequence, thiophene oligomers and polymers are among the most investigated compounds for applications in organic electronics, optoelectronics and thin film devices such as field effect transistors (FETs), light emitting diodes (LEDs) and photovoltaic devices (PVDs). Our research aims to explore the self-assembly features and the optical, electrical and photovoltaic properties of a class of thiophene based materials so far scarcely investigated, namely that of oligo- and polythiophenes head-to-head substituted with alkyl or S-alkyl chains. In particular, we synthesized these compounds in short reaction times, high yields, high purity and environmentally friendly procedures taking advantage of ultrasound (US) and microwave (MW) enabling technologies in Suzuki-Miyaura cross-couplings.

RNA-basierte Impfstoffe zur Induktion optimaler Immunantworten

Antigen-kodierende RNA wird als eine sichere und effiziente Alternative zu traditionellen Impfstoff-Formulierungen, wie Peptid-, Protein-, rekombinanten viralen oder DNA basierten Impfstoffen betrachtet. Der endgültige klinische Nutzen RNA-basierter Impfstoffe wird von der Optimierung verschiedener Parameter abhängig sein, die zur Induktion und effizienten Expansion der humoralen und zellvermittelten Immunantwort beitragen. Vor diesem Hintergrund war die Zielsetzung der vorliegenden Arbeit, die Etablierung pharmakologischer und immunologischer Parameter für die Generierung effektiver Immunantworten durch RNA-Impfstoffe sowie deren Wirksamkeit in vitro und im Mausmodell unter Nutzung von Modellantigenen zu testen. Zur Untersuchung und Optimierung der RNA-Pharmakokinetik, als einem Schlüsselaspekt der klinischen Medikamentenentwicklung, wurde der Einfluss von strukturellen Modifikationen auf die Transkriptstabilität und Translationseffizienz von Reporter-Proteinen in einer zeitabhängigen Kinetik evaluiert. Es wurde gezeigt, dass ein poly(A) Schwanz von 120 Adenosinen, verglichen mit einem kürzeren, ein freies 3´ poly(A) Ende, verglichen mit einem verdeckten und eine doppelte β-globin 3´ UTR, unabhängig voneinander zu einer Erhöhung der IVT-RNA Stabilität und zu einer Verbesserung der Translationseffizienz beitrugen und dadurch insgesamt zu einer erhöhten Proteinexpression führten. Antigen-kodierende IVT-RNA mit diesen molekularen Merkmalen in Kombination führte, im Vergleich zur Standard IVT-RNA, zu einer erhöhten Dichte und Stabilität von Peptid/MHC-Komplexen auf der Zelloberfläche transfizierter DCs und dadurch zu einer verbesserten Stimulation von CD4+ und CD8+ T-Zellen im murinen und humanen System. Mit dem Ziel, die RNA kodierte Antigenform für die Induktion einer verstärkten Antikörperantwort zu modifizieren, wurde im zweiten Teil der Arbeit ein Antigen-IgM Fusionskonstrukt hergestellt und hinsichtlich seiner Eignung als neues Impfstoff-Format untersucht. Die Ausgangshypothese, dass die RNA kodierten Antigen-IgM Fusionsproteine polymerisieren, von transfizierten Zellen sezerniert werden und aufgrund der repetitiven Antigenstruktur im Vergleich mit dem monomeren Antigen zu einer Verstärkung der Antikörperantwort führen, wurde in vitro und in vivo im Mausmodell bestätigt. Die Entwicklung und Evaluierung von Zytokinfusionsproteinen zur selektiven Verstärkung der antigenspezifischen Immunantworten bildeten den dritten Schwerpunkt der vorliegenden Arbeit. Zur weiteren Verstärkung der Antikörperantwort wurde basierend auf den Resultaten aus dem zweiten Teil ein IL2-IgM Fusionskonstrukt hergestellt. Die Ko-Transfektion von Antigen-IgM und IL2-IgM kodierender IVT-RNA führte zu einer signifikant stärkeren Antikörperantwort als die Ko-Transfektion von Antigen-IgM und IL2. Für die Initiierung einer erfolgreichen anti-Tumor-Immunantwort ist das Priming antigenspezifischer T-Zellen essentiell. Um die Effizienz dieses Prozesses zu steigern, wurde ein bifunktionelles IL2-mCD40L Fusionskonstrukt hergestellt und sein Einfluss auf die Effektorfunktion von DCs in vitro und in vivo untersucht. Es wurde gezeigt, dass ein RNA kodiertes IL2-mCD40L Fusionsprotein als genetisches Adjuvanz zu einer Effizienzsteigerung des Priming zytotoxischer T-Zellen führt. Somit wurden in dieser Arbeit durch die Optimierung der Pharmakokinetik, die Modifikation der Antigenform und die Herstellung und Evaluierung von Zytokinfusionskonstrukten als genetische Adjuvantien, RNA-basierte Impfstoffe für eine optimierte Induktion von antigenspezifischen Immunantworten weiter verbessert.

On the development of novel cocaine-analogues for in vivo imaging of the dopamine transporter status

The present thesis is concerned with the development of novel cocaine-derived dopamine transporter ligands for the non-invasive exploration of the striatal and extra-striatal dopamine transporter (DAT) in living systems. The presynaptic dopamine transporter acquires an important function within the mediation of dopaminergic signal transduction. Its availability can serve as a measure for the overall integrity of the dopaminergic system. The DAT is upregulated in early Parkinson’s disease (PD), resulting in an increased availability of DAT-binding sites in the striatal DAT domains. Thereby, DAT imaging has become an important routine diagnostic tool for the early diagnosis of PD in patients, as well as for the differentiation of PD from symptomatically similar medical conditions. Furthermore, the dopaminergic system is involved in a variety of psychiatric diseases. In this regard, DAT-selective imaging agents may provide detailed insights into the scientific understanding of the biochemical background of both, the progress as well as the origins of the symptoms. DAT-imaging may also contribute to the determination of the dopaminergic therapeutic response for a given medication and thereby contribute to more convenient conditions for the patient. From an imaging point of view, the former demands a high availability of the radioactive probe to facilitate broad application of the modality, whereas the latter profits from short-lived probes, suitable for multi-injection studies. Therefore, labelling with longer-lived 18F-fluoride and in particular the generator nuclide 68Ga is worthwhile for clinical routine imaging. In contrast, the introduction of a 11C-label is a prerequisite for detailed scientific studies of neuronal interactions. The development of suitable DAT-ligands for medical imaging has often been complicated by the mixed binding profile of many compounds that that interact with the DAT. Other drawbacks have included high non-specific binding, extensive metabolism and slow accumulation in the DAT-rich brain areas. However, some recent examples have partially overcome the mentioned complications. Based on the structural speciality of these leads, novel ligand structures were designed and successfully synthesised in the present work. A structure activity relationship (SAR) study was conducted wherein the new structural modifications were examined for their influence on DAT-affinity and selectivity. Two of the compounds showed improvements in in vitro affinity for the DAT as well as selectivity versus the serotonin transporter (SERT) and norepinephrine transporter (NET). The main effort was focussed on the high-affinity candidate PR04.MZ, which was subsequently labelled with 18F and 11C in high yield. An initial pharmacological characterisation of PR04.MZ in rodents revealed highly specific binding to the target brain structures. As a result of low non-specific binding, the DAT-rich striatal area was clearly visualised by autoradiography and µPET. Furthermore, the radioactivity uptake into the DAT-rich brain regions was rapid and indicated fast binding equilibrium. No radioactive metabolite was found in the rat brain. [18F]PR04.MZ and [11C]PR04.MZ were compared in the primate brain and the plasma metabolism was studied. It was found that the ligands specifically visualise the DAT in high and low density in the primate brain. The activity uptake was rapid and quantitative evaluation by Logan graphical analysis and simplified reference tissue model was possible after a scanning time of 30 min. These results further reflect the good characteristics of PR04.MZ as a selective ligand of the neuronal DAT. To pursue 68Ga-labelling of the DAT, initial synthetic studies were performed as part of the present thesis. Thereby, a concept for the convenient preparation of novel bifunctional chelators (BFCs) was developed. Furthermore, the suitability of novel 1,4,7-triazacyclononane based N3S3-type BFCs for biomolecule-chelator conjugates of sufficient lipophilicity for the penetration of the blood-brain-barrier was elucidated.

Synthese, biochemische und physikochemische Charakterisierung von Liganden der Glycin-Bindungsstelle des NMDA-Rezeptors

Die exzitatorische Neurotransmission erfolgt über ionotrope Glutamat-Rezeptoren von denen dem NMDA-(N-Methyl-D-aspartat)-Rezeptor durch seine hohe Leitfähigkeit für Ca2+-Ionen eine besondere Rolle zugesprochen wird. Bei seiner Überaktivierung kommt es zu exzitotoxischen Prozessen, die direkt mit neurodegenerativen Erkrankungen einhergehen und nach einem Schlaganfall, bei akuten Epilepsien, Morbus Parkinson, Alzheimer Demenz aber auch im Bereich der neuropathischen Schmerzentstehung eine wichtige Rolle spielen.rnDurch das Eingreifen in die glutamatvermittelten pathologischen Prozesse verspricht man sich daher die Möglichkeit einer Neuroprotektion bei der Therapie verschiedener neurodegenerativer Erkrankungen, die primär auf völlig unterschiedliche Ursachen zurückzuführen sind.rnAusgehend von in früheren Arbeiten synthetisierten Hydantoin-substituierten Dichlor-indol-2-carbonsäure-Derivaten, die hochaffine Eigenschaften zur Glycin-Bindungsstelle des NMDA-Rezeptors aufweisen, sollten neue Derivate entwickelt und untersucht werden, die hinsichtlich ihrer Affinität zur Glycin-Bindungsstelle des NMDA-Rezeptors, ihrer Pharmakokinetik sowie physikochemischen Parameter in präparativ-organischen, radiopharmazeutischen und zell- bzw. tierexperimentellen Studien in vitro sowie in vivo charakterisiert werden sollten. Von besonderem Interesse war dabei die Evaluierung der synthetisierten Verbindungen in einem Verdrängungsassay mit dem Radioliganden [3H]MDL105,519 mit dem der Einfluss der strukturellen Modifikationen auf die Affinität zur Glycin-Bindungsstelle des Rezeptors untersucht wurde, sowie die Selektivität und die Potenz der Liganden abgeschätzt wurde.rnIm Rahmen der Struktur-Wirkungs-Untersuchungen mit Hilfe der Bindungsexperimente konnten bestimmte Strukturmerkmale als essentiell herausgestellt bzw. bekräftigt werden. Die Testverbindungen zeigten dabei IC50-Werte im Bereich von 0,0028 bis 51,8 μM. Die entsprechenden Ester dagegen IC50-Werte von 23,04 bis >3000 μM. Als vielversprechende Strukturen mit Affinitäten im niedrigen nanomolaren Bereich stellten sich Derivate mit einer 4,6-Dichlor-oder Difluor-Substitution am Indolgrundgerüst (2,8 bis 4,6 nM) heraus. Auch die Substitution des Phenylhydantoin-Teils durch das bioisostere Thienylhydantoin führte zu einer gleichbleibenden ausgeprägten Affinität (3,1 nM). rnZur Abschätzung der Bioverfügbarkeit, insbesondere der Fähigkeit zur Überwindung der Blut-Hirn-Schranke, wurden die Lipophilien bei einer Auswahl der Testverbindungen durch Bestimmung ihrer log P-Werte ermittelt. Neben dem Verfahren der potentiometrischen Titration wurde eine HPLC-Methode an einer RP-Phase verwendet.rnUm das Zytotoxizitätsprofil der synthetisierten Strukturen frühzeitig abschätzen zu können, wurde ein schnell durchführbares, zellbasiertes in vitro-Testsystem, der kommerziell erhältliche „Cell Proliferation Kit II (XTT-Test)“, eingesetzt. rnIm Rahmen von Positronen-Emissions-Tomographie-Experimenten an Ratten wurde eine Aussage bezüglich der Aufnahme und Verteilung eines radioaktiv markierten, hochaffinen Liganden an der Glycinbindungsstelle des NMDA-Rezeptors im Gehirn getroffen. Dabei wurden sowohl ein Carbonsäure-Derivat sowie der korrespondierende Ethylester dieser Testung unterworfen.rn

The quest for planarizing distortions in hydrocarbons: two stereoisomeric 4.5.5.5 fenestranes

According to semiempirical calculations the planarizing distortions in the central C(C)4 substructure of fenestranes, represented as 1, can be enhanced by a variety of structural modifications. Based on these results we selected the 7-hydroxy-c,c,c,c- and c,t,c,c[4.5.5.5]fenestranones 13 and 16 as precursors for the introduction of a bridgehead double bond. The efficient synthesis of these precursors and their chemical transformations are reported. Attempts to activate the hydroxyl group in 16 for introduction of a bridgehead double bond led to the rearrangement of the [4.5.5.5]fenestrane to a triquinacane skeleton. (C) 2011 Elsevier Ltd. All rights reserved.

Influence of different spacers on the biological profile of a DOTA-somatostatin analogue

Radiolabeled somatostatin analogues have been successfully used for targeted radiotherapy and for imaging of somatostatin receptor (sst1-5)-positive tumors. Nevertheless, these analogues are subject to improving their tumor-to-nontarget ratio to enhance their diagnostic or therapeutic properties, preventing nephrotoxicity. In order to understand the influence of lipophilicity and charge on the pharmacokinetic profile of [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)]-somatostatin-based radioligands such as [DOTA,1-Nal3]-octreotide (DOTA-NOC), different spacers (X) based on 8-amino-3,6-dioxaoctanoic acid (PEG2), 15-amino-4,7,10,13-tetraoxapentadecanoic acid (PEG4), N-acetyl glucosamine (GlcNAc), triglycine, beta-alanine, aspartic acid, and lysine were introduced between the chelator DOTA and the peptide NOC. All DOTA-X-NOC conjugates were synthesized by Fmoc solid-phase synthesis. The partition coefficient (log D) at pH = 7.4 indicated that higher hydrophilicity than [111In-DOTA]-NOC was achieved with the introduction of the mentioned spacers, except with triglycine and beta-alanine. The high affinity of [InIII-DOTA]-NOC for human sst2 (hsst2) was preserved with the structural modifications, while an overall drop for hsst3 affinity was observed, except in the case of [InIII-DOTA]-beta-Ala-NOC. The new conjugates preserved the good affinity for hsst5, except for [InIII-DOTA]-Asn(GlcNAc)-NOC, which showed decreased affinity. A significant 1.2-fold improvement in the specific internalization rate in AR4-2J rat pancreatic tumor cells (sst2 receptor expression) at 4 h was achieved with the introduction of Asp as a spacer in the parent compound. In sst3-expressing HEK cells, the specific internalization rate at 4 h for [111In-DOTA]-NOC (13.1% +/- 0.3%) was maintained with [111In-DOTA]-beta-Ala-NOC (14.0% +/- 1.8%), but the remaining derivatives showed <2% specific internalization. Biodistribution studies were performed with Lewis rats bearing the AR4-2J rat pancreatic tumor. In comparison to [111In-DOTA]-NOC (2.96% +/- 0.48% IA/g), the specific uptake in the tumor at 4 h p.i. was significantly improved for the 111In-labeled sugar analogue (4.17% +/- 0.46% IA/g), which among all the new derivatives presented the best tumor-to-kidney ratio (1.9).

In situ dehydration behavior of zeolite-like pentagonite: A single-crystal X-ray study

The structural modifications upon heating of pentagonite, Ca(VO)(Si4O10)·4H2O (space group Ccm21, a=10.3708(2), b=14.0643(2), c=8.97810(10) Å, V=1309.53(3) Å3) were investigated by in situ temperature dependent single-crystal X-ray structure refinements. Diffraction data of a sample from Poona district (India) have been measured in steps of 25 up to 250 °C and in steps of 50 °C between 250 and 400 °C. Pentagonite has a porous framework structure made up by layers of silicate tetrahedra connected by V4+O5 square pyramids. Ca and H2O molecules are extraframework occupants. Room temperature diffraction data allowed refinement of H positions. The hydrogen-bond system links the extraframework occupants to the silicate layers and also interconnects the H2O molecules located inside the channels. Ca is seven-fold coordinated forming four bonds to O of the tetrahedral framework and three bonds to extraframework H2O. The H2O molecule at O9 showing a high displacement parameter is not bonded to Ca. The dehydration in pentagonite proceeds in three steps. At 100 °C the H2O molecule at O8 was released while O9 moved towards Ca. As a consequence the displacement parameter of H2O at O9 halved compared to that at room temperature. The unit-cell volume decreased to 1287.33(3) Å3 leading to a formula with 3H2O per formula unit (pfu). Ca remained seven-fold coordinated. At 175 °C Ca(VO)(Si4O10)·3H2O transformed into a new phase with 1H2O molecule pfu characterized by doubling of the c axis and the monoclinic space group Pn. Severe bending of specific TOT angles led to contraction of the porous three-dimensional framework. In addition, H2O at O9 was expelled while H2O at O7 approached a position in the center of the channel. The normalized volume decreased to 1069.44(9) Å3. The Ca coordination reduced from seven- to six-fold. At 225 °C a new anhydrous phase with space group Pna21 but without doubling of c had formed. Release of H2O at O7 caused additional contraction of TOT angles and volume reduction (V=1036.31(9) Å3). Ca adopted five-fold coordination. During heating excursion up to 400 °C this anhydrous phase remained preserved. Between room temperature and 225 °C the unit-cell volume decreased by 21% due to dehydration. The dehydration steps compare well with the thermo-gravimetric data reported in the literature.

The structure of some [4.5.5.5]fenestranes

cis,cis,cis,cis-[4.5.5.5]Fenestrane 11 was prepared by a novel route. The energy hypersurface of some stereoisomeric and substituted [4.5.5.5]fenestranes and -fenestrenes was explored by DFT calculations. The impact of some structural modifications, which enhance the planarizing deformation in the central C(C)4 substructures are discussed.

Asymmetric cyclopropanation of olefins catalysed by Cu(I) complexes of chiral pyridine-containing macrocyclic ligands (Pc-L*)

The synthesis and characterisation of copper(I) complexes of chiral pyridine-containing macrocyclic ligands (Pc-L*) and their use as catalysts in asymmetric cyclopropanation reactions are reported. All ligands and metal complexes were fully characterised, including crystal structures of some species determined by X-ray diffraction on single crystals. This allowed characterising the very different conformations of the macrocycles which could be induced by different substituents or by metal complexation. The strategy adopted for the ligand synthesis is very flexible allowing several structural modifications. A small library of macrocyclic ligands possessing the same donor properties but with either C-1 or C-2 symmetry was synthesized. Cyclopropane products with both aromatic and aliphatic olefins were obtained in good yields and enantiomeric excesses up to 99%.

Highlights in Analytical Chemistry in Switzerland: OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids

Oligonucleotides comprising unnatural building blocks, which interfere with the translation machinery, have gained increased attention for the treatment of gene-related diseases (e.g. antisense, RNAi). Due to structural modifications, synthetic oligonucleotides exhibit increased biostability and bioavailability upon administration. Consequently, classical enzyme-based sequencing methods are not applicable to their sequence elucidation and verification. Tandem mass spectrometry is the method of choice for performing such tasks, since gas-phase dissociation is not restricted to natural nucleic acids. However, tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. The gas-phase dissociation of oligonucleotides is characterized by the cleavage of one of the four bonds along the phosphodiester chain, by the accompanying loss of nucleases, and by the generation of internal fragments due to secondary backbone cleavage. For example, an 18-mer oligonucleotide yields a total number of 272’920 theoretical fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. The existing web-based and stand-alone software applications are primarily designed for the sequence analysis of natural nucleic acids, but do not account for chemical modifications and adducts. Consequently, we developed a software to support the interpretation of mass spectrometric data of natural and modified nucleic acids and their adducts with chemotherapeutic agents.

Elucidation of the gas-phase structure of a sugar-modified DNA analogue

Antisense oligonucleotides are medical agents for the treatment of genetic diseases that are designed to interact specifically with mRNA. This interaction either induces enzymatic degradation of the targeted RNA or modifies processing pathways, e.g. by inducing alternative splicing of the pre-mRNA. The latter mechanism applies to the treatment of Duchenne muscular dystrophy with a sugar-modified DNA analogue called tricyclo-DNA (tcDNA). In tcDNA the ribose sugar-moiety is extended to a three-membered ring system, which augments the binding affinity and the selectivity of the antisense oligonucleotide for its target. The advent of chemically modified nucleic acids for antisense therapy presents a challenge to diagnostic tools, which must be able to cope with a variety of structural analogues. Mass spectrometry meets this demand for non-enzyme based sequencing methods ideally, because the technique is largely unaffected by structural modifications of the analyte. Sequence coverage of a fully modified tcDNA 15mer can be obtained in a single tandem mass spectrometric experiment. Beyond sequencing experiments, tandem mass spectrometry was applied to elucidate the gas-phase structure and stability of tcDNA:DNA and tcDNA:RNA hybrid duplexes. Most remarkable is the formation of truncated duplexes upon collision-induced dissociation of these structures. Our data suggest that the cleavage site within the duplex is directed by the modified sugar-moiety. Moreover, the formation of truncated duplexes manifests the exceptional stability of the hybrid duplexes in the gas-phase. This stability arises from the modified sugar-moiety, which locks the tcDNA single strand into a conformation that is similar to RNA in A-form duplexes. The conformational particularity of tcDNA in the gas-phase was confirmed by ion mobility-mass spectrometry experiments on tcDNA, DNA, and RNA.

Gas-phase fragmentation and conformation of the sugar-modified antisense oligonucleotide tcDNA

Tricyclo-DNA (tcDNA) is a sugar- and backbone-modified analogue of DNA that is currently tested as antisense oligonucleotide for the treatment of Duchenne muscular dystrophy. The name tricyclo-DNA is derived from the modified sugar-moiety: the deoxyribose is extended to a three-membered ring system. This modification is designed to limit the flexibility of the structure, thus giving rise to entropically stabilized hybrid duplexes formed between tcDNA and complementary DNA or RNA oligonucleotides. While the structural modifications increase the biostability of the therapeutic agent, they also render the oligonucleotide inaccessible to enzyme-based sequencing methods. Tandem mass spectrometry constitutes an alternative sequencing technique for partially and fully modified oligonucleotides. For reliable sequencing, the fragmentation mechanism of the structure in question must be understood. Therefore, the presented work evaluates the effect of the modified sugar-moiety on the gas-phase dissociation of single stranded tcDNA. Moreover, our experiments reflect the exceptional gas-phase stability of hybrid duplexes that is most noticeable in the formation of truncated duplex ions upon collision-induced dissociation. The stability of the duplex arises from the modified sugar-moiety, as the rigid structure of the tcDNA single strand minimizes the change of the entropy for the annealing. Moreover, the tc-modification gives rise to extended conformations of the nucleic acids in the gas-phase, which was studied by ion mobility spectrometry-mass spectrometry.