eLabNotebook > Nucleic Acid Prep & Purification > Plasmid DNA Purification > Promega MagneSil*
Biomek® FX


High-Quality Plasmid Purification Using Promega's Wizard* MagneSil* Plasmid Purification System and the Biomek® FX Liquid Handling System

Monique Coles**, 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 shake 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.
  • Be sure MagneSil reagent plates are freshly dispensed.
Particle carryover in final eluate.
  • Inappropriate aspiration rate.
  • Reduce the aspiration rate when removing the final eluate from the MagneSil pellets.
  • Insufficient elution steps.
  • Add an additional magnetic capture step to remove any carryover.
  • Elution volume too low.
  • Increase the elution volume.
  • Wrong magnet installed in MagBead ALP.
  • Ensure that the Prong, not flat, magnet is installed in the MagBead ALP.
  • Insufficient time on the magnet.
  • Increase incubation time on the magnet.
Incomplete resuspension of cells.
  • Excessive storage at -20°C.
  • Store bacterial pellets for 2-6 weeks at -20°C.
  • Insufficient shaking on the Orbital Shaker.
  • Increase shake cycles in resuspension step.
  • Cell pellet too large.
  • Do not process more than 6.0 OD600 per well.
  • Cell pellet still frozen.
  • Allow plates to equilibrate to room temperature for 15 minutes minimum.
Contamination of wells.
  • Aggressive mixing.
  • Adjust shaking on the Orbital Shaker such that sloshing of wells does not occur.
Incomplete removal of solutions from plates and/or improper movement of plates.
  • Poor framing of the worksurface.
  • Reframe the worksurface of the Biomek FX.
  • Labware and/or tip box holders in wrong location.
  • Place labware and tip box holders in the appropriate location on the surface of the workstation. Be sure to have the method on the Instrument Setup step of the method when configuring reagents on the Biomek FX.
  • Alternate labware used.
  • Define alternate labware in the Labware Type Editor.
  • Use the recommended labware as indicated in the starting Instrument Setup.
  • Adjust the aspiration and dispense heights accordingly to accommodate the non-specified labware.
Low volume of final eluate.
  • Volume of final eluate too low.
  • Increase volume of Elution Buffer.
Low yield.
  • Overgrowth of bacterial culture by nontransformed cells.
  • Inoculate antibiotic-containing media with a single colony from a fresh plate. Make sure antibiotics are present in the media.
  • Incomplete resuspension.
  • Adjust shaking on the Orbital Shaker to get maximum resuspension for your conditions.
  • Residual ethanol.
  • Adjust aspiration height when removing ethanol wash solutions.
  • Add pauses to increase drying time.
  • Insufficient MagneSil Red to bind the plasmid.
  • Be sure MagneSil reagent plates are freshly dispensed.
  • Insufficient mixing.
  • Adjust Orbital Shaker for maximum resuspension of particles.
  • Shaker parameters have been optimized using the manufacturer's recommended volumes. If your volume is different, the parameters for the shaker should be adjusted.
  • Endonuclease present in final eluate.
  • Use an endA(-) strain of E. coli such as DH5(, XL10Blue, JM103 or JM109.
  • Inadequate or inappropriate culture growth conditions.
  • Ensure good aeration of the culture.
  • Use a rich media. CIRCLEGROW is recommended (Q-Biogene, Cat #3000-165/(0.5L) pack of 10).
Poor results in downstream applications.
  • 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.
Pellet does not form at corners by magnet.
  • Too many cells processed.
  • Adjust cell growth parameters such that the cell mass processed is less than 6.0 OD600 per well total cell Biomass.
  • Insufficient time on the magnet.
  • Increase incubation time on the magnet.
  • Wrong magnet installed in MagBead ALP.
  • Ensure that the prong, not flat, magnet is installed in the MagBead ALP.
Turbidity observed in cleared lysate.
  • Excessive incubation in neutralization solution.
  • Do not shake for more than 4 minutes after the addition of neutralization solution.
  • Incomplete lysis.
  • Ensure that cells are completely thawed.
  • Too many cells processed.
  • Increase lysis time from 3 minutes.
  • Do not process more than 6.0 OD600 per well total cell biomass and/or increase lysis time.
Poor or no results with automated fluorescent DNA sequencing.
  • Ethanol contamination.
  • Make sure the wash solutions have completely evaporated by using the full 10 minute 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 spectrophotometric analysis.
  • TE buffer used for elution.
  • Elute DNA in nuclease-free water.
Reagents are not delivered appropriately.
  • Incorrect positioning of reagents.
  • Consult the Initial Instrument Setup screen to ensure reagents are placed in the appropriate location.
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.
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 definition incorrect.
  • Check Labware and movement definitions.
  • Labware or ALPs are placed in the wrong positions.
  • Check Deck Editor and the Instrument Setup to confirm all ALPs and labware are in the correct location.
Orbital Shaker does not respond.
  • Wrong hardware address.
  • Set the hardware address on the Orbital Shaker to "0."
  • Device not associated with Orbital Shaker position on the deck.
  • Associate the Orbital Shaker with the position in the Deck Editor.
MagBead ALP does not respond.
  • Wrong hardware address.
  • Set the hardware address on the MagBead ALP to "0."
  • Device not associated with MagBead position on the deck.
  • Associate the MagBead with the position in the Deck Editor.
Labware and reagents are missing from the Instrument setup screen.
  • The incorrect deck has been chosen.
  • Make sure the correct deck is selected in the Deck Editor.
  • Make sure all ALP positions (e.g., P0, MagBead1) are represented when using a custom deck.

* 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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