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MethylFlash Hydroxymethylated DNA Quantification Kit (Fluorometric)


For fluorescence-based quantitation of global DNA hydroxymethylation in an ELISA-like format

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Suggested Workflow
DNA Isolation
DNA Methylation Quantification
Schematic procedure of the MethylFlash™ Hydroxymethylated DNA Quantification Kit.
Input Type: DNA
Research Area: DNA Methylation
Target Application: Amount Quantitation
Vessel Format: 96-Well Plate
100% Guarantee: 6 months
Catalog No.SizePriceQty
P-1037-4848 assays $369.00 
P-1037-9696 assays $619.00 
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Product Overview

The MethylFlash™ Hydroxymethylated DNA Quantification Kit (Fluorometric) is a complete set of optimized buffers and reagents to fluorometrically quantify global DNA hydroxymethylation by specifically measuring levels of 5-hydroxymethylcytosine (5-hmC) without cross-reactivity to methylcytosine and unmethylated cytosine.

This kit is also specifically optimized for paired use with the MethylFlash Methylated DNA Quantification Kit (Fluorometric) for simultaneously quantifying both methylated DNA and hydroxymethylated DNA.

About 5-Hydroxymethylcytosine
5-hmC is a modified form of cytosine, recently discovered in animal tissues. The function of 5-hmC in epigenetics may be different from its forerunner 5-methylcytosine (5-mC) and currently remains a mystery. It is believed, though, that 5-hmC plays an important role in switching genes on and off.  The presence of 5-hmC makes it necessary to not only re-evaluate existing DNA methylation data, but also necessary to determine the relative distribution and changes of 5-hmC in human tissues of healthy and diseased statuses. Prior to Epigentek’s MethylFlash™ technology, there were no methods that could be used for practically and routinely identifying 5-hmC and discriminating this base from 5-mC.

Distinguishing Between 5-hmC and 5-mC
Currently used methylated DNA analysis methods including restriction enzyme digestion and bisulfite or MeDIP-mediated MS-PCR and sequencing are not suitable for 5-hmC detection as 5-hmC and 5-mC are virtually indistinguishable between each other with these methods. To address this problem, Epigentek offers the MethylFlash™ Hydroxymethylated DNA Quantification Kit (Fluorometric) which uses a unique procedure to quantify global DNA hydroxymethylation. This product provides a cost-effective way to measure levels of 5-hydroxymethylcytosine and to distinguish between 5hmC, 5mC, and C. This allows for researchers to re-evaluate their DNA methylation data for DNA hydroxymethylation and to efficiently look for DNA hydroxymethylation in new DNA samples.  The kit has the following advantages and features:

  • Fluorometric assay with easy-to-follow steps for convenience and speed. The entire procedure can be completed within 3 hours and 20 minutes.
  • High sensitivity, of which the detection limit can be as low as 10 pg of hydroxymethylated DNA and accepts as low as 20 ng of input genomic DNA
  • High specificity with no cross-reactivity to methylcytosine and unmethylated cytosine. 5-hydroxymethylcytosine is separately detected. 
  • Universal positive and negative controls are included, which are suitable for quantifying hydroxymethylated DNA from any species.
  • Strip-well microplate format makes the assay flexible for either manual or high throughput analysis.
  • Simple, reliable, and consistent assay conditions.


Comparison of Available ELISA-based Global DNA Methylation Assay Methods 

 MethylFlash (Fluorometric)Competitor Z
Assay Principle Direct ELISA - Detection antibody specifically and directly detects 5-hmC Indirect ELISA - Detection antibody detects dsDNA, (detected signals is dependent only on intact DNA strands and does not quantify actual total 5-hmC)
Format 96-well plate 96-well plate
Sensitivity Excellent detection limit of 0.01 ng of 5-hmC DNA Unclear, as the detected signals are from intact DNA strands
S/N Ratio >20 with very low background  <4 with high background
Procedural Convenience No need for plate blocking and denaturation of DNA Requires plate blocking and DNA denaturation
Protocol Time  <4 hr  <5 hr
DNA Type & Species Universal for any species, both ssDNA and dsDNA Only ssDNA from limited number of species 
Specificity High, the antibody only detects 5-mC Unclear, as the assay principle is not reasonable
Quantification Type Both relative and absolute quantification Relative only
Standard Control Stable, quantitative in absolute amount of 5-mC, and can be universally used for any species Unclear
Minimum Input Amount 20 ng 100 ng
Accuracy of Detection Stable and quantified standard control with proven close correlation with HPLC-MS analysis by users Unclear, based on biased assay principle
% 5-mC Calculation Simple Complicated
Patented Method Yes No
Popularity Very high published citation count Low published citation count
Support Expertise Since 2006 Since 2012


Fig. 1. Schematic procedure of the MethylFlash™ Hydroxymethylated DNA Quantification Kit.


Product Details

Principle & Procedure
The MethylFlash™  Hydroxymethylated DNA Quantification Kit (Fluorometric) contains all reagents necessary for the fluorometric quantification of global DNA hydroxymethylation. In this assay, DNA is bound to strip wells that are specifically treated to have a high DNA affinity. The hydroxymethylated fraction of DNA is detected using capture and detection antibodies and then quantified fluorometrically by reading the RFU (relative fluorescence units) in a fluorescence microplate spectrophotometer at excitation 530 nm and emission 590 nm. The amount of hydroxymethylated DNA is proportional to the fluorescence intensity measured, which can be calculated with the kit's included formulas for relative hydroxymethylation status of two different DNA samples or absolute quantification of 5-hydroxymethylcytosine (5-hmC) using a standard curve.

Fig. 2. Demonstration of high sensitivity and specificity of 5-hydroxymethylcytosine detection achieved by the MethylFlash™ kit. Synthetic unmethylated DNA (contains only cytosine), methylated DNA (contains only 5-methylcytosine), and hydroxymethylated DNA standard (contains only 5-hydroxymethylcytosine) were added into the assay wells at different concentrations and then measured with the MethylFlash™ Hydroxymethylated DNA Quantification Kit (Fluorometric).

Easy, Fast, and Flexible
The entire fluorometric assay has easy-to-follow steps for convenience and speed, which can be completed in 3 hours and 20 minutes. The strip-well microplate format allows for a flexible assay in manual or high throughput analysis. Universal positive and negative controls are included with the kit for quantifying hydroxymethylated DNA from any species such as mammals, plants, fungi, bacteria, and viruses.

Safe and Convenient
All the needed reagents, including negative controls and positive controls, for quantification of global DNA hydroxymethylation are conveniently packaged in the kit. The direct fluorometric quantification of DNA samples replaces obsolete or inferior methods and eliminates the need for DNA digestion/denaturation, radioactivity, extraction, or chromatography.

Highly Sensitive and Specific
The novel procedure and proprietary kit compositions allow for accurate quantification of hydroxymethylated DNA to be achieved with high sensitivity and specificity. The detection limit of the input DNA can be as low as 10 pg of hydroxymethylated DNA with a dynamic range from  10 pg to 5 ng (see Fig. 2). Analytic sensitivity is about ten-fold higher than that obtained by HPLC (0.008% vs 0.08%). There is no cross-reactivity to methylcytosine and unmethylated cytosine so that only hydroxymethylated DNA (5-hmC) is detected.

Responsive, Reliable, and Practical
Based on its working principle and the microplate format, the kit can be practically and routinely used for any species from a variety of forms including from cultured cells, fresh and frozen tissues, paraffin-embedded tissues, plasma/serum samples, and body fluid samples. To demonstrate the capabilities of the kit, it has been successfully used for quantifying the content of 5-hmC in DNA from mouse brains and HeLa cells. The percentage of 5-hmC measured by the MethylFlash kit is parallel and comparable to that detected by HPLC and LC-MS methods (see Table 1). Through the use of the kit, a high abundance of 5-hmC in normal human brains and colon tissues is discovered for the first time. Furthermore, it shows that 5-hmC accounts for 32% and 16% of total methylated cytosine (5-mC plus 5-hmC) in normal human brains and colon tissues, respectively (see Table 2). In contrast, 5-hmC is low or absent in colon cancer cell lines (HCT116) and cervical cancer cell lines (HeLa).

  MethylFlash LC-MS1
Mouse Brain 0.16% 0.13%
HeLa Cells < 0.02% not determined

Table 1. Comparison of the MethylFlash™ Hydroxymethylated DNA Quantification Kit and chromatography-based methods for the detection of 5-hydroxymethylcytosine, shown in percentage of 5-hmC present in two DNA sample types.

Munzel M et al: Angewandte Chemie, 122: ePub, 2010

  % 5-hmC % 5-mC 5-hmC/(5-mC + 5-hmC)
Human Brain 0.67% 1.00% 40.00%
Mouse Brain 0.16% 1.53% 10.00%
Human Placenta 0.06% 0.67% 8.00%
Human Colon 0.47% 1.46% 24.00%
HCT116 < 0.01% 1.30% < 1.00%
HeLa < 0.02% 1.62% < 1.00%

Table 2. Percentage of 5-hmC and 5-mC in different tissues/cells, measured with the MethylFlash™ Hydroxymethylated DNA Quantification Kit and the MethylFlash™ Methylated DNA Quantification Kit, respectively.

User Guide & MSDS

[User Guide]*
*Always use the actual User Guide that shipped with your product. Is the above file locked? You can also request user guides by emailing info@epigentek.com along with your contact information and institution name.

[Safety Data Sheet]
Product Citations

Paunescu I.A. et al et. al. (December 2018). Peripheral Blood Cell DNA Methylation and Hydroxymethylation in Prostate Cancer: A Pilot Study Research and Clinical Medicine. 2(2):20-23.

Zhong A et. al. (March 2018). DNA hydroxymethylation of colorectal primary carcinoma and its association with survival. J Surg Oncol.

Seo JS et. al. (February 2017). Hinokitiol induces DNA demethylation via DNMT1 and UHRF1 inhibition in colon cancer cells. BMC Cell Biol. 18(1):14.

Bak ST et. al. (December 2016). Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples. Mol Neurobiol.

Yi-ping TIAN et. al. (November 2016). Global changes of 5-hydroxymethylcytosine and 5-methylcytosine from normal to tumor tissues are associated with carcinogenesis and prognosis in colorectal cancer JZUSB.

Yamazaki M et. al. (February 2016). Fructose consumption induces hypomethylation of hepatic mitochondrial DNA in rats. Life Sci.

Nicoletti CF et. al. (July 2015). DNA Methylation and Hydroxymethylation Levels in Relation to Two Weight Loss Strategies: Energy-Restricted Diet or Bariatric Surgery. Obes Surg.

Mendonça A. S. et. al. (July 2015). Global methylation and hydroxymethylation patterns of bovine tissues Brazilian College of Animal Reproduction. 12(3)

Erdmann RM et. al. (November 2014). 5-Hydroxymethylcytosine Is Not Present in Appreciable Quantities in Arabidopsis DNA. G3 (Bethesda).

Haseeb A et. al. (March 2014). Modulation of ten-eleven translocation 1 (TET1), Isocitrate Dehydrogenase (IDH) expression, α-Ketoglutarate (α-KG), and DNA hydroxymethylation levels by interleukin-1β in primary human chondrocytes. J Biol Chem. 289(10):6877-85.

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