Ethanol Precipitation of DNA Cycle Sequencing Reactions
"an old procedure revisited"
version dated 1-24-01

This clearly is an "old procedure revisited" but is extremely efficient because 1) the amount of resulting nested fragment set is at least 5 to 10 times more than obtained by Sephadex G-50 filtration and 2) the signal strength on the ABI 3700 is increased approximately 5 to 10 fold.**
  1. Take the 384 plate from the thermocycler and add 16ul ddH2O (depending on reaction volume) to each well using the Hydra.
  2. Centrifuge to 1000 rpm to force water to the bottom of the well. Briefly vortex the plate with a tight hold to mix sample with the water. Centrifuge again.
  3. Transfer the sample/water mix to a 96 well reaction plate using the Hydra. Add 60ul EtOH/NaOAc (made according to standard protocol) to the 96 well reaction plate using a 12 channel pipet.
  4. Place the 96 well plate in a thermocycle plate base and centrifuge immediately at 3200 rpm, 4degC, for 30 to 40 minutes. Note that this is a room temperature ethanol pptn step with centrifugation at 4degC. Identical results have been obtained with 1:12 diluted big dye reactions followed by precipitation at -20degC. In either case, no 'big-dye blob' at ~140 nucleotides was observed, because of the greatly reduced amounts of big dye in the reaction mixes.
  5. Decant the EtOH/NaOAc. This can be done a couple of ways. One way is turning the plate upside down on a paper towel and patting dry. However, because we all have a tendency to do this with varing degrees of force, a better method is to place upside down on a paper towel in a Beckman CS-6R table top microtiter plate centrifuge and begin to centrifuge. immediately turn the centrifuge off. Once stopped, remove the microtiter plates and place upright on the lab bench. The important part is to get rid of a majority of the EtOH/NaOAc and not lose any sample.
  6. Rince by adding 70ul of 70% EtOH using a 12 channel pipet and centrifuge at 3200 rpm, 4degC, for 10-15 minutes.
  7. Decant the EtOH by placing the plate upside down on a paper towel and centrifuge up to 300 rpm as above and dry in vacuum for 10-15 minutes. The 70% ethanol wash can be repeated prior to drying, but only is necessary if dye blobs are seen during the sequencing run.
  8. Dry the pelleted reaction products in a vacuum for 10-15 minutes.
  9. Dissolve the dryed reaction products in 20 ul of water and load onto the ABI 3700 as recommended. Sit back and enjoy 5 to 10 times higher signal strength.


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Bruce Roe, broe@ou.edu