eLabNotebook > Nucleic Acid Prep & Purification > PCR Cleanup > MagneSil PCR Cleanup Biomek® FX


Fully-Automated Method for Purifying PCR* Products using Promega's Wizard MagneSil* PCR Clean-Up System on the Biomek® FX Liquid Handling System

**Chad Pittman, ***Graham Threadgill, Ph.D., and **Laura Pajak, Ph.D. 
Beckman Coulter, Inc.
**Indianapolis, Indiana and ***Fullerton, California

For additional information try our Maintenance and Troubleshooting section or post a question to our Biomek User Forum.  New members can subscribe to our User Forum here.

Problem Possible Cause Solution
Inconsistent yield across the plate.
  • Inconsistent particle dispense.
  • Mix particles thoroughly. Add additional mix cycles as necessary.
  • Increase speed and number of dispenses.
  • Thoroughly mix resin prior to dispensing into reservoirs for use on the workstation.
  • Particle Loss.
  • Aspirate slowly when removing supernatants from MagneSil pellets.
  • Increase time on magnet.
  • Raise aspiration heights.
  • Adjust magnet height of that labware for the MagBead ALP.
Particle carryover in final eluate.
  • Inappropriate aspiration rate.
  • Reduce the aspiration rate when removing the final eluate from the MagneSil pellets.
  • Adjust magnet height of that labware for the MagBead ALP.
  • Insufficient elution steps.
  • Add an additional magnetic capture step to remove any carryover.
  • Decrease second capture elution volume.
  • Insufficient time on the magnet.
  • Increase incubation time on the magnet.
White precipitate when samples are dried down. Possible salt contamination.
  • Insufficient mixing.
  • Ensure adequate mixing is occurring. Adjust the Orbital Shaker accordingly.
  • Insufficient Washing.
  • Add an additional wash step with ethanol.
  • Incorrect Elution Reagent used.
  • Ensure that the nuclease-free water is used in the elution step.
  • Insufficient removal of solutions from MagneSil pellets.
  • Adjust aspiration steps removing liquid from MagneSil pellets to allow for maximum removal of solutions.
  • Aggressive mixing.
  • Adjust Orbital shaker parameters such that sloshing of wells does not occur.
Contamination of wells.
  • Aggressive mixing.
  • Adjust shaking on the Orbital Shaker such that sloshing of wells does not occur.
  • Dispensing rate.
  • Adjust the rate at which wash solution is added such that sloshing of wells does not occur.
  • Tips not washing.
  • Ensure Tip Wash working properly and all tips are being cleaned.
Incomplete removal of solutions from plates and/or improper movement of plates.
  • Poor framing of the worksurface.
  • Reframe the worksurface of the Biomek FX.  Ensure Orbital Shaker is "Home" prior to framing.
  • Labware in wrong location.
  • Place labware in the appropriate locations on the surface of the workstation.
  • Alternate labware used.
  • Define alternate labware in the Labware Editor.
  • Use the recommended labware as indicated in the starting Worksurface Layout.
  • Adjust the aspiration and dispense heights accordingly to accommodate the non-specified labware.
  • Plate is warped.
  • Select for MagBead ALP to clamp the plate before pipetting from that labware.
Evaporation/low volume of final eluate.
  • Elution plates not stored.
  • After running the method properly store elution plates so they do not evaporate.
  • Volume of final eluate too low.
  • Increase volume of Elution Buffer.
Low yield.
  • Inappropriate or incomplete PCR amplification.
  • Use a Triton X-100-FREE PCR buffer.
  • Increase number of amplification cycles.
  • Optimize PCR conditions.
  • Small PCR Products.
  • Increase size of amplification product. 150-300 bp products are expected to give lower yields than larger products.
  • Residual ethanol.
  • Adjust aspiration height when removing ethanol wash solutions.
  • Increase drying time.
  • Insufficient MagneSil Red to bind the plasmid.
  • Be sure MagneSil reagent plates are freshly dispensed.
  • Insufficient mixing.
  • Adjust Shaker for maximum resuspension of particles.
  • Shaker parameters have been optimized using a 50µL PCR reaction volume. If your volume is different, you should adjust the shaker parameters.
  • Increase elution volume to 150µL.
  • Inhibitors in PCR reagents.
  • Use reagents containing less that 1M Beatine or 5% DMSO.  The effect of other PCR additives on yield may have to be determined empirically.
  • Promega PCR Master Mix (P/N M7505) is recommended for optimal yield performance.
Primer carryover.
  • Insufficient Mixing/Washing.
  • Include an additional wash step prior to the ethanol washes.
  • Increase number of mixes on the Orbital Shaker.
  • Adjust Orbital Shaker to get maximum resuspension of particles.
Impure final product.
  • Aberrant amplification. 
  • Adjust amplification reaction to eliminate non-specific amplification products.
  • Non-specific amplification products greater than 100bp will not be completely removed.
Poor or no results with automated fluorescent DNA sequencing.
  • Ethanol contamination.
  • Make sure the wash solutions have completely evaporated by using the full drying time.
  • Too much or too little DNA used in sequencing reaction.
  • Quantitate DNA accurately by using agarose gel/ethidium bromide electrophoresis in addition to PicoGreen or spectrophotmetric analysis.
  • TE buffer used for elution.
  • Elute DNA in nuclease-free water.
Reagents are not delivered appropriately.
  • Incorrect positioning of reagents.
  • Consult the Instrument Setup to ensure reagents are placed in the appropriate locations.
Magnetic beads in dispense head.
  • Inaccurate framing of worksurface.
  • Caution: Reframe the worksurface as necessary. Be sure the Orbital Shaker is properly installed and framed.
  • Aspirating too low in plates containing MagneSil.
  • Caution: Increase aspiration height. This is particularly important while mixing MagneSil.
  • Do NOT aspirate MagneSil from the very bottom of plates and/or reservoirs.
Plates are not secure on shaker.
  • Inaccurate framing of Orbital Shaker.
  • Frame shaker as recommended in the manual.
  • Wrong labware used.
  • Ensure shaker is "Home" prior to framing and thumb screws are tightly secured.
Crashes occur when moving labware with Gripper.
  • Gripper fingers are worn, torn, or bent.
  • Replace worn or torn finger pads and bent fingers as needed.
  • The Gripper or worksurface is inaccurately framed.
  • Reframe the worksurface and Grippers as necessary.
  • Labware placed in the wrong positions.
  • Check Deck Editor and the Instrument Setup to confirm all ALPs and labware are in the correct locations.

* All trademarks are the property of their respective owners. Where applicable, the PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Hoffman-LaRoche, Ltd.

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