Methylated DNA Analysis

Cloned DNA methyltransferases are used for in vivo footprinting to determine nucleosome positioning on chromatin (1). DamID is used to determine sequence specificity of DNA binding proteins – via methylation profiling, after expression of the methyltransferase-DNA binding fusion protein (2). DNA (cytosine-5) Methyltransferases (DNMTs) are also used for targeted gene silencing studies by expression as fusion proteins with a specific DNA-binding domain to direct methylation events to the promoters of target genes.

DNMT isoforms include DNMT1, DNMT1b, DNMT2, DNMT3a, and DNMT3b (and a host of DNMT3 splice variants). The activity of DNMTs can be quantitated via several methods (3). These include ELISA, radioactive filter-binding assay or a real time assay using a break light oligonucleotide in which the methylation of an unmethylated 5′-CG-3′ site is enzymatically coupled to the development of a fluorescent signal (4,5). The localization of DNMTs can be revealed by specific antibodies used in immunolocalization methods.

Methyltransferases are also used to block cleavage by restriction enzymes. In vitro methylation of genomic DNA, plasmids or purified PCR products is best accomplished by CpG Methyltransferase.

A new method for DNA methylation analysis at the single base level, NEBNext® Enzymatic Methyl-seq (EM-seq™), is now available. This enzyme-based technology minimizes damage to DNA and produces high quality libraries that enable superior detection of 5mC and 5hmC from fewer sequencing reads. More information is available here.

  1. Mehrnaz Fatemi et al. (2005) Nucl. Acids Res. 33(20): e176. PMID: 16314307
  2. Bas van Steensel, Jeffrey Delrow & Steven Henikoff (2001) Nature Genetics 27:304. PMID: 11242113
  3. Jurkowska RZ, (2011) Methods Mol Biol, 791:157-77. PMID: 21913079
  4. Carina Frauer and Heinrich Leonhardt (2009) Nucl. Acids Res. 37 (3): e22. PMID: 19129216
  5. Robert J. Wood et al. (2010) Nucl. Acids Res. 38(9): e107. PMID: 20139415

Choose Type:

FAQs for Methylated DNA Analysis
Protocols for Methylated DNA Analysis
    Publications related to Methylated DNA Analysis
    • Woodcock, C.B.l, Yu, D., Hajian, T., Li, J., Huang, Y., Dai, N., Corrêa, I.R., Jr., Wu, T., Vedadi, M., Zhang, X., Cheng, X (2019) Human MettL3 MettL14 complex is a sequence specific DNA adenine methyltransferase active on single strand and unpaired DNA in vitro Cell Discov ; 5:63, PubMedID: 31885874, DOI: 10.1038/s41421-019-0136-4
Legal Information

Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email busdev@neb.com.

This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.


  • What is Epigenetics?

    What Is Epigenetics?

    If all cells are created from the same genetic material, why are there so many different cell types? Listen to Sriharsa Pradhan, Senior Scientist, RNA Biology at NEB, as he describes how DNA is methylated and how this affects the path of reading the DNA code the same way an obstruction would derail a train off its tracks.