Epigenetics

<h2>What are epigenetics enzymes and inhibitors?</h2>
&nbsp;
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>
&nbsp;
<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>
&nbsp;
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.

Enzymes & Inhibitors

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

<h2>What are 5-hmC ELISA kits?</h2>
&nbsp;
5-hmC ELISA kits are antibody-based assays formulated specifically to quantify 5-hydroxymethylcytosine, the oxidized derivative of 5-methylcytosine produced by TET family enzymes, in a genomic DNA sample. The assay typically uses denatured single-stranded DNA coated on a plate well, recognized by an anti-5-hmC primary antibody and developed with an HRP-conjugated secondary antibody for a colorimetric readout proportional to the global level of 5-hmC in the sample.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">DNA hydroxymethylation ELISA assay kits for 5-hmC levels quantification</li>
<li dir="ltr" role="presentation">DNA methylation ELISA kits for comparative gene regulation analysis and measurement of 5-mC&nbsp;</li>
<li dir="ltr" role="presentation">DNA standards for accurate methylation and hydroxymethylation quantification&nbsp;</li>
<li dir="ltr" role="presentation">Control DNA sets and assay controls for experimental accuracy, validation, and reproducibility</li>
<li dir="ltr" role="presentation">HRP-based antibodies for the specific detection in ELISA workflows</li>
<li dir="ltr" role="presentation">ELISA coating and reaction buffers for enhanced assay performance and setup</li>
<li dir="ltr" role="presentation">Signal development reagents for quantitative readout and chemiluminescent or colorimetric detection</li>
</ul>
&nbsp;
<h2>How to use 5-hmC ELISA kits</h2>
&nbsp;
Confirm 5-hmC is detectable at relevant levels in your cell type or tissue
5-hmC is most abundant in neurons and embryonic stem cells, where it can constitute up to 20% of total modified cytosines in neuronal DNA, while most cultured cell lines have much lower 5-hmC levels that may fall below a plate-based antibody assay's reliable detection limit. Checking published 5-hmC abundance for your specific cell type helps confirm whether ELISA-level detection is appropriate before committing samples to the assay.
Use a set of mixed methylation standards to build a calibration curve
Running defined mixtures of 5-hmC-containing and unmethylated DNA at known ratios generates a standard curve that lets you convert the raw absorbance signal to an actual global hydroxymethylation percentage, since the assay signal alone cannot be interpreted as an absolute level without this calibration.
Confirm your antibody's specificity for 5-hmC versus 5-mC
Anti-5-hmC antibodies used in these kits are selected for specificity to 5-hydroxymethylcytosine rather than 5-methylcytosine, but published cross-reactivity data for the specific antibody in your kit is worth checking, particularly when studying sample types where both marks are present at similar levels.
Plan your experimental design to include appropriate negative and positive controls
Including a negative control (unmethylated DNA, expected to give background-level signal) and a positive control (5-hmC-containing DNA of known level) in every plate confirms the assay is performing as expected and catches plate-to-plate variability before it affects result interpretation.
Understand ELISA gives global level, not locus-specific 5-hmC information
A 5-hmC ELISA measures the average hydroxymethylation level across all DNA in the sample; it does not reveal which specific CpG sites carry 5-hmC, which requires hMeDIP-seq or TAB-seq for regional or base-level resolution respectively.
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<h2>Specifications context</h2>
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Anti-5-hmC antibodies used in ELISA formats are validated specifically for 5-hydroxymethylcytosine and selected for minimal cross-reactivity with 5-methylcytosine, since distinguishing these two modifications is the primary purpose of a dedicated 5-hmC assay rather than a general methylation assay. As of 2026, 5-hmC ELISA kits remain a standard first-pass tool in studies where many samples need to be screened for differences in global hydroxymethylation level before committing a smaller subset to high-resolution sequencing methods.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at Molecular Biology Products Inc. (MBP) and find reliable ELISA kits and reagents for your lab.

ELISA Kits & Reagents

10X ELISA Buffer

For use with Zymo Research purification products.

10X ELISA Buffer (30 ml)

10X ELISA Buffer (60 ml)

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.

<h2>What are non-bisulfite methylation kits and reagents?</h2>
&nbsp;
Non-bisulfite methylation kits and reagents are alternatives to sodium bisulfite conversion that achieve the same goal &mdash; distinguishing methylated from unmethylated cytosines at single-base or regional resolution &mdash; without the harsh chemical treatment that bisulfite introduces. The most widely adopted approach is enzymatic methyl-seq (EM-seq), which uses TET2 to oxidize 5-methylcytosine and 5-hydroxymethylcytosine and T4-BGT to protect them from subsequent APOBEC3A-mediated deamination, so that only unmodified cytosines are converted to uracil.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">qMethyl PCR assay kit uses PCR amplification for quantitative DNA methylation detection</li>
<li dir="ltr" role="presentation">One-step qMethyl PCR system for efficient methylation analysis and optimized workflow setup&nbsp;</li>
<li dir="ltr" role="presentation">Test reaction premixes for validation and optimization of assays&nbsp;</li>
</ul>
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<h2>How to choose non-bisulfite methylation reagents</h2>
&nbsp;
Choose EM-seq for superior library quality over bisulfite at the same resolution
EM-seq outperforms bisulfite-converted libraries on all major quality metrics: higher library yield, fewer duplicates, more usable reads, more even GC distribution, and accurate methylation calling, without requiring any changes to downstream bioinformatic analysis pipelines since the output is the same C-to-T chemistry as bisulfite conversion.
Understand EM-seq's two-step enzymatic mechanism
In the first EM-seq step, TET2 oxidizes 5-mC and 5-hmC to protected forms while T4-BGT glucosylates 5-hmC; in the second step, APOBEC3A deaminates only the unprotected unmodified cytosines to uracil. The net result is the same as bisulfite conversion &mdash; unmethylated C reads as T &mdash; but without bisulfite's destructive chemistry.
Consider TAPS for mild, nondestructive conversion that directly marks modified cytosines
TET-assisted pyridine borane sequencing (TAPS) is a bisulfite-free method that combines TET oxidation of 5-mC and 5-hmC with pyridine borane reduction, converting modified cytosines to a thymine read while leaving unmodified cytosines intact. Unlike bisulfite and EM-seq, TAPS positively marks the modified bases rather than converting the unmodified ones, and can preserve DNA fragments over 10 kilobases.
Choose MeDIP for genome-wide enrichment without per-cytosine resolution
Methylated DNA immunoprecipitation uses an antibody specific to 5-methylcytosine or 5-hydroxymethylcytosine to pull down methylated DNA fragments, providing regional enrichment data at lower cost and without bisulfite-related DNA damage, though at lower resolution than sequencing-based conversion methods.
Confirm whether your method distinguishes 5-mC from 5-hmC or co-detects both
EM-seq detects both 5-mC and 5-hmC together and cannot distinguish them without additional steps, while TAPS also co-detects both; TAPS&beta;, a variant, can specifically call 5-mC by blocking 5-hmC before oxidation. MeDIP can be targeted specifically to 5-hmC (hMeDIP) using an anti-5-hmC antibody.
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<h2>Specifications context</h2>
&nbsp;
EM-seq was effective using as little as 100 pg of DNA input, and libraries showed higher yields with fewer PCR cycles than bisulfite-converted libraries at all input amounts tested, with more even GC distribution, reduced sequencing duplicates, and more CpGs detected within genomic features per sequencing read. As of 2026, enzymatic conversion via EM-seq is broadly recommended over bisulfite conversion for new methylome analysis projects, particularly those working with limited, degraded, or high-value samples where the DNA damage of bisulfite treatment is most consequential.
This category sits within DNA/RNA Methylation, alongside Bisulfite Conversion Kits, and is closely related to DNA Hydroxymethylation for 5-hmC-specific approaches. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us" title="Contact the expert team at Molecular Biology Products Inc. (MBP)">Contact the expert team at Molecular Biology Products Inc. (MBP)</a> to find dependable non-bisulfite kits and reagents for your lab.

Non-Bisulfite Kits & Reagents

2X Test Reaction PreMix

2X Test Reaction PreMix (D5310) by Zymo Research — 500 µl, contains MSREs and SYTO 9 dye for bisulfite-free locus-specific DNA methylation quantification in the OneStep qMethyl Kit. Compatible with Bio-Rad CFX, QuantStudio, and LightCycler 480. Store at −20°C. Made in the USA.

2X Reference Reaction PreMix

2X Test Reaction-Lite PreMix

The 2X Test Reaction-Lite PreMix (D5311) by Zymo Research is the dye-free bisulfite-free DNA methylation quantitation component for the OneStep qMethyl-Lite system. Uses methylation-sensitive restriction enzymes (MSREs) to calculate percent methylation from qPCR ΔCt values — no bisulfite conversion required. Researcher supplies compatible fluorescent dye or TaqMan probe; input 5 ng–1 µg DNA; amplicons &gt;150 bp.

2X Reference Reaction-Lite PreMix

5-Hydroxymethylcytosine DNA Standard (2 µg)

D5405-3 by Zymo Research is a 5-Hydroxymethylcytosine DNA Standard — a 897 bp linear dsDNA in which 100% of cytosines are 5-hmC. Each vial contains 2 µg at 50 ng/µl for use as a positive control or calibration reference in 5-hmC ELISA, dot blot, and LC-MS/MS workflows.

Concentration

Sample Storage

<h2>What are methylated dNTPs?</h2>
&nbsp;
Methylated dNTPs are base-modified deoxynucleotide analogs, the most important being 5-methyl-dCTP (2'-deoxy-5-methylcytidine 5'-triphosphate), in which the cytosine base carries a methyl group at the carbon-5 position. This is the same position methylated in naturally occurring genomic 5-methylcytosine, the primary DNA methylation mark studied in epigenetics research. Substituting 5-methyl-dCTP for standard dCTP in a PCR reaction or in vitro synthesis produces a defined, fully cytosine-methylated DNA template from a known sequence.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
5-Methyl dCTP (10 mM) (100 &micro;l): for high-purity enzymatic incorporation into methylated DNA strands.
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
5-Methylcytosine dNTP Mix (10 mM) (250 &micro;l): pre-validated nucleotide blends for controlled epigenetic assay workflows.
</li>
</ul>
&nbsp;
<h2>How to use methylated dNTPs</h2>
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Substitute 5-methyl-dCTP for dCTP in PCR to synthesize defined methylated DNA
A PCR reaction using 5-methyl-dCTP in place of standard dCTP produces a fully methylated amplicon in which every cytosine carries the 5-methyl modification, providing a positive control with a known and consistent methylation status distinct from the partial, variable methylation of a genomic DNA control.
Use methylated DNA as a positive control for bisulfite or enzymatic conversion workflows
Running 5-methyl-dCTP-synthesized fully methylated DNA through your bisulfite or enzymatic conversion protocol confirms the method correctly preserves methylated cytosines while converting unmethylated ones, catching conversion efficiency problems at the control stage before they affect interpretation of real samples.
Test methylation-sensitive restriction enzymes using 5-methyl-dCTP-produced substrates
Some restriction enzymes cut methylated sequences while others are inhibited by methylation at their recognition site, and a PCR-synthesized, fully methylated substrate of known sequence provides a clean, defined test of whether a specific enzyme is methylation-sensitive or methylation-dependent.
Use as an in vitro substrate for TET enzyme oxidation studies
Since 5-methylcytosine is the starting substrate for TET family enzyme oxidation into 5-hydroxymethylcytosine and further products, fully methylated DNA synthesized with 5-methyl-dCTP provides a defined, homogeneous substrate for in vitro TET enzyme activity assays.
Store methylated dNTPs appropriately to maintain activity
Methylated dNTP analogs are generally stored at -20&deg;C, similar to standard dNTPs, with short-term exposure to ambient temperature acceptable but prolonged room-temperature storage avoided to prevent hydrolysis of the phosphate groups.
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<h2>Specifications context</h2>
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5-methyl-dCTP is typically supplied as a 10 mM solution at pH 7.0 and can be diluted using sterile distilled water or TE buffer, and it can be used in PCR, RT-PCR, and other DNA synthesis applications at the same concentration as standard dCTP in a reaction mix, with 5-methylated DNA probes made this way serving as methylation reference fragments or as pull-down substrates for 5-hydroxymethylcytosine-binding proteins. As of 2026, 5-methyl-dCTP-synthesized control DNA remains a standard tool in epigenetics research labs specifically because it provides a modification-defined substrate without relying on the variable or partially characterized methylation patterns of genomic positive controls.
<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP</a> and get high-quality methylated (dNTPs) for your lab.

Methylated

DataSheet

5-Methyl dCTP (10 mM) (100µl)

Zymo Research D1035: 5-Methyl dCTP at 10 mM, 100 µl (1 µmol). &gt;99% purity by HPLC; free of DNase, RNase, and phosphatase. Compatible with ZymoTaq, QuestTaq, and standard thermostable polymerases. Store at –20°C.

Applicable For 

Protocol

5-Methylcytosine & 5-Hydroxymethylcytosine DNA Standard Set

The D5405 DNA Standard Set by Zymo Research contains three sequence-identical 897 bp dsDNA standards at 50 ng/µl (2 µg each): unmodified cytosine (D5405-1), 5-methylcytosine (D5405-2), and 5-hydroxymethylcytosine (D5405-3). Ideal reference controls for HPLC, LC/MS, and TLC cytosine modification quantitation studies.

Applicable For

5-Methylcytosine DNA Standard (2 µg)

5-Methylcytosine DNA Standard (2 µg) (D5405-2) by Zymo Research — fully synthetic 897 bp dsDNA with 100% 5-mC at all cytosines. 50 ng/µl, 40 µl (2 µg total) in modified TE buffer. For bisulfite conversion controls, MeDIP, LC/MS, and HPLC assays.

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.

Standard Reaction Time

Storage

Unit Definition

5-hmC Glucosyltransferase (100 U)

5-hmC Glucosyltransferase (200 U)

<h2>What are ELISA kits for methylation in this category?</h2>
&nbsp;
ELISA kits for DNA and RNA methylation in this category are antibody-based assays that quantify the global level of a specific epigenetic mark, most commonly 5-methylcytosine in genomic DNA, 5-hydroxymethylcytosine in genomic DNA, or N6-methyladenosine in RNA, using a plate-based immunoassay format without requiring bisulfite conversion or sequencing. Denatured, single-stranded DNA or RNA from a sample is coated on a plate well, and a mark-specific primary antibody followed by an HRP-conjugated secondary antibody generates a colorimetric signal proportional to the level of the target modification.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">5-mC DNA ELISA kits for quantitative analysis of DNA methylation&nbsp;</li>
<li dir="ltr" role="presentation">DNA controls for validation and calibration of the assay to ensure experimental&nbsp; reproducibility and accuracy&nbsp;</li>
<li dir="ltr" role="presentation">Secondary antibody reagents for specific signal generation and detection in ELISA assays</li>
<li dir="ltr" role="presentation">Coating buffers for consistent assay performance and optimized plate preparation&nbsp;</li>
</ul>
&nbsp;
<h2>How to choose methylation ELISA kits and reagents</h2>
&nbsp;
Match your kit to the specific epigenetic mark you're quantifying
Different kits use antibodies against specific modifications: 5-methylcytosine ELISA kits quantify global DNA methylation, 5-hmC ELISA kits quantify global hydroxymethylation, and m6A ELISA kits quantify RNA N6-methyladenosine. Using a kit with the wrong antibody specificity will not report the mark you intend to measure.
Use methylation standards to build a calibration curve for quantitative results
Running a series of methylation standards with defined percentages alongside your samples allows the absorbance readout to be converted to a specific, meaningful methylation percentage, since the raw ELISA signal alone cannot be interpreted as absolute methylation level without a calibration.
Understand that ELISA measures global levels, not locus-specific methylation
A methylation ELISA gives the overall average percentage of methylation across the genome in a sample, which is useful for comparing broad methylation changes between conditions but cannot identify which specific genes or regions are differentially methylated the way bisulfite sequencing can.
Confirm the required DNA denaturation step is appropriate for your sample type
ELISA kits for DNA methylation typically require single-stranded, denatured DNA coated directly on the plate, and confirming this denaturation step is properly performed is necessary for consistent antibody binding and reproducible signal across wells.
Be aware of cross-reactivity with similar modifications when interpreting results
An antibody against 5-methylcytosine may have some cross-reactivity with 5-hydroxymethylcytosine, and confirming the antibody's published cross-reactivity data helps interpret whether your signal specifically reflects 5-mC, 5-hmC, or both, which matters for studies in cell types where 5-hmC is abundant.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
The 5-methylcytosine ELISA workflow uses an indirect ELISA methodology where denatured, single-stranded DNA samples are coated directly on the plate well surfaces and a 5-mC monoclonal antibody and an HRP-conjugated secondary antibody are added sequentially, generating a colorimetric signal proportional to the total level of methylated cytosine in the sample. As of 2026, methylation ELISA kits are particularly valued for high-throughput screening studies comparing global methylation levels across many treatment conditions or patient groups where single-base-resolution data is not the primary goal.
This category sits within DNA/RNA Methylation, alongside Methylation Standards for calibration, and is related to DNA Hydroxymethylation and Non-Bisulfite Kits &amp; Reagents for higher-resolution methylation analysis. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team of&nbsp; Molecular Biology Products Inc. (MBP)</a> to get high-quality ELISA Kits and Reagents for your lab.

D5325-1-15/D5325-1-30 - MSDS

5-mC Coating Buffer

D5325-1-15 5-mC Coating Buffer by Zymo Research — 15 ml, stored at 4°C — coating medium for denatured ssDNA in 5-methylcytosine quantification ELISA assays. Compatible with 5-mC DNA ELISA Kit (D5325, D5326).

5-mC Coating Buffer (15 ml)

5-mC Coating Buffer (30 ml)

5-mC ELISA Buffer (250 ml)

5-mC DNA ELISA Kit (2 x 96 Preps.)

D5326 by Zymo Research is a 5-mC DNA ELISA Kit for colorimetric quantification of global 5-methylcytosine in purified DNA. Accepts 10–200 ng DNA per well, detects methylation above 0.5% 5-mC, and completes in under 3 hours. Kit contains reagents for 2 × 96 reactions.