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EZ Nucleosomal DNA Prep Kit

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

Product Size Catalog # Price Qty
EZ Nucleosomal DNA Prep Kit 20 Preps. D5220

About EZ Nucleosomal DNA Prep Kit

The EZ Nucleosomal DNA Prep Kit is a streamlined procedure for the isolation of mammalian and yeast nucleosome-associated DNA. The kit includes procedures and reagents for: cell nuclei isolation, intact nuclei micrococcal nuclease digestion, and nucleosomal DNA purification. Non-nucleosomal DNA is specifically degraded using micrococcal nuclease and an optimized reaction buffer; while purification of "protected" nucleosome-associated DNA is performed using Zymo Research's proven Fast-Spin column technology. The result is pure nucleosomal DNA ready for analysis in less than 30 minutes!

Format Spin Column
DNA Recovery Typically, up to 25 µg total DNA can be eluted into as little as 25 µl water. For DNA 75 bp to 10 kb the recovery is 70-90%. For DNA 11 kb to 23 kb the recovery is 50-70%.
Sample Sources Nucleosome associated DNA isolation and purification from mammalian and yeast cells.
DNA Purity High quality, purified DNA is eluted with elution buffer or water and is especially well suited for PCR amplification, arrays, Southern blot analysis, DNA quantification, sequencing, and other molecular applications.
Product Detergent Tolerance ≤5% Triton X-100, ≤5% Tween-20, ≤5% Sarkosyl, ≤0.1% SDS

Mammalian Nucleosomal DNA Preparation: Mammalian nuclei was treated with 0.1 U, 0.25 U, and 0.5 U (unit) Atlantis dsDNase for the 20 min at 42°C. DNA was subsequently resolved in a 2% agarose gel. 100 bp DNA ladder (Zymo Research Corp.). Asterisks (1N, 2N, 3N) represent mono-, di-, and tri-nucleosomal DNAs, respectively.
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Featured Citations

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.
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.
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.
An MNase digestion assay was performed using the EZ Nucleosomal DNA Prep Kit to study the kinetics of micrococcal nuclease digestion in wild type and LAP2α deficient HeLa cells.
Mononucleosomal DNA from p16-methylated AGS and p16-unmethylated MGC803 cell lines was isolated using the EZ Nucleosomal DNA Prep Kit. The isolated mononucleosomal DNA was used to study the chromatin accessibility across the p16 promoter by quantitative PCR.
The EZ Nucleosomal DNA Prep Kit from Zymo Research was used to isolate nuclei from mouse pituitary tissue and B cells. The purified DNA was further isolated into mononucleosome core fragments and sequenced for nucleosome mapping studies of the human growth hormone gene.
Nucleosomal DNA was isolated from mouse splenocytes using the EZ Nucleosomal DNA Prep Kit from Zymo Research. Nucleosomal DNA was used to demonstrate the effect of topo I on binding of anti-dsDNA antibodies. Surprisingly, topo I increased binding of these antibodies in the plasma of lupus-prone mice. This data, combined with additional findings, suggests a possible therapeutic target in topo I for Lupus patients.
Researchers from the University of Rochester performed micrococcal nuclease digestion of DNA using the EZ Nucleosomal DNA Prep Kit from Zymo Research. The authors showed that SIRT6 KO mouse embryonic fibroblasts had disturbed higher order chromatin structures. Further studies demonstrated that L1 loci were particularly sensitive to the micrococcal nuclease treatment and that SIRT6 is required for packaging L1 loci into transcriptionally repressive heterochromatin.

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