Refine
Has Fulltext
- yes (6)
Is part of the Bibliography
- yes (6)
Document Type
- Doctoral Thesis (5)
- Master Thesis (1)
Keywords
- Einzelmolekülmikroskopie (3)
- Mikroskopie (2)
- Optik (2)
- dSTORM (2)
- 3D (1)
- Aberration (1)
- Adaptive Optics (1)
- Adaptive Optik (1)
- Dimension 3 (1)
- Dimerisierung (1)
Institute
- Physikalisches Institut (6) (remove)
In this work fluorescence-based single molecule detection at low concetration is investigated, with an emphasis on the usage of active transport and waveguides.
Active transport allows to overcome the limits of diffusion-based systems in terms of the lowest detectable threshold of concentration.
The effect of flow in single molecule experiments is investigated and a theoretical model is derived for laminar flow.
Waveguides on the other hand promise compact detection schemes and show great potential for their possible integration into lab-on-a-chip applications. Their properties in single molecule experiments are analyzed with help of a method based on the reciprocity theorem of electromagnetic theory.
This thesis reviews the fundamentals of three-dimensional super-resolution localization imaging. In order to infer the axial coordinate of the emission of single fluorophores, the point spread function is engineered following a technique usually referred to as astigmatic imaging by the introduction of a cylindrical lens to the detection path of a microscope.
After giving a short introduction to optics and localization microscopy, I outline sources of aberrations as frequently encountered in 3D-localization microscopy and will discuss their respective impact on the precision and accuracy of the localization process. With the knowledge from these considerations, experiments were designed and conducted to verify the validity of the conclusions and to demonstrate the abilities of the proposed microscope to resolve biological structures in the three spatial dimensions. Additionally, it is demonstrated that measurements of huge volumes with virtually no aberrations is in principle feasible.
During the course of this thesis, a new method was introduced for inferring axial coordinates. This interpolation method based on cubic B-splines shows superior performance in the calibration of a microscope and the evaluation of subsequent measurement and will therefore be used and explained in this work.
Finally, this work is also meant to give future students some guidance for entering the field of 3D localization microscopy and therefore, detailed protocols are provided covering the specific aspects of two color 3D localization imaging.
For determination of structures and structural dynamics of proteins organic fluorophores are a standard instrument. Intra- and intermolecular contact of biomolecular structures are determined in time-resolved and stationary fluorescence microscopy experiments by quenching of organic fluorophores due to Photoinduced Electron Transfer (PET) and dimerization interactions. Using PET we show in this work that end-to-end contact dynamics of serine-glycine peptides are slowed down by glycosylation. This slow down is due to a change in reaction enthalpy for end-to-end contact and is partly compensated by entropic effects. In a second step we test how dimerization of MR121 fluorophore pairs reports on end-to-end contact dynamics. We show that in aqueous solutions containing strong denaturants MR121 dimerization reports advantageously on contact dynamics for glycine-serine oligopeptides compared to the previously used MR121/tryptophane PET reporters. Then we analyze dimer interactions and quenching properties of different commercially available fluorophores being standards in Förster Resonance Energy Transfer (FRET) measurements. Distances in biomolecules are determinable using FRET, but for very flexible biomolecules the analysis of masurement data can be distorted if contact of the two FRET fluorophores is likely. We quantify how strong the quenching of fluorophore pairs with two different or two identical fluorophores is. Dimer spectra and association constants are quantified to estimate if fluophores are applicable in various applications, e.g. in FRET measurements with unstructured peptides and proteins.
Die Fluoreszenzmikroskopie ist eine vielseitig einsetzbare Untersuchungsmethode für biologische Proben, bei der Biomoleküle selektiv mit Fluoreszenzfarbstoffen markiert werden, um sie dann mit sehr gutem Kontrast abzubilden. Dies ist auch mit mehreren verschiedenartigen Zielmolekülen gleichzeitig möglich, wobei üblicherweise verschiedene Farbstoffe eingesetzt werden, die über ihre Spektren unterschieden werden können.
Um die Anzahl gleichzeitig verwendbarer Färbungen zu maximieren, wird in dieser Arbeit zusätzlich zur spektralen Information auch das zeitliche Abklingverhalten der Fluoreszenzfarbstoffe mittels spektral aufgelöster Fluoreszenzlebensdauer-Mikroskopie (spectrally resolved fluorescence lifetime imaging microscopy, sFLIM) vermessen. Dazu wird die Probe in einem Konfokalmikroskop von drei abwechselnd gepulsten Lasern mit Wellenlängen von 485 nm, 532nm und 640nm angeregt. Die Detektion des Fluoreszenzlichtes erfolgt mit einer hohen spektralen Auflösung von 32 Kanälen und gleichzeitig mit sehr hoher zeitlicher Auflösung von einigen Picosekunden. Damit wird zu jedem detektierten Fluoreszenzphoton der Anregungslaser, der spektrale Kanal und die Ankunftszeit registriert. Diese detaillierte multidimensionale Information wird von einem Pattern-Matching-Algorithmus ausgewertet, der das Fluoreszenzsignal mit zuvor erstellten Referenzpattern der einzelnen Farbstoffe vergleicht. Der Algorithmus bestimmt so für jedes Pixel die Beiträge der einzelnen Farbstoffe.
Mit dieser Technik konnten pro Anregungslaser fünf verschiedene Färbungen gleichzeitig dargestellt werden, also theoretisch insgesamt 15 Färbungen. In der Praxis konnten mit allen drei Lasern zusammen insgesamt neun Färbungen abgebildet werden, wobei die Anzahl der Farben vor allem durch die anspruchsvolle Probenvorbereitung limitiert war. In anderen Versuchen konnte die sehr hohe Sensitivität des sFLIM-Systems genutzt werden, um verschiedene Zielmoleküle voneinander zu unterscheiden, obwohl sie alle mit demselben Farbstoff markiert waren. Dies war möglich, weil sich die Fluoreszenzeigenschaften eines Farbstoffmoleküls geringfügig in Abhängigkeit von seiner Umgebung ändern. Weiterhin konnte die sFLIM-Technik mit der hochauflösenden STED-Mikroskopie (STED: stimulated emission depletion) kombiniert werden, um so hochaufgelöste zweifarbige Bilder zu erzeugen, wobei nur ein einziger gemeinsamer STED-Laser benötigt wurde.
Die gleichzeitige Erfassung von mehreren photophysikalischen Messgrößen sowie deren Auswertung durch den Pattern-Matching-Algorithmus ermöglichten somit die Entwicklung von neuen Methoden der Fluoreszenzmikroskopie für Mehrfachfärbungen.
Point-spread function engineering for single-molecule localization microscopy in brain slices
(2022)
Single-molecule localization microscopy (SMLM) is the method of choice to study biological specimens on a nanoscale level. Advantages of SMLM imply its superior specificity due to targeted molecular fluorescence labeling and its enhanced tissue preservation compared to electron microscopy, while reaching similar resolution. To reveal the molecular organization of protein structures in brain tissue, SMLM moves to the forefront: Instead of investigating brain slices with a thickness of a few µm, measurements of intact neuronal assemblies (up to 100 µm in each dimension) are required. As proteins are distributed in the whole brain volume and can move along synapses in all directions, this method is promising in revealing arrangements of neuronal protein markers. However, diffraction-limited imaging still required for the localization of the fluorophores is prevented by sample-induced distortion of emission pattern due to optical aberrations in tissue slices from non-superficial planes. In particular, the sample causes wavefront dephasing, which can be described as a summation of Zernike polynomials. To recover an optimal point spread function (PSF), active shaping can be performed by the use of adaptive optics. The aim of this thesis is to establish a setup using a deformable mirror and a wavefront sensor to actively shape the PSF to correct the wavefront phases in a super-resolution microscope setup. Therefore, fluorescence-labeled proteins expressed in different anatomical regions in brain tissue will be used as experiment specimen. Resolution independent imaging depth in slices reaching tens of micrometers is aimed.
Single molecule localization microscopy has seen a remarkable growth since its first
experimental implementations about a decade ago. Despite its technical challenges,
it is already widely used in medicine and biology and is valued as a unique tool
to gain molecular information with high specificity. However, common illumination techniques do not allow the use of single molecule sensitive super-resolution
microscopy techniques such as direct stochastic optical reconstruction microscopy
(dSTORM) for whole cell imaging. In addition, they can potentially alter the
quantitative information.
In this thesis, I combine dSTORM imaging in three dimensions with lattice lightsheet illumination to gain quantitative molecular information from cells unperturbed by the illumination and cover slip effects. Lattice light-sheet illumination
uses optical lattices for beam shaping to restrict the illumination to the detectable
volume. I describe the theoretical background needed for both techniques and detail
the experimental realization of the system as well as the software that I developed
to efficiently evaluate the data.
Eventually, I will present key datasets that demonstrate the capabilities of the
developed microscope system with and without dSTORM. My main goal here was
to use these techniques for imaging the neural cell adhesion molecule (NCAM, also
known as CD56) in whole cells. NCAM is a plasma membrane receptor known to
play a key role in biological processes such as memory and learning. Combining
dSTORM and lattice light-sheet illumination enables the collection of quantitative
data of the distribution of molecules across the whole plasma membrane, and shows
an accumulation of NCAM at cell-cell interfaces. The low phototoxicity of lattice
light-sheet illumination further allows for tracking individual NCAM dimers in living cells, showing a significant dependence of its mobility on the actin skeleton of
the cell.