A5052481780- DNA and Nucleic Acid Chemistry
- Advanced Fluorescence Microscopy Techniques
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Force Microscopy Techniques and Applications
- RNA Research and Splicing
- Mesoporous Materials and Catalysis
- Bacteriophages and microbial interactions
- Molecular Junctions and Nanostructures
- DNA Repair Mechanisms
- Porphyrin and Phthalocyanine Chemistry
- Advanced Electron Microscopy Techniques and Applications
- Toxin Mechanisms and Immunotoxins
- Photosynthetic Processes and Mechanisms
- Near-Field Optical Microscopy
- Amyotrophic Lateral Sclerosis Research
- Photochemistry and Electron Transfer Studies
- RNA Interference and Gene Delivery
- Bacterial Genetics and Biotechnology
- Spectroscopy and Quantum Chemical Studies
- Epigenetics and DNA Methylation
- Advanced Biosensing Techniques and Applications
- RNA modifications and cancer
- Protein Structure and Dynamics
Universität Ulm
2015-2024
Center for Integrated Quantum Science and Technology
2020
Institute of Biophysics
2014-2017
Ludwig-Maximilians-Universität München
2006-2013
Center for Integrated Protein Science Munich
2007-2013
Center for NanoScience
2006-2013
Max Planck Institute of Biochemistry
2012
Max Planck Society
2012
Max Planck Institute for Polymer Research
2008
Nanosystems Initiative Munich
2007
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro vivo. However, generalized protocols FRET standards ensure the reproducibility accuracy measurements efficiencies are currently lacking. Here we report results a comparative blind study which 20 labs determined (E) several dye-labeled DNA duplexes. Using unified, straightforward method, obtained with s.d. between ±0.02 ±0.05. We...
Abstract Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro vivo. We performed an international blind involving 19 laboratories to assess uncertainty FRET for proteins with respect measured efficiency histograms, determination distances, detection quantification structural dynamics. Using two protein systems distinct conformational changes dynamics, we obtained ≤0.06, corresponding interdye distance precision...
TFIIE and the archaeal homolog TFE enhance DNA strand separation of eukaryotic RNAPII RNAP during transcription initiation by an unknown mechanism. We have developed a fluorescently labeled recombinant M. jannaschii system to probe complex, consisting promoter DNA, TBP, TFB, TFE, RNAP. localized position winged helix (WH) Zinc ribbon (ZR) domains on using single-molecule FRET. The interaction sites WH domain elongation factor Spt4/5 overlap, both factors compete for binding. Binding...
The bacteriophage φ29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of portal motor complex. Several mechanical models for the generation these high complex predict coupling translocation rotation head-tail connector dodecamer. Putative is investigated here combining methods single-molecule force spectroscopy with polarization-sensitive fluorescence. In our experiment, we observe function in several packaging complexes parallel using video...
Stimulated-emission depletion (STED) microscopy improves image resolution by encoding additional spatial information in a second stimulated-decay channel with spatially-varying strength. Here we demonstrate that is also encoded the fluorophore lifetime and this can be used to improve of STED microscopy. By solving kinetic model for emission presence time-varying pulse, derive effective as function pulse duration. We find best given power achieved infinitesimally short duration; however,...
Post-translational modifications of proteins have emerged as a major mechanism for regulating gene expression. However, our understanding how histone directly affect chromatin function remains limited. In this study, we investigate acetylation H3 at lysine 64 (H3K64ac), previously uncharacterized on the lateral surface octamer. We show that H3K64ac regulates nucleosome stability and facilitates eviction hence expression in vivo. line with this, demonstrate is enriched vivo transcriptional...
Significance How transcription factors (TFs) activate is a long-standing but still unsolved question. We analyzed serum response factor (SRF), stimulus-responsive TF mediating immediate early gene (IEG) and cytoskeletal expression at single-molecule resolution. Cell stimulation enhanced SRF activity by increasing the number of long chromatin-associated molecules in an oscillating pattern. Further, chromatin residence time, binding events segregated into three distinct time regimes (short,...
Abstract Type I interferon (IFN) signalling is tightly controlled. Upon recognition of DNA by cyclic GMP-AMP synthase (cGAS), stimulator genes (STING) translocates along the endoplasmic reticulum (ER)-Golgi axis to induce IFN signalling. Termination achieved through autophagic degradation or recycling STING retrograde Golgi-to-ER transport. Here, we identify GTPase ADP-ribosylation factor 1 (ARF1) as a crucial negative regulator cGAS-STING Heterozygous ARF1 missense mutations cause...
Single-pair fluorescence resonance energy transfer was used to track RNA exiting from polymerase II (Pol II) in elongation complexes. Measuring the distance between 5' end and three known locations within complex allows us determine its position by means of triangulation. leaves active center cleft via previously proposed exit tunnel then disengages enzyme surface. When reaches lengths 26 29 nt, associates with Pol at base dock domain. Because initiation factor TFIIB binds domain tunnel, may...
We apply mesoporous thin silica films with nanometer-sized pores as drug carriers and incorporate the widely used anticancer Doxorubicin. Through single-molecule based measurements, we gain mechanistic insights into diffusion inside film, which governs drug-delivery at target-site. Drug dynamics nanopores is controlled by pore size surface modification. The release kinetics determined live-cell measurements prove applicability of system for drug-delivery. This study demonstrates that...
The histone variant H2A.Z has been implicated in many biological processes, such as gene regulation and genome stability. Here, we present the identification of H2A.Z.2.2 (Z.2.2), a novel alternatively spliced provide comprehensive characterization its expression chromatin incorporation properties. Z.2.2 mRNA is found all human cell lines tissues with highest levels brain. We show proper splicing vivo existence this protein humans. Furthermore, demonstrate binding to H2A.Z-specific TIP60...
Crystallographic studies of the RNA polymerase II (Pol II) elongation complex (EC) revealed locations downstream DNA and DNA-RNA hybrid, but not course nontemplate strand in transcription bubble upstream duplex. Here we used single-molecule Fluorescence Resonance Energy Transfer (smFRET) experiments to locate with our recently developed Nano Positioning System (NPS). In resulting complete model Pol EC, separation from template at position +2 involves interaction fork loop 2. The passes...
We describe the design and implementation of a stimulated emission depletion (STED) microscope which allows simultaneous three-dimensional super-resolution imaging in two colors. A super-continuum laser source is used to provide all spectral bands necessary for excitation efficient achieve lateral axial resolution ~35 nm ~90 respectively. characterize systems' performance by colloidal particles single fluorescent molecules. Its biological applicability demonstrated dual-color nuclear pore...
Fused in Sarcoma (FUS) is a multifunctional RNA-/DNA-binding protein, which involved the pathogenesis of neurodegenerative disorders amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A common hallmark these abnormal accumulation mutated FUS protein cytoplasm. Under normal conditions confined to nuclear compartment, neurons, however, additional somatodendritic localization can be observed. In this study, we carefully analyzed subcellular endogenous at synaptic sites...
Abstract Bottom‐up strategies to fabricate patterned polymers at the nanoscale represent an emerging field in development of advanced nanodevices, such as biosensors, nanofluidics, and nanophotonics. DNA origami techniques provide access distinct architectures various sizes shapes present manifold opportunities for functionalization with highest precision. Herein, we conduct situ atom‐transfer radical polymerization (ATRP) on origami, yielding differently nanopatterned heights. After...
The molecular architecture of RNAP II-like transcription initiation complexes remains opaque due to its conformational flexibility and size. Here we report the three-dimensional complete open complex (OC) composed promoter DNA, TATA box-binding protein (TBP), factor B (TFB), E (TFE) 12-subunit RNA polymerase (RNAP) from Methanocaldococcus jannaschii. By combining single-molecule Förster resonance energy transfer Bayesian parameter estimation-based Nano-Positioning System analysis, model...
Histone post-translational modifications (PTMs) are key players in chromatin regulation. The identification of novel histone acylations raises important questions regarding their role transcription. In this study, we characterize the an acylation on lateral surface octamer, H3K122 succinylation (H3K122succ), function and Using succinylated at vitro transcription assays, show that presence H3K122succ is sufficient to stimulate line with this, found our ChIP assays enriched promoters active...
TAR DNA binding protein 43 (TDP-43) is closely related to the pathogenesis of amyotrophic lateral sclerosis (ALS) and translocates stress granules (SGs). The role SGs as aggregation-promoting "crucibles" for TDP-43, however, still under debate. We analyzed TDP-43 mobility localization different recovery conditions using live cell single-molecule tracking super-resolution microscopy. Besides reduced within SGs, a induced decrease in cytoplasm nucleus was observed. Stress removal led mobility,...
Single dye molecules incorporated into a mesoporous matrix can act as highly sensitive reporters of their environment. Here, we use single TDI guests hexagonal films containing structured domains. The allow us to map the size these domains which extend over 100 μm. Investigation translational and orientational dynamics via molecule fluorescence techniques gives structural well dynamical information about host material. In an air atmosphere, guest show no movement but perfect orientation...