Core/facility: Keck Oligo Synthesis Resource Offering: Protocols

Protocol: Manual removal of 5’-trityl (DMT)

Manual removal of 5’-trityl (DMT) from trityl-ON DNA oligos following deprotection


Oligonucleotides can be prepared on the DNA synthesizer either trityl-ON or trityl-OFF (trityl = DMT) by making the selection at the beginning of the synthesis. Virtually all applications require DNA to be trityl-OFF, or detritylated, so that they have a free 5' hydroxyl.

However, the trityl-ON option is selected when purifying using an OPC cartridge or certain types of HPLC. After purification, trityl-ON oligonucleotides must be detritylated manually. The 5' dimethoxytrityl (DMT) is readily cleaved by limited exposure to mild acidic conditions to minimize depurination.


Materials

 
  • 80% acetic acid


Procedure

 
  1. Dissolve the dried, deprotected oligo in 1 ml 80% acetic acid. Mix by vortexing.
  2. Incubate for 1 hour at room temperature.
  3. Dry the detritylated oligo using vacuum centrifugation.
  4. A reverse-phase desalting procedure may then be used to remove the free DMT from the oligo solution.


Reference

 

Evaluating and Isolating Synthetic Oligonucleotides - The Complete Guide. Applied BioSystems, Inc., 1992, p A-7.