Materials for electrophoresis
ELECTROPHORESIS OF DNA AND RNA FRAGMENTS REQUIRES HIGH QUALITY REAGENS DEVOID OF ANY DNASE and RNASE ACTIVITY
PCR loading buffers are solutions of high density, which simplify loading of the samples into electrophoretic gels. Loading buffers contain dyes which migrate during electrophoresis in agarose gel together with DNA. Bromophenol blue and xylene cyanol are widely used dyes in loading buffers. Bromophenol blue and xylene cyanol migrate in agarose gel in 0.5x TBE buffer similarly to double stranded DNA of about 300 bps and 4000 bps, respectively. This relative mobility is not affected by agarose gel concentration at a range 0.5 - 1.4%.
Presence of the dyes could, however affect visibility and quantification of DNA fragments in gels stained with ethidium bromide. Therefore, loading buffer containing bromophenol blue alone was also introduced (loading buffer Edge). Size of many PCR products is about 300 bps and therefore other dyes are also used. Yellow load loading buffer includes orange G, which migrates at position of individual nucleotides. Even faster migration exhibits a new dye in Read Load. The same red dye is also present in some PCR Master Mixes or PCR Purple Taq DNA polymerase and therefore this loading buffer is useful alternative in such studies.