Institute of Biochemistry and Technical Biochemistry

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Funding Information Agency: DFG

1 to 10 of 29 Results

Synthesis and Hydrolysis of Cephalexin Feb 15, 2022 - EnzymeML at work Lagerman, Colton, 2022, "Synthesis and Hydrolysis of Cephalexin", https://doi.org/10.18419/darus-2468, DaRUS, V1 Investigated was the synthesis and hydrolysis of cephalexin, and the hydrolysis of phenylglycine methyl ester by an amino ester hydrolase. The concentrations of all reactants over time were measured, for four different initial concentrations of cephalexin and phenylglycine methyl...
Self-diffusion coefficients of simulated aqueous methanol mixtures Oct 28, 2022 - ThermoML Gültig, Matthias; Range, Jan Peter; Schmitz, Benjamin; Pleiss, Jürgen, 2022, "Self-diffusion coefficients of simulated aqueous methanol mixtures", https://doi.org/10.18419/darus-3114, DaRUS, V1 In order to make thermophysical properties of complex liquid mixtures available to a comprehensive analysis, we developed a data management and analysis platform based on the standard data exchange format ThermoML. The practicability of integrating thermophysical data from experi...
Self-diffusion coefficients of simulated aqueous glycerol mixtures Oct 28, 2022 - ThermoML Gültig, Matthias; Range, Jan Peter; Schmitz, Benjamin; Pleiss, Jürgen, 2022, "Self-diffusion coefficients of simulated aqueous glycerol mixtures", https://doi.org/10.18419/darus-3115, DaRUS, V1 In order to make thermophysical properties of complex liquid mixtures available to a comprehensive analysis, we developed a data management and analysis platform based on the standard data exchange format ThermoML. The practicability of integrating thermophysical data from experi...
Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects" Feb 1, 2022 - MD Simulations Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2463, DaRUS, V1 Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"
Propioin Synthesis using Benzoin Aldolase Feb 15, 2022 - EnzymeML at work Spöring, Jan-Dirk, 2022, "Propioin Synthesis using Benzoin Aldolase", https://doi.org/10.18419/darus-2466, DaRUS, V1 Investigated was the ligation of two molecules propanal in organic conditions, catalysed by the benzoin aldolase, which was added in the form of lyophillised whole cells. The reaction was performed in triplicate, with 200 mM as the starting concentration of the propanal in all ca...
Oxidation of ABTS by Trametes versicolor laccase Feb 15, 2022 - EnzymeML at work Ngubane, Sandile, 2022, "Oxidation of ABTS by Trametes versicolor laccase", https://doi.org/10.18419/darus-2467, DaRUS, V1 Investigated was the oxidation of ABTS and syringaldazine by Trametes versicolor laccase. For this, the concentration of the substrate over time was measured, for different initial concentrations. All measurements were repeated for three replicates.
NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation Sep 27, 2022 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2022, "NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation", https://doi.org/10.18419/darus-2993, DaRUS, V1 The naming of the files is described in the Supplemental Tables 1 of the accompanying manuscript.
NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons Mar 4, 2024 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Dossmann, Leonie; Emperle, Max, 2024, "NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons", https://doi.org/10.18419/darus-3386, DaRUS, V1 Cloning and site-directed mutagenesis The gene of the catalytic, C-terminal domain of murine DNMT3C (amino acid residues 439-740 of P0DOY1) was obtained in E. coli codon optimized form from IDT Integrated DNA Technologies. The gene fragment was cloned with the StrataClone PCR Clo...
NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3 Nov 25, 2021 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2 Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem...
NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1 Jan 10, 2024 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Albrecht, Claudia, 2024, "NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1", https://doi.org/10.18419/darus-3790, DaRUS, V1 Method overview For targeted DNA demethylation of the H19/IGF2 ICR1, HEK293 cells were transfected with two plasmids, one containing dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter pr...

Synthesis and Hydrolysis of Cephalexin

Feb 15, 2022 - EnzymeML at work

Lagerman, Colton, 2022, "Synthesis and Hydrolysis of Cephalexin", https://doi.org/10.18419/darus-2468, DaRUS, V1

Investigated was the synthesis and hydrolysis of cephalexin, and the hydrolysis of phenylglycine methyl ester by an amino ester hydrolase. The concentrations of all reactants over time were measured, for four different initial concentrations of cephalexin and phenylglycine methyl...

Self-diffusion coefficients of simulated aqueous methanol mixtures

Oct 28, 2022 - ThermoML

Gültig, Matthias; Range, Jan Peter; Schmitz, Benjamin; Pleiss, Jürgen, 2022, "Self-diffusion coefficients of simulated aqueous methanol mixtures", https://doi.org/10.18419/darus-3114, DaRUS, V1

In order to make thermophysical properties of complex liquid mixtures available to a comprehensive analysis, we developed a data management and analysis platform based on the standard data exchange format ThermoML. The practicability of integrating thermophysical data from experi...

Self-diffusion coefficients of simulated aqueous glycerol mixtures

Oct 28, 2022 - ThermoML

Gültig, Matthias; Range, Jan Peter; Schmitz, Benjamin; Pleiss, Jürgen, 2022, "Self-diffusion coefficients of simulated aqueous glycerol mixtures", https://doi.org/10.18419/darus-3115, DaRUS, V1

Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

Feb 1, 2022 - MD Simulations

Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2463, DaRUS, V1

Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

Propioin Synthesis using Benzoin Aldolase

Feb 15, 2022 - EnzymeML at work

Spöring, Jan-Dirk, 2022, "Propioin Synthesis using Benzoin Aldolase", https://doi.org/10.18419/darus-2466, DaRUS, V1

Investigated was the ligation of two molecules propanal in organic conditions, catalysed by the benzoin aldolase, which was added in the form of lyophillised whole cells. The reaction was performed in triplicate, with 200 mM as the starting concentration of the propanal in all ca...

Oxidation of ABTS by Trametes versicolor laccase

Feb 15, 2022 - EnzymeML at work

Ngubane, Sandile, 2022, "Oxidation of ABTS by Trametes versicolor laccase", https://doi.org/10.18419/darus-2467, DaRUS, V1

Investigated was the oxidation of ABTS and syringaldazine by Trametes versicolor laccase. For this, the concentration of the substrate over time was measured, for different initial concentrations. All measurements were repeated for three replicates.

NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

Sep 27, 2022 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2022, "NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation", https://doi.org/10.18419/darus-2993, DaRUS, V1

The naming of the files is described in the Supplemental Tables 1 of the accompanying manuscript.

NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons

Mar 4, 2024 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Dossmann, Leonie; Emperle, Max, 2024, "NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons", https://doi.org/10.18419/darus-3386, DaRUS, V1

Cloning and site-directed mutagenesis The gene of the catalytic, C-terminal domain of murine DNMT3C (amino acid residues 439-740 of P0DOY1) was obtained in E. coli codon optimized form from IDT Integrated DNA Technologies. The gene fragment was cloned with the StrataClone PCR Clo...

NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3

Nov 25, 2021 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2

Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem...

NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1

Jan 10, 2024 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Albrecht, Claudia, 2024, "NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1", https://doi.org/10.18419/darus-3790, DaRUS, V1

Method overview For targeted DNA demethylation of the H19/IGF2 ICR1, HEK293 cells were transfected with two plasmids, one containing dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter pr...

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