Magnetic particle-based genomic DNA purification from seed, young leaf, fruit, difficult plant or fungal tissue, and SDS-assisted high-weight genomic DNA workflows.
Manual workflow timing is shown as a practical laboratory estimate. Always follow the product insert for official operating conditions.
Grind plant seeds into a fine powder using a high-speed grinder and transfer 30–100 mg powder to a 2 ml microcentrifuge tube.
Seed input and grinding consistency strongly affect downstream lysate clarity and binding efficiency.
Add one 3 mm tungsten carbide bead and 0.8 ml Buffer SOL. Homogenize using a TissueLyser or GeneGrinder for about 3–5 minutes at 30–50 Hz, or vortex at high speed for 10 minutes.
The displayed timeline uses the mechanical homogenizer route; vortex homogenization can extend the entry step.
Incubate the homogenized lysate at 65°C for 10 minutes.
Keep the material suspended during lysis when possible, especially for starchy or oily seed powders.
Centrifuge the lysate for 5 minutes at >10,000 × g.
A compact debris pellet makes the 400 µl supernatant transfer more reliable.
Transfer 400 µl of the clarified supernatant to a clean tube without disturbing the cell-debris pellet.
The DNA-containing fraction used for purification is the clarified supernatant, not the pellet.
Combine the supernatant with 30 µl MagPure Particles and 600 µl Buffer MPB. Mix by pipetting 20 times or by shaking for 5 minutes until the suspension is homogeneous.
MagPure Particles should be shaken vigorously before use so that the particle suspension is uniform.
Place the tube on a magnetic stand for 1 minute until the particles have separated, then remove and discard the supernatant.
After binding, target DNA is associated with the magnetic particles; do not aspirate the bead pellet.
Add 600 µl Buffer GW1, resuspend the beads by pipette mixing 10 times or shaking for 1 minute, place on the magnetic stand for 1 minute, and remove the supernatant.
Ensure that ethanol has been added to Buffer GW1 before use.
Add 600 µl 80% ethanol, fully resuspend the beads, place on the magnetic stand for 1 minute, and remove the supernatant.
This wash helps remove residual salts and binding components.
Repeat the 80% ethanol wash once more, then remove the ethanol wash as completely as practical.
Residual ethanol can interfere with downstream reactions if not removed before drying and elution.
Air-dry the magnetic-particle pellet for 10 minutes.
Insufficient drying can leave ethanol in the eluate; excessive drying can make the pellet difficult to resuspend.
Add approximately 100 µl Elution Buffer, resuspend the particles by vortexing, and incubate at 65°C for 10 minutes with shaking. Place on the magnetic rack for 2 minutes.
If no shaking device is available, vortex 2–3 times during incubation to improve elution contact.
Transfer the supernatant containing purified DNA to a clean 1.5 ml centrifuge tube.
Avoid carrying magnetic particles into the final eluate.
Place tender young leaf or fruit tissue into a 2 ml safe-lock tube containing one 3 mm tungsten bead. About 50 mg fresh or frozen tissue is generally sufficient.
This route is intended for tender samples that can be rapidly homogenized.
Add 0.7 ml Buffer SOL and homogenize for 3–10 minutes at 30–50 Hz using a TissueLyser or GeneGrinder.
The displayed timeline uses a near-midpoint value for the 3–10 minute homogenization range.
Incubate the homogenized lysate at 65°C for 10 minutes.
Complete disruption before incubation is important because the lysis step is short.
Centrifuge the lysate for 5 minutes at >10,000 × g.
Transfer only the clarified supernatant into the shared magnetic purification route.
Transfer 400 µl of the clarified supernatant to a clean tube without disturbing the cell-debris pellet.
The DNA-containing fraction used for purification is the clarified supernatant, not the pellet.
Combine the supernatant with 30 µl MagPure Particles and 600 µl Buffer MPB. Mix by pipetting 20 times or by shaking for 5 minutes until the suspension is homogeneous.
MagPure Particles should be shaken vigorously before use so that the particle suspension is uniform.
Place the tube on a magnetic stand for 1 minute until the particles have separated, then remove and discard the supernatant.
After binding, target DNA is associated with the magnetic particles; do not aspirate the bead pellet.
Add 600 µl Buffer GW1, resuspend the beads by pipette mixing 10 times or shaking for 1 minute, place on the magnetic stand for 1 minute, and remove the supernatant.
Ensure that ethanol has been added to Buffer GW1 before use.
Add 600 µl 80% ethanol, fully resuspend the beads, place on the magnetic stand for 1 minute, and remove the supernatant.
This wash helps remove residual salts and binding components.
Repeat the 80% ethanol wash once more, then remove the ethanol wash as completely as practical.
Residual ethanol can interfere with downstream reactions if not removed before drying and elution.
Air-dry the magnetic-particle pellet for 10 minutes.
Insufficient drying can leave ethanol in the eluate; excessive drying can make the pellet difficult to resuspend.
Add approximately 100 µl Elution Buffer, resuspend the particles by vortexing, and incubate at 65°C for 10 minutes with shaking. Place on the magnetic rack for 2 minutes.
If no shaking device is available, vortex 2–3 times during incubation to improve elution contact.
Transfer the supernatant containing purified DNA to a clean 1.5 ml centrifuge tube.
Avoid carrying magnetic particles into the final eluate.
Disrupt 50 mg plant or fungal tissue using bead-beating methods.
This route is used when sample texture makes simple grinding or rapid homogenization insufficient.
Add 0.6 ml Buffer SOL and homogenize for approximately 2 minutes at 30–50 Hz.
The estimated time includes buffer addition, tube handling and homogenization.
Incubate the homogenized lysate at 65°C for 10 minutes.
If the lysate remains visibly heterogeneous, sample amount or disruption conditions may need optimization.
Centrifuge the lysate for 5 minutes at >10,000 × g.
Avoid disturbing the pellet during supernatant transfer.
Transfer 400 µl of the clarified supernatant to a clean tube without disturbing the cell-debris pellet.
The DNA-containing fraction used for purification is the clarified supernatant, not the pellet.
Combine the supernatant with 30 µl MagPure Particles and 600 µl Buffer MPB. Mix by pipetting 20 times or by shaking for 5 minutes until the suspension is homogeneous.
MagPure Particles should be shaken vigorously before use so that the particle suspension is uniform.
Place the tube on a magnetic stand for 1 minute until the particles have separated, then remove and discard the supernatant.
After binding, target DNA is associated with the magnetic particles; do not aspirate the bead pellet.
Add 600 µl Buffer GW1, resuspend the beads by pipette mixing 10 times or shaking for 1 minute, place on the magnetic stand for 1 minute, and remove the supernatant.
Ensure that ethanol has been added to Buffer GW1 before use.
Add 600 µl 80% ethanol, fully resuspend the beads, place on the magnetic stand for 1 minute, and remove the supernatant.
This wash helps remove residual salts and binding components.
Repeat the 80% ethanol wash once more, then remove the ethanol wash as completely as practical.
Residual ethanol can interfere with downstream reactions if not removed before drying and elution.
Air-dry the magnetic-particle pellet for 10 minutes.
Insufficient drying can leave ethanol in the eluate; excessive drying can make the pellet difficult to resuspend.
Add approximately 100 µl Elution Buffer, resuspend the particles by vortexing, and incubate at 65°C for 10 minutes with shaking. Place on the magnetic rack for 2 minutes.
If no shaking device is available, vortex 2–3 times during incubation to improve elution contact.
Transfer the supernatant containing purified DNA to a clean 1.5 ml centrifuge tube.
Avoid carrying magnetic particles into the final eluate.
Disrupt plant or fungal tissue by liquid-nitrogen grinding or bead-beating methods.
For this route, use up to 50 mg wet tissue or 15 mg dried tissue.
Add 500 µl Buffer SOL and 50 µl Buffer SDS to the disrupted sample and vortex vigorously.
The SDS route is provided for high-weight genomic DNA preparation and should be mixed thoroughly without unnecessary overhandling.
Incubate the lysate at 65°C for 10 minutes.
The protocol uses SOL plus SDS before clarification and magnetic binding.
Centrifuge the lysate for 5 minutes at >10,000 × g.
Transfer only the clarified supernatant and avoid pellet carryover.
Transfer 400 µl of the clarified supernatant to a clean tube without disturbing the cell-debris pellet.
The DNA-containing fraction used for purification is the clarified supernatant, not the pellet.
Combine the supernatant with 30 µl MagPure Particles and 600 µl Buffer MPB. Mix by pipetting 20 times or by shaking for 5 minutes until the suspension is homogeneous.
MagPure Particles should be shaken vigorously before use so that the particle suspension is uniform.
Place the tube on a magnetic stand for 1 minute until the particles have separated, then remove and discard the supernatant.
After binding, target DNA is associated with the magnetic particles; do not aspirate the bead pellet.
Add 600 µl Buffer GW1, resuspend the beads by pipette mixing 10 times or shaking for 1 minute, place on the magnetic stand for 1 minute, and remove the supernatant.
Ensure that ethanol has been added to Buffer GW1 before use.
Add 600 µl 80% ethanol, fully resuspend the beads, place on the magnetic stand for 1 minute, and remove the supernatant.
This wash helps remove residual salts and binding components.
Repeat the 80% ethanol wash once more, then remove the ethanol wash as completely as practical.
Residual ethanol can interfere with downstream reactions if not removed before drying and elution.
Air-dry the magnetic-particle pellet for 10 minutes.
Insufficient drying can leave ethanol in the eluate; excessive drying can make the pellet difficult to resuspend.
Add approximately 100 µl Elution Buffer, resuspend the particles by vortexing, and incubate at 65°C for 10 minutes with shaking. Place on the magnetic rack for 2 minutes.
If no shaking device is available, vortex 2–3 times during incubation to improve elution contact.
Transfer the supernatant containing purified DNA to a clean 1.5 ml centrifuge tube.
Avoid carrying magnetic particles into the final eluate.
This workflow separates four sample-entry routes from the shared magnetic-particle purification route. Seed powder, tender young leaf or fruit, difficult-to-grind material and SDS-assisted high-weight genomic DNA preparation differ mainly in disruption and lysis conditions; after clarification, the workflow converges at supernatant transfer, MPB-assisted magnetic binding, washing, drying and elution. It is intended as a practical companion to the product manual rather than a replacement for 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, tube transfer, centrifuge handling, magnetic-rack placement, bead resuspension, supernatant removal, residual-liquid removal, drying control, elution and final tube transfer. For short protocol ranges, the timeline uses the midpoint or a near-midpoint value. 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. For this D6352 workflow, sample weighing and homogenizer handling are also included in the practical time estimate. The displayed timelines represent standard manual runs and end at 70, 66, 65 and 66 min for the four routes. Because the main timing anchors are fixed, the final ranges are kept close to the timelines: the seed high-yield route remains slightly wider because grinding and homogenization can vary more, while the young leaf / fruit, difficult-sample and SDS high-weight gDNA routes are kept to a narrower 60–75 min range.
D6352 is a phenol-free and chloroform-free magnetic DNA workflow for seed and plant materials. Buffer SOL provides the main lysis environment, while the SDS route adds Buffer SDS for high-weight genomic DNA preparation. DNA in the clarified supernatant is captured by MagPure Particles in the presence of Buffer MPB, washed with GW1 and 80% ethanol, dried, and eluted from the particles with Elution Buffer at 65°C.
Sample powder or tissue must be fully disrupted before lysis. Do not transfer debris pellets into the binding step, because particulate carryover can reduce bead handling quality. MagPure Particles must be homogeneous before dispensing, and the beads must be fully resuspended during binding, washing and elution. Remove wash solutions completely before drying, but avoid over-drying the bead pellet. During final transfer, avoid carrying magnetic particles into the purified DNA.