15 datasets found

Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3B. Reactions were stopped...

Methylation of long hemimethylated DNA substrates: Methylation of the 349 bp long hemimethylated substrate with DNMT1 was carried out in 1X methylation buffer (100 mM HEPES, 1...

Methylation of random flank substrates: Libraries of double stranded DNA substrates with unmethylated or hemimethylated CpG sites in randomized sequence context were methlyated...

Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3A or DNMT3B. Reactions...

Method overview To achieve targeted locus and allele-specific DNA demethylation, HEK293 cells were transfected with two plasmids. One plasmid contains, dCas9 fused to a SunTag...

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...

Method overview To achieve targeted ASM, transient transfection of the dCas9-10X SunTag-BFP, scFv-DNMT3A-3L-sfGFP, and sgRNA-DsRed plasmids was performed in HEK293 cells....

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...

Expression and purification of DNMT1 for biochemical work Full length murine DNMT1 (UniProtKB P13864) was overexpressed and purified as described (Adam, et al. 2020) using the...

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

In the publication "Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression" bacterial DNA-adenine...

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

Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were...

Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with different distance between CpG sites were obtained...

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...