Plasmid DNA Purification Using Filterprep With an Optional Endotoxin Removal Step

This protocol presents a modified version of the Filterprep method originally reported in New Biotechnology, adding an optional step to reduce endotoxin levels. Filterprep is a simple, rapid, and cost-effective approach to plasmid DNA purification that couples ethanol precipitation with a single spin-column filtration step, eliminating chaotropic salts and silica binding. The formulations and parameters are fully transparent and do not rely on proprietary buffers, using only standard laboratory reagents and widely available miniprep columns. Under matched conditions, the method recovers high-purity plasmid DNA with yields up to fivefold higher than those obtained with representative commercial midiprep kits. The workflow is readily adoptable in most molecular biology laboratories and, under routine conditions, can be completed in approximately 40 min. The resulting DNA is suitable for molecular cloning, PCR, sequencing, and other downstream biochemical applications. Endotoxin is a lipopolysaccharide (LPS) found in the outer membrane of Gram-negative bacteria and may carry over during plasmid preparation. For experiments requiring lower endotoxin input, an optional modification resuspends the DNA pellet in a Triton X-114 wash buffer before column loading to decrease lipopolysaccharide carryover. The method is modular and extensible, allowing adjustment of precipitation and wash conditions, variation in the number of washes, selection of alternative column formats, and integration of endotoxin-reduction modules without altering the core principle. These features facilitate troubleshooting and quality control, enable scaling from routine batches to larger culture volumes and higher throughput, and allow seamless integration with existing workflows. Key features • Modular, chaotrope-free workflow [1] combining ethanol precipitation and single-column cleanup; transparent chemistry allows RNase, endotoxin reduction, or extra washes without changing the core principle. • Uses only standard reagents, a microcentrifuge, and common miniprep columns, with no proprietary kits, vacuum manifolds, or specialized equipment, enabling broad adoption across laboratories. • Extensible across scales from small miniprep volumes to larger cultures while remaining compatible with cloning, PCR, sequencing, and transfection-grade applications. • Optional low-endotoxin modification resuspends the DNA pellet in Triton X-114 wash buffer before column filtration to reduce lipopolysaccharide carryover.