A5047962510- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Genomics and Chromatin Dynamics
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- DNA and Nucleic Acid Chemistry
- Enzyme Structure and Function
- Force Microscopy Techniques and Applications
- Photosynthetic Processes and Mechanisms
- Click Chemistry and Applications
- Advanced Electron Microscopy Techniques and Applications
- HIV/AIDS drug development and treatment
- DNA Repair Mechanisms
- Plasmonic and Surface Plasmon Research
- Electron Spin Resonance Studies
- Photonic and Optical Devices
- Monoclonal and Polyclonal Antibodies Research
- HIV Research and Treatment
- Advanced Biosensing Techniques and Applications
University of Regensburg
2016-2025
Czech Academy of Sciences, Institute of Microbiology
2023-2024
Technische Universität Braunschweig
2012-2016
Institute of Structural and Molecular Biology
2009-2013
University College London
2009-2013
Ludwig-Maximilians-Universität München
2010
Center for Integrated Protein Science Munich
2010
University of Lübeck
2006-2008
University Hospital Schleswig-Holstein
2006-2008
Philipps University of Marburg
2008
Many tiny force sensors Several techniques can measure forces on biomolecules, but the need to connect molecule macroscopic world often limits rate at which data be taken. Nickels et al. created large arrays of nanoscale by using DNA origami structures. Single-stranded molecules different lengths attached interest acted as entropic springs, with shorter strands exerting more force. The authors used their setup study bending induced TATA-binding protein. Science , this issue p. 305
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...
Spt5 is the only known RNA polymerase-associated factor that conserved in all three domains of life. We have solved structure Methanococcus jannaschii Spt4/5 complex by X-ray crystallography, and characterized its function interaction with archaeal RNAP a wholly recombinant vitro transcription system. Archaeal Spt4 form stable associates independently DNA-RNA scaffold elongation complex. The association results stimulation processivity, both absence presence non-template strand. A domain...
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...
High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, full-length transcripts based on the single-molecule platform from Oxford Nanopore Technologies (ONT) was introduced is widely used to sequence eukaryotic viral RNAs. However, experimental approaches implementing this technique prokaryotic transcriptomes remain scarce. Here, we present an bioinformatic workflow ONT RNA-seq bacterial...
Hcf136 encodes a hydrophilic protein localized in the lumen of stroma thylakoids. Its mutational inactivation Arabidopsis thaliana results photosystem II (PHII)-less phenotype. Under standard illumination, PSII is not detectable and amount I (PSI) reduced, which implies that HCF136p may be required for biogenesis general. However, at low light, comparison mutants with defects PSII, PSI, cytochrome b(6)f complex reveals regulates selectively PSII. We demonstrate by vivo radiolabeling hcf136...
Controlling maleimide hydrolysis allows the modular construction of bromomaleimide-mediated bioconjugates which are either stable or cleavable in an aqueous, thiol-mediated reducing environment.
Argonaute can be found in all three domains of life and is the functional core eukaryotic RNA-silencing machinery. In order to shed light on conformational changes that drive action, we performed single-molecule FRET measurements employing a so far uncharacterized member family, namely from archaeal organism Methanocaldococcus jannaschii (MjAgo). We show MjAgo catalytically active variant hydrolyzing exclusively DNA target strands out DNA/DNA hybrid. studied interplay between nucleic acids...
Significance DNA-dependent RNA polymerases (RNAPs) are complex enzymes that synthesize in a factor-dependent fashion. Like mechanical engines, RNAPs consist of rigid and flexible parts; the catalytic function critically relies on conformational changes. Based single-molecule FRET measurements directly report movements RNAP clamp archaeal 12-subunit RNAP, we show domain exists alternative states distinguishable by width DNA binding channel. The conformation is adjusted through transcription...
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...
Site specific incorporation of molecular probes such as fluorescent- and nitroxide spin-labels into biomolecules, subsequent analysis by Förster resonance energy transfer (FRET) double electron-electron (DEER) can elucidate the distance distance-changes between probes. However, have an intrinsic conformational flexibility due to linker which they are conjugated biomolecule. This property minimizes influence label side chain on structure target molecule, but complicates direct correlation...
Abstract Initiation of gene transcription by RNA polymerase (Pol) III requires the activity TFIIIB, a complex formed Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment Pol to promote transition from closed an open pre-initiation complex, process dependent on Bdp1 subunit. Here, we present crystal structure Brf2–TBP–Bdp1 bound DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis in vitro biochemical assays. Our study provides structural...
Abstract The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like are important constituents of all eukaryotic initiation complexes. reason for the emergence strict requirement additional Bdp1 in RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect this context is effect DNA strain arising from compaction transcriptional activity on complex formation. We made use origami-based force clamp to follow assembly human complexes RNAP II systems at...
Abstract Human Argonaute 2 (hAgo2) constitutes the functional core of RNA interference pathway. Guide RNAs direct hAgo2 to target mRNAs, which ultimately leads hAgo2-mediated mRNA degradation or translational inhibition. Here, we combine site-specifically labeled with time-resolved single-molecule FRET measurements monitor conformational states and dynamics hAgo2-RNA complexes in solution that remained elusive so far. We observe dynamic anchoring release guide’s 3’-end from PAZ domain during...
Transcription elongation in vitro is affected by the interactions between RNA polymerase (RNAP) subunits and nucleic acid scaffold of ternary complex (TEC, RNAP-DNA-RNA). We have investigated role RNAP F/E (homologous to eukaryotic RPB4/7) during transcription termination using a wholly recombinant archaeal synthetic scaffolds. The greatly stimulates processivity RNAP, it enhances formation full length products, reduces pausing, increases facilitated weak signals. Mutant variants that are...
Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well their interactions. The immobilization, however, can invoke perturbation to activity biomolecules causing incongruities between single molecule ensemble measurements. Here we introduce recently developed DNA origami a platform transfer assays level without changing nano-environment biomolecules. idea is stepwise common functional first surface origami, which...