Nuclear isolation is crucial for studying gene expression and regulatory mechanisms in eukaryotic cells. This study aimed to improve nuclear isolation and compare the yield, purity, and efficiency of several methods. Human umbilical vein endothelial cells were used to evaluate four different techniques: sucrose centrifugation, a simplified method, homogenization, and the NE-PER kit. For sucrose centrifugation, cells were scraped in Tween buffer, washed with sucrose buffer, and homogenized in a Dounce homogenizer. The pellet was washed with glycerol buffer to isolate the nuclei. In the simplified method, cells were scraped in scraping buffer, washed with sucrose buffer, and the pellet was washed with glycerol buffer to isolate the nuclei. For homogenization, cells were washed with phosphate buffered saline, followed by two washes in extract buffer and lysed with 10 strokes in a Kontes Dounce homogenizer. The NE-PER kit was used according to the manufacturer's protocol. Nuclei isolated by each method were tested by immunoblotting, co-immunoprecipitation (Co-IP), and chromatin immunoprecipitation (Ch-IP) assays. The simplified method produced nuclei with fewer organelles and less cytoplasm than those isolated by homogenization or the NE-PER kit. It was similarly effective as sucrose centrifugation but faster. Co-IP and Ch-IP assays confirmed that the simplified method enriched target proteins and DNA fragments. Overall, the simplified method provides a highly pure nuclear sample optimal for downstream applications requiring purified nuclei.
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