Strategies to identify and further characterize novel and known genes involved in regulation of skeletogenesis

372 osteochondrodysplasias and genetically determined dysostoses were reported in 2007 [Superti-Furga and Unger, 2007]. For 215 of these conditions, an association with one or more genes can be stated, while the molecular changes for the remaining syndromes remain illusive to date. Thus, the present dissertation aims at the identification of novel genes involved in processes regarding cartilage/ bone formation, growth, differentiation and homeostasis, which may serve as candidate genes for the above mentioned conditions. Two different approaches were undertaken. Firstly, a high throughput EST sequencing project from a human fetal cartilage library was performed to identify novel genes in early skeletal development (20th week of gestation until 2nd year of life) that could be investigated as potential candidate genes. 5000 EST sequences were generated and analyzed representing 1573 individual transcripts, corresponding to known (1400) and to novel, yet uncharacterized genes (173). About 7% of the proteins were already described in cartilage/ bone development or homeostasis, showing that the generated library is tissue specific. The remaining profile of this library was compared to previously published libraries from different time points (8th–12th, 18th–20th week and adult human cartilage) that also showed a similar distribution, reflecting the quality of the presented library analyzed. Furthermore, three potential candidate genes (LRRC59, CRELD2, ZNF577) were further investigated and their potential involvement in skeletogenesis was discussed. Secondly, a disease-orientated approach was undertaken to identify downstream targets of LMX1B, the gene causing Nail-Patella syndrome (NPS), and to investigate similar conditions. Like NPS, Genitopatellar syndrome (GPS) is characterized by aplasia or hypoplasia of the patella and renal anomalies. Therefore, six GPS patients were enrolled in a study to investigate the molecular changes responsible for this relatively rare disease. A 3.07 Mb deletion including LMX1B and NR5A1 (SF1) was found in one female patient that showed features of both NPS and GPS and investigations revealed a 46,XY karyotype and ovotestes indicating true hermaphroditism. The microdeletion was not seen in any of the five other patients with GPS features only, but a potential regulatory element between the two genes cannot be ruled out yet. Since Lmx1b is expressed in the dorsal limb bud and in podocytes, proteomic approaches and expression profiling were performed with murine material of the limbs and the kidneys to identify its downstream targets. After 2D-gel electrophoresis with protein extracts from E13.5 fore limb buds and newborn kidneys of Lmx1b wild type and knock-out mice and mass spectrometry analysis, only two proteins, agrin and carbonic anhydrase 2, remained of interest, but further analysis of the two genes did not show a transcriptional down regulation by Lmx1b. The focus was switched to expression profiles and RNA from newborn Lmx1b wild type and knock-out kidneys was compared by microarray analysis. Potential Lmx1b targets were almost impossible to study, because of the early death of Lmx1b deficient mice, when the glomeruli, containing podocytes, are still immature. Because Lmx1b is also expressed during limb development, RNA from wild type and knock-out Lmx1b E11.5 fore limb buds was investigated by microarray, revealing four potential Lmx1b downstream targets: neuropilin 2, single-stranded DNA binding protein 2, peroxisome proliferative activated receptor, gamma, co-activator 1 alpha, and short stature homeobox 2. Whole mount in situ hybridization strengthened a potential down regulation of neuropilin 2 by Lmx1b, but further investigations including in situ hybridization and protein-protein interaction studies will be needed.

Three-dimensional electron microscopy of myriapod hemocyanin, planorbid snail acetylcholine-binding protein and cyanobacterial Vipp1

Three-dimensional electron microscopy (3-D EM) provides a framework for the analysis of large protein quaternary structures. The advantage over the generally higher resolving meth- od of X-ray crystallography is the embedding of the proteins in their physiological environ- ment. However, results of the two methods can be combined to obtain superior structural information. In this work, three different protein types – (i) Myriapod hemocyanin, (ii) vesi- cle-inducing protein in plastids 1 (Vipp1) and (iii) acetylcholine-binding protein (AChBP) – were structurally analyzed by 2-D and 3-D EM and, where possible, functionally interpreted.rnMyriapod hemocyanins have been previously shown to be 6x6-meric assemblies that, in case of Scutigera coleoptrata hemocyanin (ScoHc), show two 3x6-mer planes whith a stag- gering angle of approximately 60°. Here, previously observed structural differences between oxy- and deoxy-ScoHc could be substantiated. A 4° rotation between hexamers of two dif- ferent 3x6-mer planes was measured, which originates at the most central inter-hexamer in- terface. Further information about allosteric behaviour in myriapod hemocyanin was gained by analyzing Polydesmus angustus hemocyanin (PanHc), which shows a stable 3x6-mer and divergent histidine patterns in the inter-hexamer interfaces when compared to ScoHc. Both findings would conclusively explain the very different oxygen binding properties of chilopod and diplopod hemocyanin.rnVipp1 is a protein found in cyanobacteria and higher plants which is essential for thyla- koid membrane function and forms highly variable ring-shaped structures. In the course of this study, the first 3-D analysis of Vipp1 was conducted and yielded reconstructions of six differently sized Vipp1 rings from negatively stained images at resolutions between 20 to 30 Å. Furthermore, mutational analyses identified specific N-terminal amino acids that are essential for ring formation. On the basis of these analyses and previously published results, a hypothetical model of the Vipp1 tertiary and quaternary structure was generated.rnAChBP is a water-soluble protein in the hemolymph of mollusks. It is a structural and functional homologue of the ligand-binding domain of nicotinic acetylcholine receptors. For the freshwater snail Biomphalaria glabrata, we previously described two types of AChBP (BgAChBP1 and BgAChBP2). In this work, a 6 Å 3-D reconstruction of native BgAChBP is presented, which shows a dodecahedral assembly that is unprecedented for an AChBP. Single particle analysis of recombinantely expressed BgAChBP types led to preliminary results show- ing a dodecahedral assembly of BgAChBP1 and a dipentameric assembly of BgAChBP2. This indicates divergent biological functions of the two types.

High pressure surface plasmon spectroscopy

Der Einfluß von Druck auf die Eigenschaften dünner dielektrischer Filme wurde mit Hilfe von Oberflächenplasmonen-Spektroskopie untersucht. Die Arbeit kann aus der Perspektive der Materialcharakterisierung und aus apparativer Sicht betrachtet werden, da z.B. eine neue Hochdruckzelle konstruiert wurde, die kombinierte Oberflächenplasmonen-Elektrochemie Messungen erlaubt. SiO2-Solgel Filme wurden optimiert und auf ihre Widerstandsfähigkeit in Bufferlösungen und ihre Oberflächeneigenschaften hin untersucht. Eine Anwendung lag in der Charakterisierung von thermoresponsiven Acrylsäureisopropylamid Hydrogelen, die einen Volumenphasenübergang aufwiesen, dessen Eigenschaften durch Druck und die Beschränktheit des Films auf die Oberfläche beeinflußt wurden.Die Charakterisierung von DNA Hybridisierungsreaktionen an Oberflächen wurde mit einer Fluoreszenz-erweiterten Hochdruckapparatur durchgeführt. Zunächst wurde die Stabilität der zugrundeliegenden Bindematrix sichergestellt. Bei DNA Einzelsträngen führten Temperatur und Druck zu jeweils verringertem bzw. erhöhtem Signal. Entropie und Änderungen der Lösungsmitteleigenschaften wurden für die Signaländerungen verantwortlich gemacht. Die Eigenschaften der Doppelhelix wurden im Langmuir-Bild beschrieben. Der Brechungsindex von Kohlendioxid wurde bis zu 200 MPa gemessen und mit vorhandenen Gleichungen verglichen. Weiterhin wurde das Schwellverhalten von PMMA in scCO2/MMA-Mischungen untersucht. Mit Druck und MMA-Konzentration nimmt das Polymer vermehrt Kohlendioxid auf. Dadurch schwillt es an und sein Brechungsindex nimmt ab. Berechnungen unter Annahme einer idealen Mixtur ergaben gute qualitative Übereinstimmung mit den Meßwerten.Abschließend wurde eine neue Elektrochemie-Hochdruckzelle vorgestellt, die an Kaliumhexacyanoferrat(III)-(II) getestet wurde. Die Elektropolymerisation von Thiophen optisch untersucht.

DNA block copolymers – from micelles to machines

DNA block copolymer, a new class of hybrid material composed of a synthetic polymer and an oligodeoxynucleotide segment, owns unique properties which can not be achieved by only one of the two polymers. Among amphiphilic DNA block copolymers, DNA-b-polypropylene oxide (PPO) was chosen as a model system, because PPO is biocompatible and has a Tg < 0 °C. Both properties might be essential for future applications in living systems. During my PhD study, I focused on the properties and the structures of DNA-b-PPO molecules. First, DNA-b-PPO micelles were studied by scanning force microscopy (SFM) and fluorescence correlation spectroscopy (FCS). In order to control the size of micelles without re-synthesis, micelles were incubated with template-independent DNA polymerase TdT and deoxynucleotide triphosphates in reaction buffer solution. By carrying out ex-situ experiments, the growth of micelles was visualized by imaging in liquid with AFM. Complementary measurements with FCS and polyacrylamide gel electrophoresis (PAGE) confirmed the increase in size. Furthermore, the growing process was studied with AFM in-situ at 37 °C. Hereby the growth of individual micelles could be observed. In contrast to ex-situ reactions, the growth of micelles adsorbed on mica surface for in-situ experiments terminated about one hour after the reaction was initiated. Two reasons were identified for the termination: (i) block of catalytic sites by interaction with the substrate and (ii) reduced exchange of molecules between micelles and the liquid environment. In addition, a geometrical model for AFM imaging was developed which allowed deriving the average number of mononucleotides added to DNA-b-PPO molecules in dependence on the enzymatic reaction time (chapter 3). Second, a prototype of a macroscopic DNA machine made of DNA-b-PPO was investigated. As DNA-b-PPO molecules were amphiphilic, they could form a monolayer at the air-water interface. Using a Langmuir film balance, the energy released owing to DNA hybridization was converted into macroscopic movements of the barriers in the Langmuir trough. A specially adapted Langmuir trough was build to exchange the subphase without changing the water level significantly. Upon exchanging the subphase with complementary DNA containing buffer solution, an increase of lateral pressure was observed which could be attributed to hybridization of single stranded DNA-b-PPO. The pressure versus area/molecule isotherms were recorded before and after hybridization. I also carried out a series of control experiments, in order to identify the best conditions of realizing a DNA machine with DNA-b-PPO. To relate the lateral pressure with molecular structures, Langmuir Blodgett (LB) films were transferred to highly ordered pyrolytic graphite (HOPG) and mica substrates at different pressures. These films were then investigated with AFM (chapter 4). At last, this thesis includes studies of DNA and DNA block copolymer assemblies with AFM, which were performed in cooperation with different group of the Sonderforschungsbereich 625 “From Single Molecules to Nanoscopically Structured Materials”. AFM was proven to be an important method to confirm the formation of multiblock copolymers and DNA networks (chapter 5).

Rupture forces of split aptamers

Rupture forces of ligand-receptor interactions, such as proteins-proteins, proteins-cells, and cells-tissues, have been successfully measured by atomic force spectroscopy (AFS). For these measurements, the ligands and receptors were chemically modified so that they can be immobilized on the tip and on a substrate, respectively. The ligand interact the receptor when the tip approaches the substrate. This interaction can be studied by measuring rupture force upon retraction. However, this technique is not feasible for measurements involving small molecules, since they form only few H-bonds with their corresponding receptors. Modifying small molecules for immobilization on surfaces may block or change binding sites. Thus, recorded rupture forces might not reflect the full scope of the involved small ligand-receptor interactions.rnIn my thesis, a novel concept that allows measuring the rupture force of small involved ligand-receptor interactions and does not require molecular modification for immobilization was introduced. The rupture force of small ligand-receptor interaction is not directly measured but it can be determined from measurements in the presence and in the absence of the ligand. As a model system, the adenosine mono phosphate (AMP) and the aptamer that binds AMP were selected. The aptamer (receptor) is a single stranded DNA that can partially self-hybridize and form binding pockets for AMP molecules (ligands). The bonds between AMP and aptamer are provided by several H-bonds and pair stacking.rnIn the novel concept, the aptamer was split into two parts (oligo a and oligo b). One part was immobilized on the tip and the other one on the substrate. Approaching the tip to the substrate, oligo a and oligo b partially hybridized and the binding pockets were formed. After adding AMP into the buffer solution, the AMP bound in the pockets and additional H-bonds were formed. Upon retraction of the tip, the rupture force of the AMP-split aptamer complex was measured. In the presence of excess AMP, the rupture force increased by about 10 pN. rnThe dissociation constant of the AMP-split aptamer complex was measured on a single molecular level (~ 4 µM) by varying the AMP concentrations and measuring the rupture force at each concentration. Furthermore, the rupture force was amplified when more pockets were added to the split aptamer. rnIn the absence of AMP, the thermal off-rate was slightly reduced compared to that in the presence of AMP, indicating that the AMP stabilized the aptamer. The rupture forces at different loading rates did not follow the logarithmic fit which was usually used to describe the dependence of rupture forces at different loading rates of oligonucleotides. Two distinguished regimes at low and high loading rates were obtained. The two regimes were explained by a model in which the oligos located at the pockets were stretched at high loading rates. rnThe contribution of a single H-bond formed between the AMP molecule and the split aptamer was measured by reducing the binding groups of the AMP. The rupture forces reduce corresponding to the reduction of the binding groups. The phosphate group played the most important role in the formation of H-bond network between the AMP molecule and the split aptamer. rn

Investigations on DNA methylation by Dnmt2 and impact of tRNA modifications on TLR7 stimulation

The incorporation of modified nucleotides into ribonucleic acids (RNAs) is important for their structure and proper function. These modifications are inserted by distinct catalytic macromolecules one of them being Dnmt2. It methylates the Cytidine (C) at position 38 in tRNA to 5-methylcytidine (m5C). Dnmt2 has been a paradigm in this respect, because all of its nearest neighbors in evolution are DNA-cytosine C5-methyltransferases and methylate DNA, while its (own) DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. This work determines whether the biochemical potential for DNA methylation is present in the enzyme. It was discovered that DNA fragments, when presented as covalent RNA:DNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate. Additional minor deviations from a native tRNA structure that were seen to be tolerated by Dnmt2 were used for a stepwise development of a composite system of guide RNAs that enable the enzyme to perform cytidine methylation on single stranded DNA in vitro. Furthermore, a proof-of-principle is presented for utilizing the S-adenosyl methionine-analog cofactor SeAdoYn with Dnmt2 to search for new possible substrates in a SELEX-like approach.rnIn innate immunity, nucleic acids can function as pathogen associated molecular patterns (PAMPs) recognized by pattern recognition receptors (PRRs). The modification pattern of RNA is the discriminating factor for toll-like receptor 7 (TLR7) to distinguish between self and non-self RNA of invading pathogens. It was found that a 2'-O-methylated guanosine (Gm) at position18, naturally occurring at this position in some tRNAs, antagonizes recognition by TLR7. In the second part of this work it is pointed out, that recognition extends to the next downstream nucleotide and the effectively recognized molecular detail is actually a methylated dinucleotide. The immune silencing effect of the ribose methylation is most pronounced if the dinucleotide motif is composed of purin nucleobases whereas pyrimidines diminish the effect. Similar results were obtained when the Gm modification was transposed into other tRNA domains. Point mutations abolishing base pairings important for a proper tertiary structure had no effect on the immune stimulatory potential of a Gm modified tRNA. Taken together these results suggest a processive type of RNA inspection by TLR7.rn

Strukturbildung durch Selbstorganisation von Oligonukleotiden

Die DNA-Doppelhelix ist eine relativ dicke (Ø ≈ 2 nm), kompakte und dadurch auf kurzen Längenskalen relativ steife Verbindung (lp[dsDNA] ≈ 50-60 nm), mit einer klar definierten Struktur, die durch biologische Methoden sehr präzise manipuliert werden kann. Die Auswirkungen der primären Sequenz auf die dreidimensionale Strukturbildung ist gut verstanden und exakt vorhersagbar. Des Weiteren kann DNA an verschiedenen Stellen mit anderen Molekülen verknüpft werden, ohne dass ihre Selbsterkennung gestört wird. Durch die helikale Struktur besteht außerdem ein Zusammenhang zwischen der Lage und der räumlichen Orientierung von eingeführten Modifikationen. Durch moderne Syntheseverfahren lassen sich beliebige Oligonukleotidsequenzen im Bereich bis etwa 150-200 Basen relativ preiswert im Milligrammmaßstab herstellen. Diese Eigenschaften machen die DNA zu einem idealen Kandidaten zur Erzeugung komplexer Strukturen, die durch Selbsterkennung der entsprechenden Sequenzen gebildet werden. In der hier vorgelegten Arbeit wurden einzelsträngige DNA-Abschnitte (ssDNA) als adressierbare Verknüpfungsstellen eingesetzt, um verschiedene molekulare Bausteine zu diskreten nicht periodischen Strukturen zu verbinden. Als Bausteine dienten flexible synthetische Polymerblöcke und semiflexible Doppelstrang-DNA-Abschnitte (dsDNA), die an beiden Enden mit unterschiedlichen Oligonukleotidsequenzen „funktionalisiert“ sind. Die zur Verknüpfung genutzten Oligonukleotidabschnitte wurden so gewählt (n > 20 Basen), dass ihre Hybridisierung zu einer bei Raumtemperatur stabilen Doppelstrangbildung führt. Durch Kombination der Phosphoramiditsynthese von DNA mit einer festkörpergestützten Blockkopplungsreaktion konnte am Beispiel von Polyethylenoxiden ein sehr effektiver Syntheseweg zur Herstellung von ssDNA1-PEO-ssDNA2-Triblockcopolymeren entwickelt werden, der sich problemlos auf andere Polymere übertragen lassen sollte. Die Längen und Basenabfolgen der beiden Oligonukleotidsequenzen können dabei unabhängig voneinander frei gewählt werden. Somit wurden die Voraussetzungen geschaffen, um die Selbsterkennung von Oligonukleotiden durch Kombination verschiedener Triblockcopolymere zur Erzeugung von Multiblockcopolymeren zu nutzen, die mit klassischen Synthesetechniken nicht zugänglich sind. Semiflexible Strukturelemente lassen sich durch die Synthese von Doppelstrangfragmenten mit langen überstehenden Enden (sticky-ends) realisieren. Die klassischen Ansätze der molekularen Genetik zur Erzeugung von sticky-ends sind in diesem Fall nicht praktikabel, da sie zu Einschränkungen im Bezug auf Länge und Sequenz der überhängenden Enden führen. Als Methode der Wahl haben sich zwei verschiedene Varianten der Polymerase Kettenreaktion (PCR) erwiesen, die auf der Verwendung von teilkomplementären Primern beruhen. Die eigentlichen Primersequenzen wurden am 5´-Ende entweder über ein 2´-Desoxyuridin oder über einen kurzen Polyethylenoxid-Spacer (n = 6) mit einer frei wählbaren „sticky-end-Sequenz“ verknüpft. Mit diesen Methoden sind sowohl 3´- als auch 5´-Überhänge zugänglich und die Länge der Doppelstrangabschnitte kann über einen breiten Molmassenbereich sehr exakt eingestellt werden. Durch Kombination derartiger Doppelstrangfragmente mit den biosynthetischen Triblockcopolymeren lassen sich Strukturen erzeugen, die als Modellsysteme zur Untersuchung verschiedener Biomoleküle genutzt werden können, die in Form eines mehrfach gebrochenen Stäbchens vorliegen. Im letzten Abschnitt wurde gezeigt, dass durch geeignete Wahl der überstehenden Enden bzw. durch Hybridisierung der Doppelstrangfragmente mit passenden Oligonukleotiden verzweigte DNA-Strukturen mit Armlängen von einigen hundert Nanometern zugänglich sind. Im Vergleich zu den bisher veröffentlichten Methoden bietet diese Herangehensweise zwei entscheidende Vorteile: Zum einen konnte der Syntheseaufwand auf ein Minimum reduziert werden, zum anderen ist es auf diesem Weg möglich die Längen der einzelnen Arme, unabhängig voneinander, über einen breiten Molmassenbereich zu variieren.

Structure formation of amphiphilic molecules at the air,water interface and after film transfer

One of the basic concepts of molecular self-assembly is that the morphology of the aggregate is directly related to the structure and interaction of the aggregating molecules. This is not only true for the aggregation in bulk solution, but also for the formation of Langmuir films at the air/water interface. Thus, molecules at the interface do not necessarily form flat monomolecular films but can also aggregate into multilayers or surface micelles. In this context, various novel synthetic molecules were investigated in terms of their morphology at the air/water interface and in transferred films. rnFirst, the self-assembly of semifluorinated alkanes and their molecular orientation at the air/water interface and in transferred films was studied employing scanning force microscopy (SFM) and Kelvin potential force microscopy. Here it was found, that the investigated semifluorinated alkanes aggregate to form circular surface micelles with a diameter of 30 nm, which are constituted of smaller muffin-shaped subunits with a diameter of 10 nm. A further result is that the introduction of an aromatic core into the molecular structure leads to the formation of elongated surface micelles and thus implements a directionality to the self-assembly. rnSecond, the self-assembly of two different amphiphilic hybrid materials containing a short single stranded desoxyribonucleic acid (DNA) sequence was investigated at the air/water interface. The first molecule was a single stranded DNA (11mer) molecule with two hydrophobically modified 5-(dodec-1-ynyl)uracil nucleobases at the terminal 5'-end of the oligonucleotide sequence. Isotherm measurements revealed the formation of semi-stable films at the air/water interface. SFM imaging of films transferred via Langmuir-Blodgett technique supported this finding and indicated mono-, bi- and multilayer formation, according to the surface pressure applied upon transfer. Within these films, the hydrophilic DNA sequence was oriented towards air covering 95% of the substrate.rnSimilar results were obtained with a second type of amphiphile, a DNA block copolymer. Furthermore, the potential to perform molecular recognition experiments at the air/water interface with these DNA hybrid materials was evaluated.rnThird, polyglycerol ester molecules (PGE), which are known to form very stable foams, were studies. Aim was to elucidate the molecular structure of PGE molecules at the air/water interface in order to comprehend the foam stabilization mechanism. Several model systems mimicking the air/water interface of a PGE foam and methods for a noninvasive transfer were tested and characterized by SFM. It could be shown, that PGE stabilizes the air/water interface of a foam bubble by formation of multiple surfactant layers. Additionally, a new transfer technique, the bubble film transfer was established and characterized by high speed camera imaging.The results demonstrate the diversity of structures, which can be formed by amphiphilic molecules at the air/water interface and after film transfer, as well as the impact of the chemical structure on the aggregate morphology.