Yes, oligo degradation due to depurination can occur when oligos are stored in low pH conditions. For long term oligo storage, temperature is the most important factor to consider. For long term storage, whether oligos are dried down, or resuspended in water (non-DEPC treated) or TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA; such as IDTE), it’s optimal to store them frozen at –20°C.
For room temperature or 4°C storage, oligos that are resuspended in TE buffer are more stable than dry oligos. Oligos that are stored in water are the least stable. At 4°C oligos are stable for at least 60 weeks.
Please see the Technical Report, Oligonucleotide Stability Study, for data on oligonucleotide storage and a more thorough explanation.