When performing bacterial strain typing we got a problem for DNA agarose gel visualization. After performing bacterial DNA extraction, the extracts were run in an electrophoresis equipment using 1% agarose gels in TBE buffer with ethidium bromide from Sigma-Aldrich as fluorescent mark. We loaded a gel well with 4µL of a mix of 6X DNA loading dye Thermo Scientific (2 µL) with the DNA sample (2 µL). In another well we used 3.5 µL of a mix of 6X DNA loading dye (2 µL ) with DNA ladder GeneRuler 1 kb from Thermo scientific (1.5 µL). The electrophoresis was carried out at 100 V until the dye reached 2/3 of the gel, during approximately 40 min.
After that, we put the gels in the chamber of a BIOTOP Fluor Shot - gel documentation system, purchased from a Chinese biotech brand Shangai Biotech Co. The UV transilluminance lamp mode was used (312 nm, according to the manufacturer). We could not see any band in the images displayed by the equipment software. We performed the same procedure different times, and also tried incorporating EtBr to the buffer bath instead, but again we failed to visualize any bands in the gels. We also tried to run some samples of DNA enzyme digests using 2% agarose gels, but the results were the same. Initially we thought that perhaps the lamp of the equipment was not working, but we opened the door using the “gel cut” mode and could see that the transilluminator lamp was on, with the bottom screen being evenly illuminated with violet light.
Ragarding the gel documentation equipment: we purchased the equipment about 2 years ago. Unfortunately we could not test it until recently since we were just acquiring the complete set of apparatus for molecular biology assays. I tried to contact the Chinese company customer service but they ignored my query. Please advice as to what could be causing the problems for visualizing the DNA agarose gels.