Stainsall stain solution

Native PAGE was applied to purify AM and BM (BM-FQ) duplex strands to remove excess strands and avoid undesired system leakage caused by sequence defects. The ssDNA components of AM and BM (BM-FQ) were annealed at concentrations of around 50 μM in 1× TAE/Mg²⁺ buffer (40 mM Tris-acetic acid, 1 mM EDTA, and 12.5 mM magnesium acetate, pH 8.0). Native PAGE gels (12%) in 1× TAE/Mg²⁺ buffer were run at 120 V for 60 min at 4 °C and stained with Stainsall stain solution (Sigma-Aldrich). Only the sharp bands were cut from the gels, chopped into small pieces, and soaked in 1× TAE/Mg²⁺ buffer for 24 h. After extracting most of the DNA from the gel pieces, the solutions were extracted and concentrated with centrifugal filter devices (Millipore, Billerica, MA). Finally, the DNA duplex sequences were quantified by UV spectrometry and kept in buffer for future use. The extinction coefficients for double-stranded complexes were calculated using the following equation:
$$\epsilon =\epsilon \left(\text{top}\hspace{0.17em}\text{strand}\right)+\epsilon \left(\text{bottom}\hspace{0.17em}\text{strand}\right)-3200N_{\text{AT}}-2000N_{\text{GC}}$$
where N_AT and N_GC are the numbers of AT pairs and GC pairs in the double-stranded domain, respectively.^{19 (link),34 (link)}