A5078712752- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- Microfluidic and Capillary Electrophoresis Applications
- Cancer-related gene regulation
- Microfluidic and Bio-sensing Technologies
- RNA and protein synthesis mechanisms
- Nanopore and Nanochannel Transport Studies
- Congenital heart defects research
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Innovative Microfluidic and Catalytic Techniques Innovation
- Genetics and Neurodevelopmental Disorders
- Bacteriophages and microbial interactions
- RNA Interference and Gene Delivery
- Zebrafish Biomedical Research Applications
- RNA Research and Splicing
- Spectroscopy and Quantum Chemical Studies
- CRISPR and Genetic Engineering
- PARP inhibition in cancer therapy
- HVDC Systems and Fault Protection
- DNA Repair Mechanisms
- Pluripotent Stem Cells Research
- Field-Flow Fractionation Techniques
Institute of Molecular Biology
2015-2024
Institute of Molecular Biology
2019
University Medical Center of the Johannes Gutenberg University Mainz
2018
Johannes Gutenberg University Mainz
2018
German Cancer Research Center
2018
DKFZ-ZMBH Alliance
2018
Heidelberg University
2018
Universitätsklinikum Würzburg
2018
York University
2005-2013
University of Oxford
2009
Aptamers are DNA (or RNA) ligands selected from large libraries of random sequences and capable binding different classes targets with high affinity selectivity. Both the chances for aptamer to be quality largely dependent on method selection. Here we introduce selection aptamers by nonequilibrium capillary electrophoresis equilibrium mixtures (NECEEM). The new has a number advantages over conventional approaches. First, NECEEM-based exceptionally efficiency, which allows development fewer...
Aptamers are typically selected from libraries of random DNA (or RNA) sequences by SELEX, which involves multiple rounds alternating steps partitioning and PCR amplification. Here we report, for the first time, non-SELEX selection aptamersa process that repetitive with no amplification between them. A highly efficient affinity method, non-equilibrium capillary electrophoresis equilibrium mixtures (NECEEM), was used partitioning. We found three NECEEM-based in approach were sufficient to...
Here we introduce a technology for biomarker discovery in which (i) DNA aptamers to biomarkers differentially expressed on the surfaces of cells being different states are selected; (ii) used isolate from cells; and (iii) isolated identified by means mass spectrometry. The is termed aptamer-facilitated (AptaBiD). AptaBiD was discover surface that distinguish live mature immature dendritic cells. We selected vitro two aptamer pools specifically bind with difference strength approximately 100...
Abstract N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking immunoprecipitation) an antibody-based approach to map m6A sites with single-nucleotide resolution. However, due broad antibody reactivity, reliable identification from data remains challenging. Here, we present miCLIP2 combination machine learning significantly improve detection. The...
Cells detect and adapt to hypoxic nutritional stress through immediate transcriptional, translational metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy DNA binding dyes acetylated histones, by the sensitivity digestion with DNAseI, fluorescence recovery after photobleaching (FRAP) core linker histones. Short-term oxygen nutrient deprivation cardiomyocyte cell line HL-1 induces a previously...
Abstract In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess X chromosome, while females (XX) undergo inactivation. To compensate for this reduction in dosage compared with two active copies of autosomes, it has been proposed that the chromosome exhibit compensation. However, existence and mechanisms X-to-autosome compensation still under debate. Here we show transcripts have fewer m 6 A modifications more stable than their autosomal counterparts. Acute...
Tau is a microtubule‐associated protein, which plays an important role in physiology and pathology of neurons. has been recently reported to bind double‐stranded DNA (dsDNA) but not single‐stranded (ssDNA) [Cell. Mol. Life Sci. 2003, 60, 413–421]. Here, we prove that tau binds only dsDNA also ssDNA. This finding was facilitated by using two kinetic capillary electrophoresis methods: (i) non‐equilibrium equilibrium mixtures (NECEEM); (ii) affinity‐mediated NECEEM. Using the new approach,...
Enhancers, not promoters, are the most dynamic in their DNA methylation status throughout development and differentiation. Generally speaking, enhancers that primed to or actually drive gene expression characterized by relatively low levels of (hypo-methylation), while inactive display hyper-methylation underlying DNA. The direct functional significance state is, however, unclear for loci. In contrast conventional epigenetic interactions at enhancers, we find enhancer activity during early...
Abstract The aim of this study was to investigate the chronic effects palmitate on fatty acid (FA) oxidation, AMPK/ACC phosphorylation/activation, intracellular lipid accumulation, and molecular mechanisms involved in these processes skeletal muscle cells. Exposure L6 myotubes for 8 h 200, 400, 600, 800 µM did not affect cell viability but significantly reduced FA oxidation by ∼26.5%, ∼43.5%, ∼50%, ∼47%, respectively. Interestingly, occurred despite significant increases AMPK (∼2.5‐fold) ACC...
The development of drugs and diagnostics with desirable characteristics requires smart small-molecule ligandsligands predefined binding parameters interaction the target. Here, we propose a general approach for selection such ligands from highly diverse combinatorial libraries small molecules by methods kinetic capillary electrophoresis (KCE). We deduct three fundamental requirements library to suit KCE-based suggest universal design selecting ligands: every molecule in is tagged DNA that...
Functional genomics requires structural and functional studies of a large number proteins. While the production proteins through over-expression in cultured cells is relatively routine procedure, subsequent protein purification from cell lysate often represents significant challenge. The most direct way affinity using an probe to target protein. It extremely difficult develop antibodies, classical probes, for lysate; their development pure Thus, isolating while developing antibodies Here we...
Although recent methods for targeted drug delivery have addressed many of the existing problems cancer therapy associated with undesirable side effects, significant challenges remain that to be met before they find clinical relevance. One such area is delicate chemical bond applied connect a cytotoxic targeting moieties like antibodies or peptides. Here we describe novel platform can utilized preparation drug-carrier conjugates in site-specific manner, which provides excellent versatility...
DNA demethylation plays a central role during development and in adult physiology. Different mechanisms of active have been established. For example, Growth Arrest Damage 45-(GADD45) Ten-Eleven-Translocation (TET) proteins act but their functional relationship is unresolved. Here we show that GADD45a physically interacts – functionally cooperates with TET1 methylcytosine (mC) processing. In reporter requires endogenous conversely GADD45a. On target genes hyperinduces 5-hydroxymethylcytosine...
Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here, we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and reagents show that mammalian physiologically PARylated different levels primary tissues. Inhibition of PAR glycohydrolase (PARG) increases PARylation, supporting the modification reversible. PARylation requires PARP1 vitro PARylates single-stranded DNA,...
Base excision repair (BER) functions not only in the maintenance of genomic integrity but also active DNA demethylation and epigenetic gene regulation. This dual role raises question if phenotypic abnormalities resulting from deficiency BER factors are due to damage or impaired demethylation. Here we investigate bifunctional glycosylases/lyases NEIL1 NEIL2, which act oxidative lesions Neil-deficiency Xenopus embryos differentiating mouse embryonic stem cells (mESCs) leads a surprisingly...
Mouse embryonic stem cell (ESC) cultures contain a rare population of “2C-like” cells resembling two-cell embryos, the key stage zygotic genome activation (ZGA). Little is known about positive regulators 2C-like state and embryos. Here we show that GADD45 (growth arrest DNA damage 45) proteins, TET (TET methylcytosine dioxygenase)-mediated demethylation, promote both states. Methylome analysis Gadd45a , b g triple-knockout (TKO) ESCs reveal locus-specific hypermethylation ∼7000 sites, which...
Temperature increase in capillary electrophoresis (CE) due to Joule heating is an inherent limitation of this powerful separation technique. Active cooling systems can decrease the temperature a large part but they leave "hot spots" at ends which completely ruin some CE analyses despite their short lengths. Here, we introduce "universal method for determining electrolyte temperatures" (UMET) that determine temperatures both efficiently- and inefficiently-cooled parts capillary. UMET be...