EZ Nucleosomal DNA Prep Kit


EZ Nucleosomal DNA Prep Kit


Cat # Name Size Price Quantity
D5220 EZ Nucleosomal DNA Prep Kit 20 Preps $137.00
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Ideal for nucleosome mapping studies


  • For the isolation of nucleosome-associated DNA from mammalian and yeast cells.
  • Ideal for use in nucleosome mapping studies.


The EZ Nucleosomal DNA Prep Kit is a streamlined procedure for the isolation of nucleosome-associated DNA. The kit includes reagents/procedures for the following: cell nuclei isolation, intact nuclei enzymatic digestion, and nucleosomal DNA purification. This kit includes two different enzymes for nucleosomal DNA preparation: Atlantis dsDNase and Micrococcal Nuclease. Enzymatic digestion yields very homogeneous populations of core nucleosomes and purification of the nucleosome-associated DNA is performed using Zymo Research’s proven spin column technology. The result is pure nucleosomal DNA ready for analysis in less than 45 minutes!

Technical Specifications

Applicable For All sensitive downstream applications such as qPCR and Next-Generation sequencing.
Processing Volume ≤106 cells
Purity Typical A260/A280 ≥ 1.8
Sample Source Nucleosome associated DNA isolation and purification from mammalian and yeast cells.
Sample Storage Eluted DNA should be stored at ≤ -20°C.
Yield Up to 25 µg total DNA can be eluted into ≥ 25 µl. For DNA 75 bp - 10 kb the recovery is 70-90%. For DNA 11 kb - 23 kb the recovery is 50-70%.

Product FAQ

Q1: What is the sensitivity of the enzyme to different cell types?

Q2: What is the difference between Atlantis dsDNase and MNase?

Q3: Do the sticky-end fragments have 5’ vs. 3’-overhangs? What is the relative abundance of different ends?

Q4: What if the nucleosomal DNA is not shearing properly and the majority of DNA is still intact?


Micrococcal nuclease digestion was performed on embryonic stem cells using the EZ Nucleosomal DNA Prep Kit and paired-end libraries were generated for sequencing. Research showed heterogeneous chromatin organization around transcription start sites as well as unique nucleosome profiles associated with epigenetic patterns that can identify pluripotency.

Yazdi PG, et. al. (2015). Nucleosome Organization in Human Embryonic Stem Cells. PLoS ONE. 10(8).

The EZ Nucleosomal DNA Prep Kit was used by researchers to isolate nucleosomal DNA from 293FT cells prior to performing Chromatin Accessibility Real Time PCR (CHART-PCR) to investigate the IL-2 promoter chromatin architecture in the presence of TATA-box binding protein (TBP-TALE) and VP64-TALE activators in non-immune cells. They found that the combination of AD’CF TALEs but not empty vector control increased DNase I hypersensitivity across the IL-2 promoter.

Anthony K et al. (2014) Activation of Silenced Cytokine Gene Promoters by the Synergistic Effect of TBP-TALE and VP64-TALE Activators. PLoS One. 2014 Apr 22;9(4):e95790.

Researchers used the EZ Nucleosomal DNA Prep Kit from Zymo Research to isolate nuclei, digest chromatin, and purify nucleosomal DNA from Hep3B cells or SW13 cells that were transfected with either an empty vector or vectors expressing WT BRG1 or ATPase-dead BRG1. Purified nucleosomal DNA was used for SYBR Green–based qPCR to determine nucleosome positioning on the CA9 and LDHA promoters.

Sena JA et al. (2013) BRG1 and BRM chromatin remodeling complexes regulate the hypoxia response by acting as a co-activator for a subset of HIF target genes. Mol Cell Biol.

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Kit Components