Each organism has to maintain the integrity of its genetic code, which is stored in its DNA. This is achieved by strongly controlled and regulated cellular processes such as DNA replication, -repair and -recombination. An essential element of these processes is the unwinding of the duplex strands of the DNA helix. This biochemical reaction is catalyzed by helicases that use the energy of nucleoside triphophate (NTP) hydrolysis. Although all helicases comprise highly conserved domains in their amino acid sequence, they exhibit large variations regarding for example their structure, their function and their target nucleic acid structures. The main objective of this thesis is to obtain insight into the DNA unwinding mechanisms of three helicases from two different organisms. These helicase vary in their structures and are involved in different pathways of DNA metabolism. In particular the replicative, hexameric helicase Large Tumor-Antigen (T-Antigen) from Simian virus 40 and the DNA repair helicases RecQ2 and RecQ3 from Arabidopsis thaliana are studied. To observe DNA unwinding by these helicases in real-time on the single molecule level, a biophysical technique, called magnetic tweezers, was applied. This technique allows to stretch single DNA molecules attached to magnetic particles. Simultaneously one can measure the DNA end-to-end distance. Special DNA hairpin templates allowed to characterize different parameters of the DNA unwinding reaction such as the unwinding velocity, the length of unwound DNA (processivity) or the influence of forces. From this mechanistic models about the functions of the helicases could be obtained. T-Antigen is found to be one of the slowest and most processive helicases known so far. In contrast to prokaryotic helicases, the unwinding velocity of T-Antigen shows a weak dependence on the applied force. Since current physical models for the unwinding velocity fail to describe the data an alternative model is developed. The investigated RecQ helicases are found to unwind and close short stretches of DNA in a repetitive fashion. This activity is shown for the first time under external forces. The experiments revealed that the repetitive DNA unwinding is based on the ability of both enzymes to switch from one single DNA strand to the other. Although RecQ2 and RecQ3 perform repetitive DNA unwinding, both enzymes differ largely in the measured DNA unwinding properties. Most importantly, while RecQ2 is a classical helicase that unwinds DNA, RecQ3 mostly rewinds DNA duplexes. These different properties may reflect different specific tasks of the helicases during DNA repair processes. To obtain high spatial resolution in DNA unwinding experiments, the experimental methods were optimized. An improved and more stable magnetic tweezers setup with sub-nanometer resolution was built. Additionally, different methods to prepare various DNA templates for helicase experiments were developed. Furthermore, the torsional stability of magnetic particles within an external field was investigated. The results led to selection rules for DNA-microsphere constructs that allow high resolution measurements. / Jeder Organismus ist bestrebt, die genetischen Informationen intakt zu halten, die in seiner DNA gespeichert sind. Dies wird durch präzise gesteuerte zelluläre Prozesse wie DNA-Replikation, -Reparatur und -Rekombination verwirklicht. Ein wesentlicher Schritt ist dabei das Entwinden von DNA-Doppelsträngen zu Einzelsträngen. Diese chemische Reaktion wird von Helikasen durch die Hydrolyse von Nukleosidtriphosphaten katalysiert. Obwohl bei allen Helikasen bestimmte Aminosäuresequenzen hoch konserviert sind, können sie sich in Eigenschaften wie Struktur, Funktion oder DNA Substratspezifität stark unterscheiden. Gegenstand der vorliegenden Arbeit ist es, die Entwindungsmechanismen von drei verschieden Helikasen aus zwei unterschiedlichen Organismen zu untersuchen, die sich in ihrer Struktur sowie ihrer Funktion unterscheiden. Es handelt sich dabei um die replikative, hexamerische Helikase Large Tumor-Antigen (T-Antigen) vom Simian-Virus 40 und die DNA-Reparatur-Helikasen RecQ2 und RecQ3 der Pflanze Arabidopsis thaliana. Um DNA-Entwindung in Echtzeit zu untersuchen, wird eine biophysikalische Einzelmolekültechnik, die \"Magnetische Pinzette\", verwendet. Mit dieser Technik kann man ein DNA-Molekül, das an ein magnetisches Partikel gebunden ist, strecken und gleichzeitig dessen Gesamtlänge messen. Mit speziellen DNA-Konstrukten kann man so bestimmte Eigenschaften der Helikasen bei der DNA-Entwindung, wie z.B. Geschwindigkeit, Länge der entwundenen DNA (Prozessivität) oder den Einfluß von Kraft, ermitteln. Es wird gezeigt, dass T-Antigen eine der langsamsten und prozessivsten Helikasen ist. Im Gegensatz zu prokaryotischen Helikasen ist die Entwindungsgeschwindigkeit von T-Antigen kaum kraftabhängig. Aktuelle Modelle sagen dieses Verhalten nicht vorraus, weshalb ein alternatives Modell entwickelt wird. Die untersuchten RecQ-Helikasen zeigen ein Entwindungsverhalten bei dem permanent kurze Abschnitte von DNA entwunden und wieder zusammengeführt werden. Dieses Verhalten wird hier zum ersten Mal unter dem Einfluß externer Kräfte gemessen. Es wird gezeigt, dass die permanente Entwindung auf die Fähigkeit beider Helikasen, von einem einzelen DNA-Strang auf den anderen zu wechseln, zurückzuführen ist. Obwohl RecQ2 und RecQ3 beide das Verhalten des permanenten Entwindens aufzeigen, unterscheiden sie sich stark in anderen Eigenschaften. Der gravierendste Unterschied ist, dass RecQ2 wie eine klassische Helikase die DNA entwindet, während RecQ3 eher bestrebt ist, die DNA-Einzelstränge wieder zusammenzuführen. Die unterschiedlichen Eigenschaften könnten die verschieden Aufgaben beider Helikasen während DNA-Reparaturprozessen widerspiegeln. Weiterhin werden die experimentellen Methoden optimiert, um möglichst hohe Auflösungen der Daten zu erreichen. Dazu zählen der Aufbau einer verbesserten und stabileren \"Magnetischen Pinzette\" mit sub-nanometer Auflösung und die Entwicklung neuer Methoden, um DNA Konstrukte herzustellen. Außerdem wird die Torsions\\-steifigkeit von magnetischen Partikeln in externen magnetischen Feldern untersucht. Dabei finden sich Auswahlkriterien für DNA-gebundene magnetische Partikel, durch die eine hohe Auflösung erreicht wird.

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Knowledge of the properties of single molecule diffusion is important for controlling dynamic self-assembly of molecular structures. A powerful experimental technique for determining diffusion coefficients is the recording of diffusion-induced signal fluctuations by a locally fixed point-like probe. Here, the signal becomes modified, whenever a molecule enters a certain detection area on the surface under the probe. The technique is minimal invasive and has a very good time resolution, enabling the investigation of highly mobile molecules. Theories are necessary for the analysis of the fluctuations and the extraction of diffusion properties. In this thesis, three methods are presented, which are based on the autocorrelation function, the distribution of peak widths and the distribution of interpeak intervals. Analytical expressions are derived for the distributions and the autocorrelation function in case of molecules, which can be described by circular or rectangular shapes. For rectangular shaped molecules, rotational diffusion can influence the recorded fluctuations. To allow for a simultaneous determination of rotational and translational diffusion coefficients the analytical treatment is extended. Furthermore, new methods are developed to determine the diffusion tensor for anisotropic stochastic molecular motion, using either one linearly extended probe or two individual probes. Coarse-graining the signal recorded by a point-like probe, which repeatedly moves on a line or a circle, is suggested for experimental implementation. All facets of the evaluation methods are verified against kinetic Monte Carlo simulations. Applications to experimental data, recorded by a locally fixed scanning tunneling microscope tip, are demonstrated for copperphthalocyanine and PTCDA molecules diffusing on Ag(100).

La nano-organisation de la membrane cellulaire est essentielle à la régulation de certaines fonctions cellulaires. Dans cette thèse, les récepteurs EGF, CPεT et de la transferrine ont été marqués avec des nanoparticules luminescentes et ont été suivis à la fois dans leur environnement local dans la membrane cellulaire vivantes pour de longues durées et sous un flux hydrodynamique. Nous avons alors appliqué des techniques d'inférence bayésienne, d’arbre de décision et de clustering de données extraire des informations quantitatives sur les paramètres caractéristiques du mouvement des récepteurs, notamment la forme de leur confinement dans des microdomaines. L’application d’une force hydrodynamique sur les nanoparticules nous a alors permis de sonder les interactions auxquelles ces récepteurs sont soumis. Nous avons appliqué cette approche in vitro pour favoriser et mesurer la dissociation in vitro de paires récepteur / ligand à haute affinité entre des récepteurs membranaires et leurs ligands pharmaceutiques, telles que HB-EGF et DTR et l’avons ensuite appliqué à l’étude d’interactions à la membrane cellulaire. Nous avons ainsi mis en évidence trois modes différents d'organisation de la membrane et de confinement des récepteurs: le confinement de CPεTR est déterminé par l'interaction entre les récepteurs et les constituants lipidiques / protéiques des microdomaines, le potentiel de confinement de l'EGFR résulte de l'interaction avec les lipides et les protéines de l’environnement du radeau et de l’interaction avec la F-actine; les récepteurs de la transferrine diffusent librement dans la membrane, uniquement limités stériquement par des barrières d’actine, selon le modèle ‘picket-and-fence’. Nous avons de plus montré que les nanodomaines de type radeau sont rattachés au cytoskelette d’actine. Ce travail présente donc à la fois un aperçu quantitatif du récepteur membranaire, des mécanismes d’organisation à l’échelle nanométrique, et établit un cadre méthodologique avec lequel différents types de propriétés membranaires peuvent être étudiés. / In this thesis, EGF, CPεT and transferrin receptors were labeled with luminescent nanoparticles, , and were tracked both in their local environment in the cell membrane and under a hydrodynamic flow. Bayesian inference, Bayesian decision tree, and data clustering techniques can then be applied to obtain quantitative information on the receptor motion parameters. Furthermore, we introduced hydrodynamic force application in vitro to study biomolecule dissociation between membrane receptors and their pharmaceutical ligands in high affinity receptor- ligand pairs, such as HB-EGF and DTR. Finally, three different modes of membrane organization and receptor confinement were revealed: the confinement of CPεTR is determined by the interaction between the receptors and the lipid/protein constituents of the raft; the confining potential of EGFR results from the interaction with lipids and proteins of the raft environment and from the interaction with F-actin; transferrin receptors diffuse freely in the membrane, only sterically limited by actin barriers, according to the “picket-and-fence” model. We moreover showed that all raft nanodomains are attached to the actin cytoskeleton.

La translocation de biopolymères à travers un nanopore intervient dans de nombreux processus biologiques et technologiques, comme le transport nucléocytoplasmique dans le pore nucléaire des cellules eucaryotes, la sécrétion de protéines, le séquençage rapide de l’ADN ou l’électrophorèse capillaire.Nous proposons une technique optique en molécule unique originale pour l’étude de la translocation de biopolymères à travers un nanopore basée sur l’effet Zero-Mode Waveguide. Nous nous sommes intéressés au passage d’ADN double-brin de plusieurs tailles, d’ADN simple-brin et d’ARN, entraînés par un flux à travers une membrane nanoporeuse track-etched. Nous montrons qu’il existe un flux critique régissant le passage des biopolymères indépendant du rayon des pores ainsi que de la taille des biopolymères et de leur nature, conformément aux prédictions théoriques de Brochard et de Gennes.Le pore nucléaire est un nanopore biologique responsable du transport sélectif entre le noyau et lecytoplasme des cellules. Nous avons étudié l’influence de la concentration en importinBeta1 – une protéine nécessaire au transport nucléocytoplasmique – sur l’organisation du canal central du pore nucléaire deXenopus laevis en mesurant la diffusion de molécules de Dextran fluorescentes à travers celui-ci. Nous observons une ouverture du canal central à basse concentration suivi d’un rétrécissement de celui-ci à plus forte concentration. Cette évolution du rayon du canal central avec la concentration en importin Beta1est conforme aux modèles en champ moyen de Opferman et coll. et de Ando et coll. et aux observations expérimentales sur des systèmes reconstitués in vitro de Lim et coll. et Zahn et coll. / The translocation of biopolymers through a nanopore is a feature common to many biological andtechnological processes such as the nucleocytoplasmic transport through the nuclear pore complex(NPC), protein secretion, fast DNA sequencing or capillary electrophoresis.We have developed an original single molecule optical detection technique for the study of biopolymerstranslocation through a nanopore based on the Zero-Mode Waveguide effect. We studied thepassage of double stranded DNA of different sizes, of single stranded DNA and of double-stranded RNAdriven by a flux through track-etched nanoporous membranes. We demonstrate that translocation isgoverned by a critical flux independent of both biopolymer size and nature and of the pore radius inagreement with the theoretical predictions of Brochard and de Gennes.The NPC is a biological nanopore responsible for the selective transport between cytoplasm andnucleus in cells. We studied the influence of importinBeta1 concentration – a protein involved in the nucleocytoplasmictransport – on the structure of the central channel of the NPC of Xenopus laevis byassessing the diffusion of fluorescently labeled Dextran molecules through the NPC. We observe anopening of the central channel at low concentration followed by a shrinking at higher concentrationin importinBeta1 in agreement with mean-field models from Opferman et al. and Ando et al. and withexperiments on biomimetic in vitro systems from Lim et al. and Zahn et al.

Mesoscopic structures in liquids have an impact on the diffusion dynamics of the constituting molecules. Smectic 8CB liquid crystals on silicon wafers show the formation of mesoscopic structures on the μm scale at a film thickness of 200 nm. Depending on the kind of substrate (thermally grown or native SiOx), we observed the formation of focal conic domains (FCDs) and a new type of terraced holes, respectively. Dynamics are described via single perylene diimide tracer molecule tracking of translational diffusion and in the case of FCDs by a combination of translation and rotation detected via fluorescence correlation spectroscopy. Tailoring perylene diimide molecules such that the optical transition dipole moment follows the liquid crystal director allows mapping out FCDs and investigating the dynamics within a single FCD.

The use of super-resolution (SR) microscopy is an important tool for understanding the inside mechanisms of bacterial cells. However, for SR imaging, the labelling of the proteins of interest is a great challenge as flourescent proteins (FPs) are often too big to be directly fused to the target protein and traditional immunolabelling with antibodies creates too long separation between the fluorophore and the target protein. In an attempt to overcome this hurdle, the Escherichia coli (E. coli) cell division protein FtsZ is in this project fused to a nanotag (NT) that is subsequently labelled with a nanobody (NB). The ALFA-tag, a short amino acid peptide, is chromosomally fused to the target protein, creating a MG1655/FtsZ-ALFA strain where all FtsZ proteins have an ALFA-tag attached. Recognising the ALFA-tag is the NB αALFA (anti-ALFA) which is fused to a FP and expressed from a plasmid. The MG1655/FtsZ-ALFA strain is labelled using standard plasmid transformation which allows for live cell imaging of the division ring in E. coli. Both FPs sfGFP and mEos3.2 are used for labelling which means that the cells can be imaged in epifluorescence microscopy and single-molecule Photo-Activated Localisation Microscopy (PALM), and even single-molecule time lapses of the constricting FtsZ-ring is possible. This system is also applicable to other bacterial proteins. / Superupplösningsmikroskopi (SUM) är ett viktigt redskap för att förstå de inre processerna i en bakteriecell. Att på ett framgångsrikt sätt tagga målproteinerna har dock visat sig vara en utmaning för SUM. Att direkttagga målproteinerna med fluorescerande protein är oftast inte möjligt på grund av de fluorescerande proteinernas storlek och traditionell märkning med antikroppar skapar ett för stort avstånd mellan fluorofor och målprotein. För att överkomma detta problem taggas här celldelningsproteinet FtsZ iEscherichia coli (E. coli) med hjälp av nanotaggar (NT) och nanokroppar (NK). ALFA-taggen, en kort aminosyrapeptid, är kromosomt bunden till FtsZ i cellinjen MG1655/FtsZ-ALFA, så att varje FtsZ protein som produceras har en ALFA-tag bunden till sig. NK αALFA (anti-ALFA) känner igen och binder till ALFA-taggen när de kommer i kontakt. NK är bunden till ett fluorescerande protein och uttryckt från en plasmid vilket gör att MG1655/FtsZ-ALFA kan bli taggad med hjälp av vanlig plasmidtransformation. Denna metod möjliggör mikroskopi av divisionsringen i levande E. coli-celler. Två olika fluorescerande protein används, sfGFP och mEos3.2, vilket innebär att både epifluorensmikroskopi och fotoaktiverad lokaliseringsmikroskopi (PALM) kan användas. Dessutom är även intervallfotografering i enmolekylmikroskopi av divisionsringens konstriktion möjligt. Denna märkningsteknik är vidare applicerbar på andra bakteriella protein.

Outer membrane proteins (OMPs) maintain the viability of Gram-negative bacteria by functioning as receptors, transporters, ion channels, lipases, and porins. Folding and assembly of OMPs involves synchronized action of chaperones and multi-protein machineries which escort the highly hydrophobic polypeptides to their target outer membrane in a folding competent state. Previous studies have identified proteins and their involvement along the OMP biogenesis pathway. Yet, the mechanisms of action and the intriguing ability of all these molecular machines to work without the typical cellular energy source of ATP, but solely based on thermodynamic principles, are still not well understood. Here, we highlight how different single-molecule studies can shed additional light on the mechanisms and kinetics of OMP biogenesis.

The rise of superbugs, including antibiotic-resistant bacteria, and virus outbreaks, such as the recent coronavirus scare, illustrate the need for rapid detection of disease pathogens. Widespread availability of rapid disease identification would facilitate outbreak prevention and specific treatment. The ARROW biosensor microchip can directly detect single molecules through fluorescence-based optofluidic interrogation. The nature of the microfluidic channels found on optofluidic sensor platforms sets some of the ultimate sensitivity and accuracy limits and can result in false negative test results. Yet higher sensitivity and specificity is desired through hydrodynamic focusing. Novel 3D hydrodynamic focusing designs were developed and implemented on the ARROW platform, an optofluidic lab-on-a-chip single-molecule detector device. Microchannels with cross-section dimensions smaller than 10 μm were formed using sacrificial etching of photoresist layers covered with plasma-enhanced chemical-vapor-deposited silicon dioxide on a silicon wafer. Buffer fluid carried to the focusing junction enveloped an intersecting sample fluid, resulting in 3D focusing of the sample stream. The designs which operate across a wide range of fluid velocities through pressure-driven flow were integrated with optical waveguides in order to interrogate fluorescing particles and confirm 3D focusing, characterize diffusion, and quantify optofluidic detection enhancement of single viruses on chip.

Nanopore technology has introduced new techniques for single particle detection and analysis. A nanopore consists of a small opening in a membrane on the nanometer scale. Nanopores are found in nature and are utilized for transporting molecules through biological membranes. Researchers have been able to mimic naturally forming biological nanopores and utilize them for a variety of sensing applications. Nanopores, fabricated either organically or inorganically, can be used for detecting biomarkers such as proteins, nucleic acids, and metabolites that translocate the membrane by way of the nanopore. Constant ionic current flow is measured through the nanopore by way of a sensitive ammeter. In the presence of a biomarker, the ionic current flow will be impeded, causing the electrical signal to drop. This drop uniquely corresponds to the type of particle passing through the nanopore. In this work, the thin membrane on which the nanopore resides is created through a newly developed meniscus shaped sacrificial technique. The sacrificial polymer material starts as a liquid and is confined to the microfluidic channel through the capillary effect, giving it the meniscus profile. It is used as a structural support on which a thin silicon dioxide layer is grown. The layer of oxide takes on the same natural meniscus shape as the sacrificial material. The polymer is subsequently etched, resulting in a hollow core liquid channel with a suspended meniscus membrane. This process allows a thin membrane to be fabricated on top of a microfluidic channel that ranges from 50-200 nm in thickness. The meniscus membrane is crucial to the success of nanopore formation. The nanoscale membrane allows for smaller, more precise nanopores to be created. Reduced nanopore dimensions are advantageous for the detection of smaller biomarkers. The platform described in this dissertation integrates solid-state naturally forming meniscus membranes with solid-core and optofluidic waveguides for nanopore detection applications. The waveguides allow for a particle trap to be introduced to the system. The ability to trap particles directly under the nanopore is critical to the speed of which the nanopore can operate. This dissertation focuses on the fabrication, characterization, and testing of an optofluidic platform that features a nanopore for rapid single molecule detection and analysis.