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We recommend the Edge BioSystems’ MagWell™ Magnetic Separator 96, Catalog #57624. The unique configuration of the magnet (milled cavities aligned on either side of an imbedded bar magnet) places the tip of the wells below the top of the bar magnets on the plate. This configuration maximizes the magnetic field strength experienced by each well while allowing the magnetic particles to be pulled both to the side and away from the bottom of the plate. In so doing, it permits effective washing of the particles in both magnetic and manual liquid handling protocols. It also permits the user to resuspend in a minimum volume of fluid e.g. 10 μl. If using an alternative magnet, the protocol will need to be optimized by the user.
No. However, we recommend that users of this sample purification system follow the instrument manufacturer’s recommendation for the appropriate solvent to be used in sample injection. If the sample must be in formamide, the sample can be eluted in water then dried down and resuspended in formamide.
Yes. Over dried resin will be attached to the plate well wall in an obvious manner and will be difficult to work with during resuspension. Over drying of the resin may result in reduced signal strength and an increase in the overall failure rate. To avoid over drying, aspirate all ethanol, and reduce drying time at room temperature to 3 minutes, or heat at 98°C for 30 seconds. Resuspend immediately. If samples appear over dried at the elution step, add the recommended volume of deionized water, and incubate at room temperature for one minute. Pipet mix to resuspend.
Blobs or unincorporated dye terminator peaks are usually a result of incomplete removal of ethanol that may contain unincorporated dye terminators. If residual ethanol is present following the first aspiration, a second aspiration is recommended. Offset the pipet to 150 μl, and aspirate as slowly as possible to remove all residual ethanol. If this step alone does not solve the problem, then try adding a third wash step to the process.
The optimum concentration of ethanol is 80%. Concentrations as low as 60% and as high as 90% have been tested. These other concentrations are reasonably effective at washing the resin. Lower concentrations of ethanol tend to reduce signal strength and read length especially for samples containing small amounts of DNA. Increased ethanol concentrations are less effective at washing away salts and unincorporated dye terminators leading to an increased frequency of dye blob contamination, noise, and reduced signal strength.