Cartridge Purification

Cartridge purification of oligonucleotides is based on the differential hydrophobicity of tritylated (full length) vs. non-tritylated (failure syntheses) oligonucleotides (a reverse phase based approach). This procedure can be carried out at a cost of $5/oligonucleotide on our 50nmole scale and $25/oligo for 200 nmole or 1 micromole scales. The protocol we use is nearly as effective as HPLC purification at removing failure syntheses (read the HPLC Purification section for reference).

It has been our experience here that cartridge purification provides highly enriched full length product (>90%) when performed on oligos of 50 or fewer bases in length. If cartridge purification is performed on longer primers, the eluted product is still predominantly composed of full length product, but a higher percentage of failure sequences end up in the eluted final product since the hydrophobicity differences between tritylated and untritylated oligos decreases as the oligo length increases. User feedback on the quality of the longer purified oligos has been very positive, but we wanted to bring the potential limitations to your attention to help in assessing your needs. Additionally, we have had no success in purifying any oligo larger than 90 bases in length.

Also keep in mind that final yield will be decreased by purification. Oligonucleotides >60 nucleotides in length inevitably will have shorter products present, even after cartridge purifcation, as noted above. If it is absoloutely essential that you have pure full-length product of a longer oligonucleotide, you will have to purify it yourself by preparative PAGE or request HPLC purification. Most of our customers who are using very long oligos in, for example, cloning projects where they ultimately will be constructing a long stretch of cloned double stranded DNA, find they don't need to purify but can just sequence several clones containing the synthesized sequence in order to find their full length construct.