Cat. No. D635601 / D635602 / D635603
Manual magnetic-bead workflow for genomic DNA purification from soil, stool and environmental samples.
Transfer 250–500 mg soil sample, 0.1 g stool sample, or 0.1–0.5 g environmental sample into a 2 ml Bead Tube.
Use the stated input range according to matrix load. Excess material can increase pigment, humic-acid and particulate carryover.
Add 700 µl Buffer SOL, 70 µl Buffer SDS and 5 µl Reagent DX to the sample. Mix thoroughly before mechanical disruption.
The SOL / SDS / Reagent DX mixture can be prepared in advance as described in the manual. For multiple samples, the manual recommends using Magen's MagMix A shaker for parallel processing.
Lyse by FastPrep 24 at 6.5 m/s twice for 45 s, or vortex at maximum speed for 10 min, then incubate at 65°C for 10 min.
The standard timeline uses the fast bead-grinding route. Vortex disruption may extend this step.
Centrifuge at 13,000 × g for 3 min at room temperature to pellet debris and large particles.
Clear separation at this stage helps reduce carryover into the inhibitor-removal step.
Transfer 500 µl supernatant into a new 1.5 ml microcentrifuge tube.
Avoid disturbing the pellet when transferring the clarified lysate.
Add 125 µl Buffer PS and vortex to mix thoroughly.
This step prepares the lysate for inhibitor adsorption and downstream magnetic binding.
Add 125 µl Absorber Solution, vortex thoroughly, let sit on ice for 5 min, then centrifuge at maximum speed (≥13,000 × g) for 5 min.
Absorber Solution is used to reduce humic acid, pigments, polysaccharides and other soil-matrix inhibitors.
Transfer 600 µl supernatant to a new 2.0 ml microcentrifuge tube.
Keep the cleared fraction clean; inhibitor-rich sediment should not be carried into magnetic binding.
Add 40 µl MagPure Particles and 700 µl Buffer GDP. Mix well by inverting, incubate for 5 min with occasional inversion, then place on a magnetic stand for 1 min and remove the supernatant.
DNA binds to magnetic particles under GDP binding conditions.
Add 500 µl Buffer GDP, vortex for 15 s to resuspend beads, place on the magnetic stand for 1 min, then remove the supernatant.
This wash helps reduce remaining matrix contaminants before ethanol-containing washes.
Add 750 µl Buffer GW1, vortex for 15 s to resuspend beads, place on the magnetic stand for 1 min, then remove the supernatant.
Confirm that ethanol has been added to Buffer GW1 before use.
Add 750 µl 75% ethanol, vortex for 15 s to resuspend beads, place on the magnetic stand for 1 min, then remove the supernatant.
Efficient ethanol washing helps remove residual salts.
Repeat the 75% ethanol wash once using the same resuspension, magnetic separation and supernatant-removal logic.
Remove the wash liquid carefully to reduce ethanol carryover.
Centrifuge briefly to collect residual liquid, place the tube on the magnetic stand, remove all liquid carefully and air-dry for 10 min.
Do not leave visible ethanol before elution; incomplete drying can affect downstream PCR or enzymatic reactions.
Add 50–100 µl Elution Buffer, resuspend the beads by vortexing and incubate at 55°C for 10 min with shaking. If no shaking device is available, vortex 2–3 times during incubation.
Warm elution improves DNA release from magnetic particles.
Place the tube on the magnetic rack for 2 min, then transfer the supernatant containing purified DNA to a clean 1.5 ml centrifuge tube.
Avoid transferring magnetic particles into the final eluate.
This workflow separates soil-matrix lysis and inhibitor cleanup from the shared magnetic-particle binding, washing, drying and elution path. It is intended as a practical companion to the product manual rather than a replacement for the official protocol. This note reflects the manual magnetic-bead workflow; automated KingFisher Flex processing can be followed according to the official protocol.
Protocol times stated in the product manual are retained where applicable. Steps without explicit timing are estimated for an experienced operator, including pipetting, vortexing, tube transfer, magnetic-rack handling, supernatant removal and tube repositioning. For short protocol ranges, the timeline uses the midpoint. For long or optional protocol ranges, the displayed standard timeline uses the shortest reasonable path, while the note and total-time range indicate where extended handling may apply. In this workflow, the standard cumulative timeline uses the rapid bead-grinding route described in the manual. If maximum-speed vortex disruption is used instead of FastPrep-style bead grinding, the lysis module may take longer and the total processing time may move toward the upper end of the displayed range. Cumulative time runs continuously from sample loading to final DNA recovery.
D6356 combines bead-tube disruption, detergent-based lysis, Absorber Solution cleanup and magnetic-particle purification. The early workflow is designed to release microbial DNA from soil, stool or environmental matrices while reducing humic acid, pigments, polysaccharides and other PCR-inhibitory contaminants before DNA binding to MagPure Particles.
The main handling risk is carrying inhibitor-rich sediment into the magnetic binding stage. Keep the clarified supernatant clean after centrifugation and Absorber Solution treatment. The standard timeline uses the fast bead-grinding option; vortex-based disruption may extend the lysis module. Complete removal of residual ethanol before elution is important for PCR, restriction digestion and next-generation sequencing compatibility.