DNA Loss from Bead Removal During Supernatant Transfer (Cell-free DNA Extraction)

Question

Accepted Answer

Variable or reduced cfDNA yields across samples. Beads may be visible in wash supernatants or final eluate, or yield decreases progressively through the protocol. Common causes: 1) Magnetic separation time less than the required 2 minutes minimum at separation steps 2) Weak magnet insufficient to fully pellet beads, leaving beads suspended in supernatant 3) Pipette tip disturbing bead pellet during supernatant removal 4) Rushing through transfers without verifying clear supernatant before pipetting Solutions: 1) Leave tubes on magnet for minimum 2 minutes at all magnetic separation steps 2) Use a strong magnet to ensure effective bead separation and clear supernatant 3) Visually confirm supernatant is completely clear and free of beads before removing 4) Carefully pipette supernatant without touching or disturbing the bead pellet 5) When transferring final elution, leave a small volume (1-2 µL) behind to avoid bead carryover