A Rapid and Simple Bead-Bashing-Based Method for Genomic DNA Extraction from Mammalian Tissue

Abstract

Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.

Molecular characterization of chlorpyrifos degrading bacteria isolated from contaminated dairy farm soils in Nakuru County, Kenya

“…The Zymo quick DNA™ Min Prep Kit (Zymo Research, USA) was used for genomic DNA extraction, with strict adherence to manufacturer instructions ( Wei et al., 2020 ). In this regard, freshly cultured bacteria isolates were suspended in normal saline (500 μL) in Eppendorf tubes.…”

Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing

“…Bead-bashing involves the mechanical agitation of cells using glass or plastic beads, which can physically break apart the cells and release nuclei. Bead-bashing is not typically utilized in conjunction with nuclear isolation methodologies, but it has demonstrated efficacy in dissociating various tissues, contingent upon the intensity of mechanical force applied and sample properties [ 22 , 23 ]. Cryogenic pulverization involves freezing tissue in liquid nitrogen and then pulverizing it into a fine powder and can be used for a wide range of tissues, including hard-to-dissociate tissues [ 24 , 25 , 26 , 27 ].…”

Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing

“…Bead bashing involves mechanical agitation of cells using glass or plastic beads, which can physically break apart the cells and release nuclei. Bead bashing is not typically utilized in conjunction with nuclear isolation methodologies, but it has demonstrated efficacy in dissociating various tissues contingent upon the intensity of mechanical force applied and sample properties (22)(23). Cryogenic pulverization involves freezing tissue in liquid nitrogen and then pulverizing it into a fine powder and can be used for a wide range of tissues including hard-to-dissociate tissues [24 -277].…”