Investigation of the electric field enhanced PNA-DNA hybridization on Au surface by using surface plasmon field-enhanced fluorescence spectroscopy (SPFS)

Recently, the surface plasmon field-enhanced fluorescence spectroscopy (SPFS) was developed as a kinetic analysis and a detection method with dual- monitoring of the change of reflectivity and fluorescence signal for the interfacial phenomenon. A fundamental study of PNA and DNA interaction at the surface using surface plasmon fluorescence spectroscopy (SPFS) will be investigated in studies. Furthermore, several specific conditions to influence on PNA/DNA hybridization and affinity efficiency by monitoring reflective index changes and fluorescence variation at the same time will be considered. In order to identify the affinity degree of PNA/DNA hybridizaiton at the surface, the association constant (kon) and the dissociation constant (koff) will be obtained by titration experiment of various concentration of target DNA and kinetic investigation. In addition, for more enhancing the hybridization efficiency of PNA/DNA, a study of polarized electric field enhancement system will be introduced and performed in detail. DNA is well-known polyelectrolytes with naturally negative charged molecules in its structure. With polarized electrical treatment, applying DC field to the metal surface, which PNA probe would be immobilized at, negatively charged DNA molecules can be attracted by electromagnetic attraction force and manipulated to the close the surface area, and have more possibility to hybridize with probe PNA molecules by hydrogen bonding each corresponding base sequence. There are several major factors can be influenced on the hybridization efficiency.

Total internal reflection fluorescence cross-correlation spectroscopy: theory and application for studying boundary slip phenomenon

I present a new experimental method called Total Internal Reflection Fluorescence Cross-Correlation Spectroscopy (TIR-FCCS). It is a method that can probe hydrodynamic flows near solid surfaces, on length scales of tens of nanometres. Fluorescent tracers flowing with the liquid are excited by evanescent light, produced by epi-illumination through the periphery of a high NA oil-immersion objective. Due to the fast decay of the evanescent wave, fluorescence only occurs for tracers in the ~100 nm proximity of the surface, thus resulting in very high normal resolution. The time-resolved fluorescence intensity signals from two laterally shifted (in flow direction) observation volumes, created by two confocal pinholes are independently measured and recorded. The cross-correlation of these signals provides important information for the tracers’ motion and thus their flow velocity. Due to the high sensitivity of the method, fluorescent species with different size, down to single dye molecules can be used as tracers. The aim of my work was to build an experimental setup for TIR-FCCS and use it to experimentally measure the shear rate and slip length of water flowing on hydrophilic and hydrophobic surfaces. However, in order to extract these parameters from the measured correlation curves a quantitative data analysis is needed. This is not straightforward task due to the complexity of the problem, which makes the derivation of analytical expressions for the correlation functions needed to fit the experimental data, impossible. Therefore in order to process and interpret the experimental results I also describe a new numerical method of data analysis of the acquired auto- and cross-correlation curves – Brownian Dynamics techniques are used to produce simulated auto- and cross-correlation functions and to fit the corresponding experimental data. I show how to combine detailed and fairly realistic theoretical modelling of the phenomena with accurate measurements of the correlation functions, in order to establish a fully quantitative method to retrieve the flow properties from the experiments. An importance-sampling Monte Carlo procedure is employed in order to fit the experiments. This provides the optimum parameter values together with their statistical error bars. The approach is well suited for both modern desktop PC machines and massively parallel computers. The latter allows making the data analysis within short computing times. I applied this method to study flow of aqueous electrolyte solution near smooth hydrophilic and hydrophobic surfaces. Generally on hydrophilic surface slip is not expected, while on hydrophobic surface some slippage may exists. Our results show that on both hydrophilic and moderately hydrophobic (contact angle ~85°) surfaces the slip length is ~10-15nm or lower, and within the limitations of the experiments and the model, indistinguishable from zero.

Tracer diffusion at water-oil interfaces studied by fluorescence correlation spectroscopy

The adsorption of particles and surfactants at water-oil interfaces has attracted continuous attention because of its emulsion stabilizing effect and the possibility to form two-dimensional materials. Herein, I studied the interfacial diffusion of single molecules and nanoparticles at water-oil interfaces using fluorescence correlation spectroscopy. rnrnFluorescence correlation spectroscopy (FCS) is a promising technique to study diffusion of fluorescent tracers in diverse conditions. This technique monitors and analyzes the fluorescence fluctuation caused by single fluorescent tracers coming in and out of a diffraction-limited observation volume “one at a time”. Thus, this technique allows a combination of high precision, high spatial resolution and low tracer concentration. rnrnIn chapter 1, I discussed some controversial questions regarding the properties of water-hydrophobic interfaces and also introduced the current progress on the stability and dynamic of single nanoparticles at water-oil interfaces. The materials and setups I used in this thesis were summarized in chapter 2. rnrnIn chapter 3, I presented a new strategy to study the properties of water-oil interfaces. The two-dimensional diffusion of isolated molecular tracers at water/n-alkane interfaces was measured using fluorescence correlation spectroscopy. The diffusion coefficients of larger tracers with a hydrodynamic radius of 4.0 nm agreed well with the values calculated from the macroscopic viscosities of the two bulk phases. However, for small molecule tracers with hydrodynamic radii of only 1.0 and 0.6 nm, notable deviations were observed, indicating the existence of an interfacial region with a reduced effective viscosity. rnrnIn chapter 4, the interfacial diffusion of nanoparticles at water-oil interfaces was investigated using FCS. In stark contrast to the interfacial diffusion of molecular tracers, that of nanoparticles at any conditions is slower than the values calculated in accordance to the surrounding viscosity. The diffusion of nanoparticles at water-oil interfaces depended on the interfacial tension of liquid-liquid interfaces, the surface properties of nanoparticles, the particle sizes and the viscosities of surrounding liquid phases. In addition, the interfacial diffusion of nanoparticles with Janus motif is even slower than that of their symmetric counterparts. Based on the experimental results I obtained, I drew some possibilities to describe the origin of nanoparticle slowdown at water-oil interfaces.

Measurement of the forward-backward asymmetry of Z boson decays in electron-positron pairs with the ATLAS detector in proton-proton collisions at root out s = 7TeV at the LHC

In this thesis the measurement of the effective weak mixing angle wma in proton-proton collisions is described. The results are extracted from the forward-backward asymmetry (AFB) in electron-positron final states at the ATLAS experiment at the LHC. The AFB is defined upon the distribution of the polar angle between the incoming quark and outgoing lepton. The signal process used in this study is the reaction pp to zgamma + X to ee + X taking a total integrated luminosity of 4.8\,fb^(-1) of data into account. The data was recorded at a proton-proton center-of-mass energy of sqrt(s)=7TeV. The weak mixing angle is a central parameter of the electroweak theory of the Standard Model (SM) and relates the neutral current interactions of electromagnetism and weak force. The higher order corrections on wma are related to other SM parameters like the mass of the Higgs boson.rnrnBecause of the symmetric initial state constellation of colliding protons, there is no favoured forward or backward direction in the experimental setup. The reference axis used in the definition of the polar angle is therefore chosen with respect to the longitudinal boost of the electron-positron final state. This leads to events with low absolute rapidity have a higher chance of being assigned to the opposite direction of the reference axis. This effect called dilution is reduced when events at higher rapidities are used. It can be studied including electrons and positrons in the forward regions of the ATLAS calorimeters. Electrons and positrons are further referred to as electrons. To include the electrons from the forward region, the energy calibration for the forward calorimeters had to be redone. This calibration is performed by inter-calibrating the forward electron energy scale using pairs of a central and a forward electron and the previously derived central electron energy calibration. The uncertainty is shown to be dominated by the systematic variations.rnrnThe extraction of wma is performed using chi^2 tests, comparing the measured distribution of AFB in data to a set of template distributions with varied values of wma. The templates are built in a forward folding technique using modified generator level samples and the official fully simulated signal sample with full detector simulation and particle reconstruction and identification. The analysis is performed in two different channels: pairs of central electrons or one central and one forward electron. The results of the two channels are in good agreement and are the first measurements of wma at the Z resonance using electron final states at proton-proton collisions at sqrt(s)=7TeV. The precision of the measurement is already systematically limited mostly by the uncertainties resulting from the knowledge of the parton distribution functions (PDF) and the systematic uncertainties of the energy calibration.rnrnThe extracted results of wma are combined and yield a value of wma_comb = 0.2288 +- 0.0004 (stat.) +- 0.0009 (syst.) = 0.2288 +- 0.0010 (tot.). The measurements are compared to the results of previous measurements at the Z boson resonance. The deviation with respect to the combined result provided by the LEP and SLC experiments is up to 2.7 standard deviations.

Diffusion in heterogeneous systems studied by laser scanning confocal microscopy and fluorescence correlation spectroscopy

Understanding and controlling the mechanism of the diffusion of small molecules, macromolecules and nanoparticles in heterogeneous environments is of paramount fundamental and technological importance. The aim of the thesis is to show, how by studying the tracer diffusion in complex systems, one can obtain information about the tracer itself, and the system where the tracer is diffusing. rnIn the first part of my thesis I will introduce the Fluorescence Correlation Spectroscopy (FCS) which is a powerful tool to investigate the diffusion of fluorescent species in various environments. By using the main advantage of FCS namely the very small probing volume (<1µm3) I was able to track the kinetics of phase separation in polymer blends at late stages by looking on the molecular tracer diffusion in individual domains of the heterogeneous structure of the blend. The phase separation process at intermediate stages was monitored with laser scanning confocal microscopy (LSCM) in real time providing images of droplet coalescence and growth. rnIn a further project described in my thesis I will show that even when the length scale of the heterogeneities becomes smaller than the FCS probing volume one can still obtain important microscopic information by studying small tracer diffusion. To do so, I will introduce a system of star shaped polymer solutions and will demonstrate that the mobility of small molecular tracers on microscopic level is nearly not affected by the transition of the polymer system to a “glassy” macroscopic state. rnIn the last part of the thesis I will introduce and describe a new stimuli responsive system which I have developed, that combines two levels of nanoporosity. The system is based on poly-N-isopropylacrylamide (PNIPAM) and silica inverse opals (iOpals), and allows controlling the diffusion of tracer molecules. rn

Complex tracer mobilities in polymer networks revealed by fluorescence correlation spectroscopy

Gels are elastic porous polymer networks that are accompanied by pronounced mechanical properties. Due to their biocompatibility, ‘responsive hydrogels’ (HG) have many biomedical applications ranging from biosensors and drug delivery to tissue engineering. They respond to external stimuli such as temperature and salt by changing their dimensions. Of paramount importance is the ability to engineer penetrability and diffusion of interacting molecules in the crowded HG environment, as this would enable one to optimize a specific functionality. Even though the conditions under which biomedical devices operate are rather complex, a bottom-up approach could reduce the complexity of mutually coupled parameters influencing tracer mobility. The present thesis focuses on the interaction-induced tracer diffusion in polymer solutions and their homologous gels, probed by means of Fluorescence Correlation Spectroscopy (FCS). This is a single-molecule-sensitive technique having the advantage of optimal performance under ultralow tracer concentrations, typically employed in biosensors. Two different types of hydrogels have been investigated, a conventional one with broad polydispersity in the distance between crosslink points and a so-called ‘ideal’, with uniform mesh size distribution. The former is based on a thermoresponsive polymer, exhibiting phase separation in water at temperatures close to the human body temperature. The latter represents an optimal platform to study tracer diffusion. Mobilities of different tracers have been investigated in each network, varying in size, geometry and in terms of tracer-polymer attractive strength, as perturbed by different stimuli. The thesis constitutes a systematic effort towards elucidating the role of the strength and nature of different tracer-polymer interactions, on tracer mobilities; it outlines that interactions can still be very important even in the simplified case of dilute polymer solutions; it also demonstrates that the presence of permanent crosslinks exerts distinct tracer slowdown, depending on the tracer type and the nature of the tracer-polymer interactions, expressed differently by each tracer with regard to the selected stimulus. In aqueous polymer solutions, the tracer slowdown is found to be system-dependent and no universal trend seems to hold, in contrast to predictions from scaling theory for non-interacting nanoparticle mobility and empirical relations concerning the mesh size in polymer solutions. Complex tracer dynamics in polymer networks may be distinctly expressed by FCS, depending on the specific synergy among-at least some of - the following parameters: nature of interactions, external stimuli employed, tracer size and type, crosslink density and swelling ratio.

The oxidation capacity of the atmosphere - OH and HO 2 radical measurements in a boreal forest environment using laser induced fluorescence spectroscopy

Das wichtigste Oxidationsmittel für den Abbau flüchtiger Kohlenwasserstoffverbindungen (VOC, engl.: volatile organic compounds) in der Atmosphäre ist das Hydroxylradikal (OH), welches sich in einem schnellen chemischen Gleichgewicht mit dem Hydroperoxylradical (HO2) befindet. Bisherige Messungen und Modellvergleiche dieser Radikalspezies in Waldgebieten haben signifikante Lücken im Verständnis der zugrundeliegenden Prozesse aufgezeigt.rnIm Rahmen dieser Doktorarbeit wurden Messungen von OH- und HO2-Radikalen mittelsrnlaserinduzierten Fluoreszensmesstechnik (LIF, engl.: laser-induced fluorescence) in einem Nadelwald in Süd-Finnland während der Messkampagne HUMPPA–COPEC–2010 (Hyytiälä United Measurements of Photochemistry and Particles in Air – Comprehensive Organic Precursor Emission and Concentration study) im Sommer 2010 durchgeführt. Unterschiedliche Komponenten des LIF-Instruments wurden verbessert. Eine modifizierte Methode zur Bestimmung des Hintergrundsignals (engl.: InletPreInjector technique) wurde in den Messaufbaurnintegriert und erstmals zur Messung von atmosphärischem OH verwendet. Vergleichsmessungen zweier Instrumente basierend auf unterschiedlichen Methoden zur Messung von OH-Radikalen, chemische Ionisationsmassenspektrometrie (CIMS - engl.: chemical ionization mass spectrometry) und LIF-Technik, zeigten eine gute Übereinstimmung. Die Vergleichsmessungen belegen das Vermögen und die Leistungsfähigkeit des modifizierten LIF-Instruments atmosphärische OH Konzentrationen akkurat zu messen. Nachfolgend wurde das LIF-Instrument auf der obersten Plattform eines 20m hohen Turmes positioniert, um knapp oberhalb der Baumkronen die Radikal-Chemie an der Schnittstelle zwischen Ökosystem und Atmosphäre zu untersuchen. Umfangreiche Messungen - dies beinhaltet Messungen der totalen OH-Reaktivität - wurden durchgeführt und unter Verwendung von Gleichgewichtszustandsberechnungen und einem Boxmodell, in welches die gemessenen Daten als Randbedingungen eingehen, analysiert. Wenn moderate OH-Reaktivitäten(k′(OH)≤ 15 s−1) vorlagen, sind OH-Produktionsraten, die aus gemessenen Konzentrationen von OH-Vorläuferspezies berechnet wurden, konsistent mit Produktionsraten, die unter der Gleichgewichtsannahme von Messungen des totalen OH Verlustes abgeleitet wurden. Die primären photolytischen OH-Quellen tragen mit einem Anteil von bis zu einem Drittel zur Gesamt-OH-Produktion bei. Es wurde gezeigt, dass OH-Rezyklierung unter Bedingungen moderater OH-Reaktivität hauptsächlich durch die Reaktionen von HO2 mit NO oder O3 bestimmt ist. Während Zeiten hoher OH-Reaktivität (k′(OH) > 15 s−1) wurden zusätzliche Rezyklierungspfade, die nicht über die Reaktionen von HO2 mit NO oder O3, sondern direkt OH bilden, aufgezeigt.rnFür Hydroxylradikale stimmen Boxmodell-Simulationen und Messungen gut übereinrn(OHmod/OHobs=1.04±0.16), während HO2-Mischungsverhältnisse in der Simulation signifikant unterschätzt werden (HO2mod/HO2obs=0.3±0.2) und die simulierte OH-Reaktivität nicht mit der gemessenen OH-Reaktivität übereinstimmt. Die gleichzeitige Unterschätzung der HO2-Mischungsverhältnisse und der OH-Reaktivität, während OH-Konzentrationen von der Simulation gut beschrieben werden, legt nahe, dass die fehlende OH-Reaktivität in der Simulation eine noch unberücksichtigte HO2-Quelle darstellt. Zusätzliche, OH-unabhängigernRO2/HO2-Quellen, wie z.B. der thermische Zerfall von herantransportiertem peroxyacetylnitrat (PAN) und die Photolyse von Glyoxal sind indiziert.

New enhancement strategies for plasmon-enhanced fluorescence biosensors

This thesis investigates metallic nanostructures exhibiting surface plasmon resonance for the amplification of fluorescence signal in sandwich immunoassays. In this approach, an analyte is captured by an antibody immobilized on a plasmonic structure and detected by a subsequently bound fluorophore labeled detection antibody. The highly confined field of surface plasmons originates from collective charge oscillations which are associated with high electromagnetic field enhancements at the metal surface and allow for greatly increased fluorescence signal from the attached fluorophores. This feature allows for improving the signal-to-noise ratio in fluorescence measurements and thus advancing the sensitivity of the sensor platform. In particular, the thesis presents two plasmonic nanostructures that amplify fluorescence signal in devices that rely on epifluorescence geometry, in which the fluorophore absorbs and emits light from the same direction perpendicular to the substrate surface.rnThe first is a crossed relief gold grating that supports propagating surface plasmon polaritons (SPPs) and second, gold nanoparticles embedded in refractive index symmetric environment exhibiting collective localized surface plasmons (cLSPs). Finite-difference time-domain simulations are performed in order to design structures for the optimum amplification of established Cy5 and Alexa Fluor 647 fluorophore labels with the absorption and emission wavelengths in the red region of spectrum. The design takes into account combined effect of surface plasmon-enhanced excitation rate, directional surface plasmon-driven emission and modified quantum yield for characteristic distances in immunoassays. Homebuilt optical instruments are developed for the experimental observation of the surface plasmon mode spectrum, measurements of the angular distribution of surface plasmon-coupled fluorescence light and a setup mimicking commercial fluorescence reading systems in epifluorescence geometry.rnCrossed relief grating structures are prepared by interference lithography and multiple copies are made by UV nanoimprint lithography. The fabricated crossed diffraction gratings were utilized for sandwich immunoassay-based detection of the clinically relevant inflammation marker interleukin 6 (IL-6). The enhancement factor of the crossed grating reached EF=100 when compared to a flat gold substrate. This result is comparable to the highest reported enhancements to date, for fluorophores with relatively high intrinsic quantum yield. The measured enhancement factor excellently agrees with the predictions of the simulations and the mechanisms of the enhancement are explained in detail. Main contributions were the high electric field intensity enhancement (30-fold increase) and the directional fluorescence emission at (4-fold increase) compared to a flat gold substrate.rnCollective localized surface plasmons (cLSPs) hold potential for even stronger fluorescence enhancement of EF=1000, due to higher electric field intensity confinement. cLSPs are established by diffractive coupling of the localized surface plasmon resonance (LSPR) of metallic nanoparticles and result in a narrow resonance. Due to the narrow resonance, it is hard to overlap the cLSPs mode with the absorption and emission bands of the used fluorophore, simultaneously. Therefore, a novel two resonance structure that supports SPP and cLSP modes was proposed. It consists of a 2D array of cylindrical gold nanoparticles above a low refractive index polymer and a silver film. A structure that supports the proposed SPP and cLSP modes was prepared by employing laser interference lithography and the measured mode spectrum was compared to simulation results.rn

Monitoring kinetic processes in polymeric colloids by fluorescence correlation spectroscopy

Polymerbasierte Kolloide mit Groen im Nanometerbereich werden als aussichts- reiche Kandidaten fur die Verkapselung und den Transport von pharmazeutischen Wirkstoen angesehen. Daher ist es wichtig die physikalischen Prozesse, die die Bil- dung, Struktur und kinetische Stabilitat der polymerbasierten Kolloide beein ussen, besser zu verstehen. Allerdings ist die Untersuchung dieser Prozesse fur nanome- tergroe Objekte kompliziert und erfordert fortgeschrittene Techniken. In dieser Arbeit beschreibe ich Untersuchungen, bei denen Zwei-Farben-Fluoreszenzkreuz- korrelationsspektroskopie (DC FCCS) genutzt wurde, um Informationen uber die Wechselwirkung und den Austausch von dispergierten, nanometergroen Kolloiden zu bekommen. Zunachst habe ich den Prozess der Polymernanopartikelherstellung aus Emul- sionstropfen untersucht, welcher einen der am haugsten angewendeten Prozesse der Nanopartikelformulierung darstellt. Ich konnte zeigen, dass mit DC FCCS eindeutig und direkt Koaleszenz zwischen Emulsionstropfen gemessen werden kann. Dies ist von Interesse, da Koaleszenz als Hauptgrund fur die breite Groenverteilung der nalen Nanopartikel angesehen wird. Weiterhin habe ich den Austausch von Mizellen bildenden Molekulen zwischen amphiphilen Diblock Kopolymermizellen untersucht. Als Modellsystem diente ein Linear-Burste Block Kopolymer, welches Mizellen mit einer dichten und kurzen Korona bildet. Mit Hilfe von DC FCCS konnte der Austausch in verschiedenen Losungsmitteln und bei verschiedenen Temperaturen beobachtet werden. Ich habe herausgefunden, dass in Abhangigkeit der Qualitat des Losungsmittels die Zeit des Austausches um Groenordnungen verschoben werden kann, was eine weitreichende Einstellung der Austauschkinetik ermoglicht. Eine Eigenschaft die all diese Kolloide gemeinsam haben ist ihre Polydispersitat. Im letzten Teil meiner Arbeit habe ich am Beispiel von Polymeren als Modellsystem untersucht, welchen Eekt Polydispersitat und die Art der Fluoreszenzmarkierung auf FCS Experimente haben. Eine Anpassung des klassischen FCS Modells kann die FCS Korrelationskurven dieser Systeme beschreiben. Die Richtigkeit meines Ansatzes habe ich mit dem Vergleich zur Gel-Permeations-Chromatographie und Brownschen Molekulardynamiksimulationen bestatigt.