Oligonucleotide Adsorption Affects Phase Transition but Not Interdigitation of diC14-Amidine Bilayers

Oligonucleotides have been extensively used in basic research of gene expression and function, vaccine design, and allergy and cancer therapy. Several oligonucleotide-based formulations have reached the clinical trial phase and one is already on the market. All these applications, however, are dependent on suitable carriers that protect oligonucleotides against degradation and improve their capture by target cells. The cationic lipid diC14-amidine efficiently delivers nucleic acids to mammalian cells. It was recently shown that diC14-amidine bilayers present an interdigitated phase which strongly correlates with a potent fusogenic activity at low temperatures. Interdigitated phases correspond to very ordered gel phases where the two bilayer leaflets are merged; they usually result from perturbations at the interfacial region such as modifications of the polar headgroup area or dehydration of the bilayer. Interdigitation has been described for asymmetric lipids or mixed-chain lipids of different chain lengths and for lipids with large effective headgroup sizes. It has also been described for symmetric lipids under pressure modifications or in the presence of alcohol, glycerol, acetonitrile, polymyxin B, or ions like thiocyanate. Surprisingly, the role of polyelectrolytes on membrane interdigitation has been only poorly investigated. In the present work, we use dynamic light scattering (DLS), differential scanning calorimetry (DSC), and electron spin resonance (ESR) to explore the effect of a small single-stranded oligonucleotide (ODN) polyelectrolyte on the structure and colloid stability of interdigitated diC14-amidine membranes.

Single polymers at surfaces: adsorption and detachment

This thesis is concerned with the adsorption and detachment of polymers at planar, rigid surfaces. We have carried out a systematic investigation of adsorption of polymers using analytical techniques as well as Monte Carlo simulations with a coarse grained off-lattice bead spring model. The investigation was carried out in three stages. In the first stage the adsorption of a single multiblock AB copolymer on a solid surface was investigated by means of simulations and scaling analysis. It was shown that the problem could be mapped onto an effective homopolymer problem. Our main result was the phase diagram of regular multiblock copolymers which shows an increase in the critical adsorption potential of the substrate with decreasing size of blocks. We also considered the adsorption of random copolymers which was found to be well described within the annealed disorder approximation. In the next phase, we studied the adsorption kinetics of a single polymer on a flat, structureless surface in the regime of strong physisorption. The idea of a ’stem-flower’ polymer conformation and the mechanism of ’zipping’ during the adsorption process were used to derive a Fokker-Planck equation with reflecting boundary conditions for the time dependent probability distribution function (PDF) of the number of adsorbed monomers. The numerical solution of the time-dependent PDF obtained from a discrete set of coupled differential equations were shown to be in perfect agreement with Monte Carlo simulation results. Finally we studied force induced desorption of a polymer chain adsorbed on an attractive surface. We approached the problem within the framework of two different statistical ensembles; (i) by keeping the pulling force fixed while measuring the position of the polymer chain end, and (ii) by measuring the force necessary to keep the chain end at fixed distance above the adsorbing plane. In the first case we treated the problem within the framework of the Grand Canonical Ensemble approach and derived analytic expressions for the various conformational building blocks, characterizing the structure of an adsorbed linear polymer chain, subject to pulling force of fixed strength. The main result was the phase diagram of a polymer chain under pulling. We demonstrated a novel first order phase transformation which is dichotomic i.e. phase coexistence is not possible. In the second case, we carried out our study in the “fixed height” statistical ensemble where one measures the fluctuating force, exerted by the chain on the last monomer when a chain end is kept fixed at height h over the solid plane at different adsorption strength ε. The phase diagram in the h − ε plane was calculated both analytically and by Monte Carlo simulations. We demonstrated that in the vicinity of the polymer desorption transition a number of properties like fluctuations and probability distribution of various quantities behave differently, if h rather than the force, f, is used as an independent control parameter.

Adsorption of macromolecules on interfaces studied by isothermal titration calorimetry

The mixing of nanoparticles with polymers to form composite materials has been applied for decades. They combine the advantages of polymers (e.g., elasticity, transparency, or dielectric properties) and inorganic nanoparticles (e.g., specific absorption of light, magneto resistance effects, chemical activity, and catalysis etc.). Nanocomposites exhibit several new characters that single-phase materials do not have. Filling the polymeric matrix with an inorganic material requires its homogeneous distribution in order to achieve the highest possible synergetic effect. To fulfill this requirement, the incompatibility between the filler and the matrix, originating from their opposite polarity, has to be resolved. A very important parameter here is the strength and irreversibility of the adsorption of the surface active compound on the inorganic material. In this work the Isothermal titration calorimetry (ITC) was applied as a method to quantify and investigate the adsorption process and binding efficiencies in organic-inorganic–hybrid-systems by determining the thermodynamic parameters (ΔH, ΔS, ΔG, KB as well as the stoichiometry n). These values provide quantification and detailed understanding of the adsorption process of surface active molecules onto inorganic particles. In this way, a direct correlation between the adsorption strength and structure of the surface active compounds can be achieved. Above all, knowledge of the adsorption mechanism in combination with the structure should facilitate a more rational design into the mainly empirically based production and optimization of nanocomposites.

The effect of elastic modulus and equilibrium vapor adsorption on capillary forces

Die Kapillarkraft entsteht durch die Bildung eines Meniskus zwischen zwei Festkörpen. In dieser Doktorarbeit wurden die Auswirkungen von elastischer Verformung und Flϋssigkeitadsorption auf die Kapillarkraft sowohl theoretisch als auch experimentell untersucht. Unter Verwendung eines Rasterkraftmikroskops wurde die Kapillarkraft zwischen eines Siliziumoxid Kolloids von 2 µm Radius und eine weiche Oberfläche wie n.a. Polydimethylsiloxan oder Polyisopren, unter normalen Umgebungsbedingungen sowie in variierende Ethanoldampfdrϋcken gemessen. Diese Ergebnisse wurden mit den Kapillarkräften verglichen, die auf einem harten Substrat (Silizium-Wafer) unter denselben Bedingungen gemessen wurden. Wir beobachteten eine monotone Abnahme der Kapillarkraft mit zunehmendem Ethanoldampfdruck (P) fϋr P/Psat > 0,2, wobei Psat der Sättigungsdampfdruck ist.rnUm die experimentellen Ergebnisse zu erklären, wurde ein zuvor entwickeltes analytisches Modell (Soft Matter 2010, 6, 3930) erweitert, um die Ethanoladsorption zu berϋcksichtigen. Dieses neue analytische Modell zeigte zwei verschiedene Abhängigkeiten der Kapillarkraft von P/Psat auf harten und weichen Oberflächen. Fϋr die harte Oberfläche des Siliziumwafers wird die Abhängigkeit der Kapillarkraft vom Dampfdruck vom Verhältnis der Dicke der adsorbierten Ethanolschicht zum Meniskusradius bestimmt. Auf weichen Polymeroberflächen hingegen hängt die Kapillarkraft von der Oberflächenverformung und des Laplace-Drucks innerhalb des Meniskus ab. Eine Abnahme der Kapillarkraft mit zunehmendem Ethanoldampfdruck hat demnach eine Abnahme des Laplace-Drucks mit zunehmendem Meniskusradius zur folge. rnDie analytischen Berechnungen, fϋr die eine Hertzsche Kontakt-deformation angenommen wurde, wurden mit Finit Element Methode Simulationen verglichen, welche die reale Deformation des elastischen Substrats in der Nähe des Meniskuses explizit berϋcksichtigen. Diese zusätzliche nach oben gerichtete oberflächenverformung im Bereich des Meniskus fϋhrt zu einer weiteren Erhöhung der Kapillarkraft, insbesondere fϋr weiche Oberflächen mit Elastizitätsmodulen < 100 MPa.rn

Plasmonic nanoparticles as sensors : a novel approach to quantify adsorption and diffusion kinetics

Biosensors find wide application in clinical diagnostics, bioprocess control and environmental monitoring. They should not only show high specificity and reproducibility but also a high sensitivity and stability of the signal. Therefore, I introduce a novel sensor technology based on plasmonic nanoparticles which overcomes both of these limitations. Plasmonic nanoparticles exhibit strong absorption and scattering in the visible and near-infrared spectral range. The plasmon resonance, the collective coherent oscillation mode of the conduction band electrons against the positively charged ionic lattice, is sensitive to the local environment of the particle. I monitor these changes in the resonance wavelength by a new dark-field spectroscopy technique. Due to a strong light source and a highly sensitive detector a temporal resolution in the microsecond regime is possible in combination with a high spectral stability. This opens a window to investigate dynamics on the molecular level and to gain knowledge about fundamental biological processes.rnFirst, I investigate adsorption at the non-equilibrium as well as at the equilibrium state. I show the temporal evolution of single adsorption events of fibrinogen on the surface of the sensor on a millisecond timescale. Fibrinogen is a blood plasma protein with a unique shape that plays a central role in blood coagulation and is always involved in cell-biomaterial interactions. Further, I monitor equilibrium coverage fluctuations of sodium dodecyl sulfate and demonstrate a new approach to quantify the characteristic rate constants which is independent of mass transfer interference and long term drifts of the measured signal. This method has been investigated theoretically by Monte-Carlo simulations but so far there has been no sensor technology with a sufficient signal-to-noise ratio.rnSecond, I apply plasmonic nanoparticles as sensors for the determination of diffusion coefficients. Thereby, the sensing volume of a single, immobilized nanorod is used as detection volume. When a diffusing particle enters the detection volume a shift in the resonance wavelength is introduced. As no labeling of the analyte is necessary the hydrodynamic radius and thus the diffusion properties are not altered and can be studied in their natural form. In comparison to the conventional Fluorescence Correlation Spectroscopy technique a volume reduction by a factor of 5000-10000 is reached.

Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Pressure Swing Adsorption on Carbon Molecular Sieves for Nitrogen Production: Modelling and Simulation with Aspen Adsorption

L’azoto è uno dei prodotti principali dell’industria chimica, utilizzato principalmente per assicurare un sicuro stoccaggio di composti infiammabili. Generatori con sistemi PSA sono spesso più economici della tradizionale distillazione criogenica. I processi PSA utilizzano una colonna a letto fisso, riempita con materiale adsorbente, che adsorbe selettivamente un componente da una miscela gassosa. L’ossigeno diffonde molto più velocemente dell'azoto nei pori di setacci molecolari carboniosi. Oltre ad un ottimo materiale adsorbente, anche il design è fondamentale per la performance di un processo PSA. La fase di adsorbimento è seguita da una fase di desorbimento. Il materiale adsorbente può essere quindi riutilizzato nel ciclo seguente. L’assenza di un simulatore di processo ha reso necessario l’uso di dati sperimentali per sviluppare nuovi processi. Un tale approccio è molto costoso e lungo. Una modellazione e simulazione matematica, che consideri tutti i fenomeni di trasporto, è richiesta per una migliore comprensione dell'adsorbente sia per l'ottimizzazione del processo. La dinamica della colonna richiede la soluzione di insiemi di PDE distribuite nel tempo e nello spazio. Questo lavoro è stato svolto presso l'Università di Scienze Applicate - Münster, Germania. Argomento di questa tesi è la modellazione e simulazione di un impianto PSA per la produzione di azoto con il simulatore di processo Aspen Adsorption con l’obiettivo di permettere in futuro ottimizzazioni di processo affidabili, attendibili ed economiche basate su computazioni numeriche. E' discussa l’ottimizzazione di parametri, dati cinetici, termodinamici e di equilibrio. Il modello è affidabile, rigoroso e risponde adeguatamente a diverse condizioni al contorno. Tuttavia non è ancora pienamente soddisfacente poiché manca una rappresentazione adeguata della cinetica ovvero dei fenomeni di trasporto di materia. La messa a punto del software permetterà in futuro di indagare velocemente nuove possibilità di operazione.

Adsorption of Components of the Plasma Kinin-forming System on the Surface of Porphyromonas gingivalis Involves Gingipains as the Major Docking Platforms

Enhanced production of proinflammatory bradykinin-related peptides, the kinins, has been suggested to contribute to the pathogenesis of periodontitis, a common inflammatory disease of human gingival tissues. In this report, we describe a plausible mechanism of activation of the kinin-generating system, also known as the contact system or kininogen-kallikrein-kinin system, by the adsorption of its plasma-derived components such as high-molecular-mass kininogen (HK), prekallikrein (PK), and Hageman factor (FXII) to the cell surface of periodontal pathogen Porphyromonas gingivalis. The adsorption characteristics of mutant strains deficient in selected proteins of the cell envelope suggested that the surface-associated cysteine proteinases, gingipains, bearing hemagglutinin/adhesin domains (RgpA and Kgp) serve as the major platforms for HK and FXII adhesion. These interactions were confirmed by direct binding tests using microplate-immobilized gingipains and biotinylated contact factors. Other bacterial cell surface components such as fimbriae and lipopolysaccharide were also found to contribute to the binding of contact factors, particularly PK. Analysis of kinin release in plasma upon contact with P. gingivalis showed that the bacterial surface-dependent mechanism is complementary to the previously described kinin generation system dependent on HK and PK proteolytic activation by the gingipains. We also found that several P. gingivalis clinical isolates differed in the relative significance of these two mechanisms of kinin production. Taken together, these data show the importance of this specific type of bacterial surface-host homeostatic system interaction in periodontal infections.

The adsorption of biomolecules to multi-walled carbon nanotubes is influenced by both pulmonary surfactant lipids and surface chemistry

Background During production and processing of multi-walled carbon nanotubes (MWCNTs), they may be inhaled and may enter the pulmonary circulation. It is essential that interactions with involved body fluids like the pulmonary surfactant, the blood and others are investigated, particularly as these interactions could lead to coating of the tubes and may affect their chemical and physical characteristics. The aim of this study was to characterize the possible coatings of different functionalized MWCNTs in a cell free environment. Results To simulate the first contact in the lung, the tubes were coated with pulmonary surfactant and subsequently bound lipids were characterized. The further coating in the blood circulation was simulated by incubating the tubes in blood plasma. MWCNTs were amino (NH2)- and carboxyl (-COOH)-modified, in order to investigate the influence on the bound lipid and protein patterns. It was shown that surfactant lipids bind unspecifically to different functionalized MWCNTs, in contrast to the blood plasma proteins which showed characteristic binding patterns. Patterns of bound surfactant lipids were altered after a subsequent incubation in blood plasma. In addition, it was found that bound plasma protein patterns were altered when MWCNTs were previously coated with pulmonary surfactant. Conclusions A pulmonary surfactant coating and the functionalization of MWCNTs have both the potential to alter the MWCNTs blood plasma protein coating and to determine their properties and behaviour in biological systems.

Self-assembly of focal point oligo-catechol ethylene glycol dendrons on titanium oxide surfaces: adsorption kinetics, surface characterization, and nonfouling properties

This work covers the synthesis of second-generation, ethylene glycol dendrons covalently linked to a surface anchor that contains two, three, or four catechol groups, the molecular assembly in aqueous buffer on titanium oxide surfaces, and the evaluation of the resistance of the monomolecular adlayers against nonspecific protein adsorption in contact with full blood serum. The results were compared to those of a linear poly(ethylene glycol) (PEG) analogue with the same molecular weight. The adsorption kinetics as well as resulting surface coverages were monitored by ex situ spectroscopic ellipsometry (VASE), in situ optical waveguide lightmode spectroscopy (OWLS), and quartz crystal microbalance with dissipation (QCM-D) investigations. The expected compositions of the macromolecular films were verified by X-ray photoelectron spectroscopy (XPS). The results of the adsorption study, performed in a high ionic strength ("cloud-point") buffer at room temperature, demonstrate that the adsorption kinetics increase with increasing number of catechol binding moieties and exceed the values found for the linear PEG analogue. This is attributed to the comparatively smaller and more confined molecular volume of the dendritic macromolecules in solution, the improved presentation of the catechol anchor, and/or their much lower cloud-point in the chosen buffer (close to room temperature). Interestingly, in terms of mechanistic aspects of "nonfouling" surface properties, the dendron films were found to be much stiffer and considerably less hydrated in comparison to the linear PEG brush surface, closer in their physicochemical properties to oligo(ethylene glycol) alkanethiol self-assembled monolayers than to conventional brush surfaces. Despite these differences, both types of polymer architectures at saturation coverage proved to be highly resistant toward protein adsorption. Although associated with higher synthesis costs, dendritic macromolecules are considered to be an attractive alternative to linear polymers for surface (bio)functionalization in view of their spontaneous formation of ultrathin, confluent, and nonfouling monolayers at room temperature and their outstanding ability to present functional ligands (coupled to the termini of the dendritic structure) at high surface densities.