Unmodified Single-stranded DNA Oligonucleotide
The purified oligonucleotides’ stability depends on the nature of the storage medium and temperature. When properly stored at -20°C, frozen oligonucleotides can remain stable for up to 2 years or longer, as a dry powder and in both TE buffer (10 mM Tris, pH 7.5-8.0, 1 mM EDTA) and nuclease-free water. Most oligonucleotides are stable for more than 60 weeks when stored dry at 4 °C or in DNase and RNase-free medium, including TE buffer and water. Unmodified single-stranded DNA oligonucleotides, either as a lyophilized dry powder or in TE buffer, can be stably stored for 3-6 months at room temperature and 1-2 months at higher temperature conditions (37°C). Any moisture present in dry oligonucleotides, even small traces, can cause damage to the oligonucleotides.
Unmodified Single-stranded RNA Oligonucleotide
On account of its chemical structure, RNA is less stable than DNA. RNA is easily autocatalyzed and degraded by RNases, which exist everywhere because they are present in sources such as shed skin cells and ubiquitous microorganisms. For short-term storage, single-stranded RNA oligonucleotides should be stored in TE buffer at -80°C. For long-term storage, storage at -80 °C in the form of ethanol sediment is preferable. Taking precautions to avoid exposure to RNases can extend shelf life. Areas for RNA storage should be cleaned regularly with RNases-removing agents, and the related equipment used should be treated by autoclaving.
Double-stranded Oligonucleotide
The double-stranded structure is more stable and more resistant to degradation. siRNA duplexes were stable for at least 3 years as the dry powder at -20°C. DNA duplexes can be stably preserved for several years in dry form at -20°C.
Modified Oligonucleotides
Most modified oligonucleotides will have similar stability to unmodified oligonucleotides. However, heavily modified oligonucleotides will be significantly more stable, especially to nuclease-dependent degradation. DNA and RNA should be stored according to the above recommendations. Notably, fluorescently labeled oligonucleotides should be stored in amber-colored test tubes or clear tubes wrapped in aluminum foil away from light to prevent exposure. Coenzyme A modified oligonucleotides should be dissolved directly prior to use, as they exhibit some instability in aqueous solutions. To prevent degradation of the modifications, aqueous solutions should be stored at 2-8°C and used within one day.
For modified oligonucleotides, long-term storage in the lyophilized state is recommended at -20°C. When storing these oligonucleotides for long periods of time, we do recommend keeping them in the dark, regardless of the storage medium, temperature and time; to prevent any negative effects on the stability of the fluorophore.
Aliquot Oligos Samples
While repeated freeze-thawing is thought to degrade genomic DNA, possibly due to shearing by ice crystal formation, oligonucleotides are likely to be less negatively affected by these processes. However, it is still best practice to store oligonucleotides in evenly divided disposable aliquots at -20°C. This prevents waste from accidents such as cross-contamination or spillage. For example, if a tube of oligonucleotide spills on the floor, it must be reordered or prepared. However, if only one aliquot is spilled, only one more needs to be thawed.
Aliquots can be 250 μL, 100 μL, or smaller, depending on how many tubes you can dispense. For UV melting studies, large aliquots (250 μL) are appropriate, while smaller aliquots (100 μL or less) are better for PCR applications. These aliquots should be used in the same tubes as those providing the oligomers (some tubes are sterile and can lead to oligomer degradation). Each tube should be carefully labeled (e.g., thawed or use by date).
Shipping of Oligonucleotides
Oligonucleotides are usually transported as lyophilized dry powders. Transport over a short period of time does not compromise the stability of dry oligonucleotides, which remain stable for up to 25 weeks when stored at 37°C (98°F). When stored in water and storage media, most oligonucleotides will remain functional for several weeks at these higher temperatures.
