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Do oligos for PCR require purification beyond standard desalting?

For general PCR assays, oligos do not typically require additional purification.  IDT synthesizes oligos from the 3' to 5' end. During PCR, the oligo primers are extended off their 3' end, so a potential 5' truncation or internal deletion will usually not adversely effect the PCR assay.
For more involved molecular biology assays, however, IDT does recommend additional purification. Many researchers incorrectly assume that synthetic oligonucleotides are 'perfect', that is, 100% of the molecules are identical and the correct sequence. However, oligonucleotide synthesis efficiency is 98-99% for each cycle of nucleotide addition. This means that deletion events will occur at each and every position albeit in a very small percentage of molecules. These undesired deletion and truncation products accumulate as the oligo elongates, so long oligos will be more affected by this problem than short oligos. For a 60nt oligo, 59% of the product made will be deletion and truncation products. It is therefore necessary to purify full length product when using long oligos for mutagenesis, gel-shift assays, cloning, or any demanding applications to avoid complications introduced by the naturally occurring deletion and truncation products.
We offer HPLC and PAGE purification. We recommend HPLC purification for any oligo up to 50 nt. It is effective in removing the n-1mers from shorter oligos and usually results in a slightly higher yield than PAGE. For oligos >50 nt, the decision is based more on whether you need a higher purity or better yield. PAGE will do a better job of removing truncations and deletions from your prep (purity will be usually 90%+), but results in a lower yield. HPLC will give you a better yield, but may only result in 80-85% purity. The turnaround time for purified oligos is 4-5 business days for HPLC purified oligos, and 5-6 days for PAGE purified oligos.

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