Enzymes & Inhibitors

<h2>What are epigenetics enzymes and inhibitors?</h2>
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Epigenetics enzymes and inhibitors are the molecular tools for directly studying or modulating the enzymatic machinery that writes, erases, or reads epigenetic marks. The major classes include: DNA methyltransferases (DNMT1, DNMT3A, DNMT3B), which catalyze the addition of a methyl group to cytosine; TET family enzymes (TET1, TET2, TET3), which oxidize 5-methylcytosine to 5-hydroxymethylcytosine; histone acetyltransferases (HATs) and histone deacetylases (HDACs), which add and remove acetyl groups from histone lysine residues; and histone methyltransferases (HMTs) including EZH2, DOT1L, and G9a. Small-molecule inhibitors of HDAC and DNMT enzymes are the most clinically and experimentally advanced of these tools.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li dir="ltr" role="presentation">Micrococcal nuclease for nucleosome mapping and controlled chromatin digestion applications</li>
<li dir="ltr" role="presentation">DNA shearing enzymes for consistent fragmentation of DNA in sequencing and epigenetic workflows</li>
<li dir="ltr" role="presentation">DNA degradation enzymes for controlled breakdown and analysis of nucleic acids&nbsp;</li>
<li dir="ltr" role="presentation">CpG methylase enzymes for targeted DNA methylation (CpG-specific )&nbsp; in epigenetic modification studies</li>
<li dir="ltr" role="presentation">5-hmC glucosyltransferase for detection and labeling of hydroxymethylcytosine in DNA</li>
<li dir="ltr" role="presentation">SAM (S-adenosylmethionine) cofactors for supporting enzyme activity and methylation reactions</li>
<li dir="ltr" role="presentation">DNA digestion enzymes for genomic DNA processing workflows</li>
<li dir="ltr" role="presentation">dsDNA nuclease systems for controlled cleavage and analysis of double-stranded DNA</li>
</ul>
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<h2>How to choose epigenetics enzymes and inhibitors</h2>
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Choose DNMT inhibitors to globally reduce or deplete DNA methylation in cells
Nucleoside analog DNMT inhibitors like 5-azacytidine and decitabine incorporate into DNA and trap DNMT1, preventing maintenance methylation and causing passive demethylation through DNA replication, while newer non-nucleoside DNMT inhibitors are in development for more selective, non-genotoxic methylation reduction.
Choose HDAC inhibitors to globally increase histone acetylation
HDAC inhibitors including pan-HDAC hydroxamates like vorinostat (SAHA) or class-selective compounds reduce histone deacetylase activity and cause hyperacetylation of histone lysine residues, broadly promoting gene expression at silenced loci. HDAC inhibitors are the most clinically advanced class of epigenetic therapeutics, with multiple FDA-approved compounds.
Use TET enzyme preparations for in vitro 5-hmC oxidation studies
Purified TET1, TET2, or TET3 enzyme preparations allow controlled in vitro oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and further oxidation products, useful for generating defined 5-hmC-containing substrate DNA or studying TET enzyme activity and selectivity.
Choose EZH2 or other HMT inhibitors for studying PRC2-dependent gene silencing
EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2), catalyzes H3K27 trimethylation (H3K27me3), a histone modification associated with repression of tumor suppressor genes, and EZH2 inhibitors like tazemetostat are used in research to probe the role of this silencing mark.
Combine inhibitors to study epistatic relationships between epigenetic marks
Because DNA methylation, histone acetylation, and histone methylation are mechanistically linked, combining HDAC inhibitors with DNMT inhibitors can produce synergistic effects on gene expression exceeding either alone, and these combination approaches are both experimental tools and the basis for combination epigenetic therapy research.
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<h2>Specifications context</h2>
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HDAC and DNMT inhibitors are the most clinically advanced classes of epigenetic therapeutics, with multiple HDAC inhibitors including vorinostat and romidepsin approved for hematological malignancies, EZH2 inhibitors including tazemetostat having received accelerated approval, and multiple BET inhibitors in clinical trials. As of 2026, CRISPR/dCas9 systems fused with DNMTs, TETs, and HDACs enable locus-specific epigenome editing, extending classic enzyme and inhibitor approaches toward targeted epigenetic modulation.
<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP</a> and find the suitable enzymes and inhibitory reagents for your lab.

MSDS

10X CpG Reaction Buffer (1 ml)

The 10X CpG Reaction Buffer (E2010-2) by Zymo Research is a 1 mL concentrate formulated for use with CpG methylase M.SssI for complete in vitro methylation of CpG dinucleotides in double-stranded DNA. Sold as a standalone buffer replacement for the E2010/E2011 CpG Methylase set.

Manufacturer

Shipping Condition

Storage Condition

20X SAM (S-adenosylmethionine) (12 mM) (200 µl)

E2010-3 by Zymo Research — 20X SAM (S-adenosylmethionine), 12 mM in 200 µL (600 µM at 1X). Methyl-donor cofactor for CpG methyltransferase (M.SssI) assays. Store at −20°C up to 12 months.

Protocol

5-hmC Glucosyltransferase

E2026 by Zymo Research is 5-hmC Glucosyltransferase supplied at 2 U/µL (100 U). The enzyme specifically transfers glucose to 5-hydroxymethylcytosine in DNA, enabling locus-specific and global 5-hmC quantification via restriction protection or sequencing. Store at −20°C; stable 12 months.

Concentration

Standard Reaction Time

Storage

Unit Definition

5-hmC Glucosyltransferase (100 U)

5-hmC Glucosyltransferase (200 U)

Atlantis Digestion Buffer (1X) (50 ml)

Atlantis Digestion Buffer (1X), SKU E2030-1 by Zymo Research — 50 mL ready-to-use companion buffer for the Atlantis dsDNase (E2030) enzyme. Used for nucleosomal DNA preparation in ChIP, ATAC-seq, and nucleosome positioning workflows. Store at −20°C; part of the EZ Nucleosomal DNA Prep Kit (D5220).

Atlantis dsDNAse (12.5 U)

E2030 by Zymo Research is Atlantis dsDNAse, 12.5&nbsp;U at 0.1&nbsp;U/&micro;l (125&nbsp;&micro;l). Selectively digests dsDNA without degrading ssDNA or RNA. Used for nucleosome mapping and ChIP-seq chromatin fragmentation. Storage: &minus;20&deg;C.

Inactivation

CpG Methylase (M. Sssl)

CpG Methylase (M. SssI) (E2010) by Zymo Research — recombinant CpG methyltransferase that completely methylates all 5′-CpG-3′ sites in dsDNA. Supplied with 10X buffer and 20X SAM. Available in 200 U and 400 U; optimal at 30°C; heat-inactivatable at 65°C.

Additional Information

Assay Condition

Heat Inactivation

Source

CpG Methylase (M. Sssl) (200 U)

CpG Methylase (M. Sssl) (400 U)

DataSheet

DNA Degradase

E2016 by Zymo Research is DNA Degradase, a nuclease mixture at 10 U/µL. Degrades DNA to individual nucleotide components in ~1 hour at 37°C. One unit degrades 1 µg of lambda DNA. Used for whole-genome methylation analysis by LC/MS, HPLC, and TLC. Store at −20°C. Available in 500 U and 2000 U sizes.

Enzyme Inactivation

DNA Degradase™ (500 U)

DNA Degradase (2000 U)

DNA Degradase Plus

E2020 by Zymo Research is a 5 U/µL DNA Degradase Plus enzyme mixture (250 units) that digests double-stranded DNA to individual nucleosides in approximately 2 hours at 37°C, enabling quantitative LC/MS analysis of DNA methylation marks including 5mC and 5hmC.

DNA Degradase Plus™ (250 U)

DNA Degradase Plus™ (1000 U)

Micrococcal Nuclease (10 U/100 µ)

The D5220-1 by Zymo Research is Micrococcal Nuclease (MNase, E.C. 3.1.31.1) at 0.1 U/µl (10 U/100 µl), a Ca²⁺-dependent endo-exonuclease that cleaves ssDNA, dsDNA, ssRNA, and dsRNA with preference for AT/AU-rich regions, producing 3′-phosphate mono- and oligonucleotides. Inactivated by EDTA; used for ChIP chromatin digestion, MNase-seq, and nucleic acid removal from lysates.

Enzyme Commission Number

dsDNA Shearase

dsDNA Shearase (E2019-200) by Zymo Research — dsDNA Shearase Plus endonuclease (1 U/µL, 200 U) bundled with DNA Clean &amp; Concentrator-5 (DCC-5). Fragments 250 ng human DNA to 100–500 bp at 42°C in 20 min; elute purified fragments in as little as 10 µL. Ready for NGS and MeDIP workflows.

dsDNA Shearase™ (200 U)

dsDNA Shearase™ Plus (50 U)

dsDNA Shearase Plus

dsDNA Shearase Plus (E2018-200) by Zymo Research — 1 U/µL, 200 U. Fragments 250 ng human DNA to 100–500 bp in 20 min at 42°C in 10 µL. Generates 5′-phosphate/3′-OH termini ready for NGS adapter ligation. Enzyme only; for the DCC-5 bundle see E2019-200.