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Oligo Purification on Acrylamide Gels

GEL PURIFICATION OF OLIGONUCLEOTIDES(Adapted from the method of Mark Fortini)

  1. Quantitate crude oligo solution via UV spectrophotometry. Assume 1.0 A260 unit is equal to 33 ug/ml. Dry down 100ug of oligo on speedivac overnight.
  2. Resuspend dried-down oligo in 40ul TE. Add 20ul formamide dye.
  3. Prepare a 12% polyacrylamide gel (20:1 acrylamide:bis-acrylamide). 6.3ml 20x TBE 32ml 7M urea 38ml 40% acrylamide/7M urea 50ml dH2O 375 ul ammonium persulphate 75ul TEMED
  4. Cast gel in 25 x 25 cm plates with 0.75mm spacers. Rainex the plate with ears. Use combs with >8mm teeth. It is important to flush the wells very thoroughly prior to pre running and loading oligos onto the gel. A build-up of urea in the well will prevent the oligo running into the gel. Pre-run gel at 400v for 15 minutes. Load samples (100ug per three of four wells) and run gel at 400v until bromophenol blue is two-thirds down the gel.
  5. Lay gel ears side up and prize off top plate. Cover gel with glad wrap and turn plate over. Gently lift off remaining glass plate, leaving gel on the glad wrap.
  6. Place gel onto a TLC plate and visualise bands by UV shadowing. Bands should appear purple on the green background of the TLC plate. Excise band with a razor blade and place into a 10ml tube with 1ml TE. Allow to elute overnight with agitation (Optional: break up gel slice by passing through a stop cock from one syringe to another before eluting over night).
  7. Filter the eluate through a pre-wetted acrodisk. Collect eluate and add 5ml butanol. Vortex for 30 seconds and spin at 3500 rpm for 5 minutes. Remove organic (top) phase and placeaqueous phase (should be ca. 100-200ul) into an ependorf. Adjust volume to 500ul with TE.  Phenol/chloroform and chloroform extract. EtOH precipitate and spin 13000 rpm for one Hour. Wash Pellet In 100ul 70% Etoh.
  8. Resuspend Pellet In 25ul Te And Quantitate.
Disclaimer: The following set of protocols were contributed by various members of our lab (past and present): Christine Andrews, Fiona Christensen, Neil Della, Ross Dickins, Debbie Donald, Andrew Holloway, Gary Hime, Colin House, Yinling Hu, Rachael Parkinson, Nadia Traficante, Hannah Robertson, Ping Fu and Dennis Wang. Special thanks to Vicki Hammond, Frank Kontgen and Maria Murphy, who contributed many of the ES cell protocols. Sections dealing with Photomicroscopy, Polyclonal and Monoclonal Antibody Production were provided by members of Gerry Rubin's Laboratory (Berkeley). Any comments in the methods (technical errors etc.) E-mail:
David Bowtell PMCI October 1998