Post Processing of DNA microarray slides made with PCR products and long oligos (70mers)

This protocol is for microarrays containing two types of targets on the same slide: PCR products and long oligos (70-mers). It combines aspects of the protocols for each type of target. Slides are UV crosslinked, and the shampoo and final rinse are both done at 50° C.


Set up three baths for slides:

  1. 400 ml Shampoo Soln, 50 °C
  2. 400 ml H2O
  3. 400 ml 95% Ethanol
Preheat Shampoo solution to 50 °C:     Shampoo Soln 400 ml
60 ml 20x SSC
4 ml 20% SDS
336 ml distilled H2O
Succinic Anhydride Blocking

Materials:     335 ml 1-methyl-2-pyrrolidinone
5.5 g Succinic Anhydride
15 ml 1M Na Borate pH 8 (premeasure into 15 ml conical)
Rotating platform shaker
Empty slide dish
400 ml 95% EtOH bath
Room Temperature H2O bath in beaker large enough to rotate slide rack

Notes: Single distilled water is fine for the H2O rinse steps. For the second rinse coming from pyrrolidinone to water, a 4 liter beaker works well for rotating the slide rack back and forth.
Chris Seidel