Purification of DNA fragments with the QIAEX II system is based on solubilization of agarose and selective adsorption of nucleic acids onto QIAEX II silica-gel particles in the presence of chaotropic salt. QIAEX II separates DNA from salts, agarose, polyacrylamide, dyes, proteins and nucleotides without phenol extraction or ethanol precipitation. QIAEX II is effective for any type of agarose in either TAE or TBE buffers.
QIAEX II particles provide a slurry for gel extraction and ensure efficient recovery without shearing, even for large DNA fragments. Optimized buffers permit DNA recovery without sodium iodide, which is difficult to remove from DNA samples, and may affect subsequent reactions.
The solubilization and binding buffer used with the QIAEX II system contains a unique pH indicator. A simple color change indicates whether the pH of the binding mixture is optimal for efficient adsorption of DNA to QIAEX II silica particles (see figure "pH indicator dye"). The colored dye also allows easy visualization of any unsolubilized agarose in the binding mixture, ensuring complete solubilization for maximum yield.
pH indicator dye in the solubilization and binding buffer allows easy visual determination of optimal pH for DNA adsorption (pH ≤7.5). An incorrect binding-mixture pH can occur if the agarose gel electrophoresis buffer was frequently used or incorrectly prepared. In this case the pH can be easily adjusted by addition of 10 µl 3 M sodium acetate, pH 5.0.