Recommended Storage Condition
Normally, oligos should be stable at -20°C and can be stored at that temperature for more than a year. Although stable in solution, oligos will be degrade if the storage solution is contaminated with nucleases. Therefore, we recommend that oligos be stored in the dried form. If you want to store oligos in solution, it is best to aliquot the oligo into several tubes and store them separately. Oligos can also be subject to degradation due to the 'Freezing and Thawing Effect' when the oligo solutions are frozen and thawed repeatedly.
Calculation of Tm
Tm (melting temperature) refers to the temperature where 50% of oligonucleotides exist in duplex form and the rest in single-strand form. The estimation method based on the GC content for long sequences is :
Calculation of MW
The molecular weight of an oligo can be calculated with the following equation:
Measurement of OD and concentration (µM, ng/µL)
The quantity of oligos is often described in O.D. units which actually express light absorbance. One O.D. corresponds to the amount of oligo in a 1mL volume that results in an optical density of 1 in a 1cm path-length cuvette. This corresponds to approximately 33 µg of oligo, although it varies for each particular oligo depending on its sequence. The concentration of an oligo of known sequence can be calculated since it is known that the extinction coefficient (in a 1cm path-length cuvette) for each of the bases at 260 nm is
Coupling efficiency is the major factor affecting the length of DNA that can be synthesized. Base composition and synthesis scales will also be contributing factors. Table 1 shows that at 99% coupling efficiency, a crude solution of synthesized 95-mers would contain 38% full-length product and 62% (nx) failure sequences. This is before other chemical effects have been taken into account such as depurination. Depurination mainly affects the base A. The frequency of depurination is small but will increase significantly with primer length. For these reasons, we specify a maximum length of 150 bases, which we believe is the maximum length that can be synthesized routinely and economically.
Purification of the oligo
For the applications such as cloning, site directed mutagenesis or quantitative gene detection, oligos of higher purity are preferred to get the satisfactory results. Since desalted oligos might not be sufficient in such cases, HPLC purification has been commonly used for that purpose.
Choice of scale
Synthesis scales refer to the amount of starting material present, not the amount of final product produced. This is the same for all manufacturers of synthetic DNA. When a 50 nmole scale synthesis is specified, approximately 50 nmoles of the first base is added to the DNA synthesizer. For an average 25-mer, at least 25% of this starting material will result in failure sequences, hence it is not possible to produce 50 nmoles of full-length product from a 50 nmole scale synthesis.
Choice of purity level
For some applications, such as PCR or sequencing, standard desalting is perfectly fine because the truncations and deletions will not affect your results appreciably.