Oligonucleotides should be subjected to minimum number of freeze-thaw cycles. Therefore, we recommend that you prepare aliquots and store microvials each having sufficient material for a day’s set of experiments and freeze at -20 °C or -80 °C.

“The repetitive freezing/thawing of an oligonucleotide strand can lead to the undesirable decomposition of a sample through the loss of a terminal phosphate group, a base or the entire oligonucleotide unit. This observation relates to the fact that during the freezing/thawing process the oligonucleotide and buffer components isolate from the solvent system. As a result this isolation increases the percentage of similar intermolecular attractions and bond breakages.”

Analysis of the degradation of oligonucleotide strands during the freezing/thawing processes using MALDI-MS. (Analytical Chemistry, Volume 72, Number 20, pages 5092 - 5096, 2000)