In the case of DGGE staining with FluoroStain™ DNA Fluorescent Staining Dye (DS1000), we can give some suggestions as stated below:
A. Similar to ethidium bromide, DS1000 could be used for staining DNA in polyacrylamide gels.
B. However, it is noted that the DS1000 is designed to stain dsDNA and thus is not appropriate for staining in DGGE due to denaturing of dsDNA.
C. For detection of ssDNA or RNA in DGGE, we strongly recommend the use of FluoroVue™ Nucleic Acid Gel Stain (NS1000) which can be used to stain both double-strands and single-strand nucleic acids.
D. Furthermore, it’s suggested staining the gel after electrophoresis (post-staining) instead of pre-staining or in-gel staining, since the fluorescent dye might be affected during acrylamide polymerization.
E. The optimal excitation wavelength of DS1000 or NS1000 is around 480~490 nm (blue light), and therefore the illuminator with blue light is preferred. Of course, UV could be used also, but the signals detected might be weaker.