Medium-throughput Column DNA Extraction Using 24-well Racks

Silica-membrane spin column extraction is the standard for high-quality DNA purification but is labor-intensive and difficult to scale manually beyond small batches. Existing automated liquid handling robots are often still too expensive for small and medium-sized laboratories. This paper presents a streamlined, semi-automated approach using custom-designed, 3D-printed racks that fit standard centrifugation plate rotors. The suggested system allows the parallel processing of up to 116 standard commercial spin columns. The rack design accommodates a "nested" configuration, enabling simultaneous lysate clarification (via filtration columns) and DNA binding (via silica columns) in a single centrifugation step. Furthermore, the design incorporates a shared waste reservoir, eliminating the need to discard flowthrough from individual tubes during washing steps. This method achieves DNA yield and purity comparable to standard manual protocols but reduces total processing time by approximately 50-70% for sample batches larger than 24 (60-90 min instead of 120-180 min). Total time required for steps including lysate filtration, washes, and waste discarding is reduced by 5-10 min regardless of the number of processed samples. This open-source hardware approach bridges the gap between manual minipreps and expensive automation.