Oligonucleotide formulations for use as size/mass markers
Our oligo length standards are available in two formulations—10/60 Ladder and 20/100 Ladder (Figure 1). These marker oligos have balanced base content, are purified, and are provided in equal mass amounts (10 µg of each oligo per tube) to normalize band intensity. Each tube contains sufficient marker for 25–100 loadings; however, recommended loading mass varies with gel comb dimensions and stain used. The oligo length standards are compatible with fluorescent stains such as SybrGold™ Stain (Molecular Probes) and GelStar® Stain (Cambrex). Non-fluorescent stains, such as Stains-All™ (Millipore Sigma), can also be used. Ethidium bromide staining works poorly with single-stranded nucleic acids, so is not recommended.
Figure 1. IDT oligo length standards. The 10/60 Ladder (left) contains marker oligos of 10, 15, 20, 25, 30, 40, 50, and 60 bases. The 20/100 Ladder (right) contains marker oligos of 20, 30, 40, 50, 60, 70, 80, 90, and 100 bases. Note: 10 nt oligos bind dyes poorly and may appear more faint than other bands.
To obtain a concentration of 0.1 µg/µL (for each oligo), resuspend your lyophilized oligo mixture in 100 µL of TE buffer (10 mM Tris pH 7.5, 0.1 mM EDTA).
Mix the desired amount of marker solution (1–4 µL) with an equal volume of a formamide- or urea-based loading buffer. Heat samples at 95ºC for 3 minutes, cool on ice, and load. For 1 mm x 4–6 mm combs, we recommend 0.1–0.2 µg/lane if using SybrGold Stain. If using GelStar Stain, we recommend 0.2–0.4 µg/lane. For non‑fluorescent stains such as Stains‑All™ (Sigma-Aldrich), use 0.3–0.4 µg/lane.