Lumiprobe dsGreen® is a DNA binding benzothiazole dye presented in the category of PCR and qPCR products. In terms of structure it is an equivalent of SYBR® Green dye and it binds DNA much stronger than the EtBr (the constant of dissociation is 280 times smaller - 3.1 nM vs 870 nM for Ethidium Bromide). As it can be expected this characteristic prevents the effective use of this dye (and also dyes with similar structures like SYBR Green) to be directly applied to a gel or electrophoresis buffer. The blurred bands are obtained after electrophoresis in case of large amounts of DNA per well (greater than 10 ng) and a significant amount of dsGreen in the gel (at least 0.5x). In case of the decreasing the dye amount in the gel (0.05x), this effect is decreased, but at the same time we obtain the reduced analysis sensitivity.

The gel staining after the electrophoresis (gel soaking) seems to be the best method in terms of separation quality of the DNA fragments and the analysis sensitivity. The appearance and shape of the bands does not change when incubated in the buffer with the dye for several hours. While for the staining it is enough 10-40 minutes, depending on the gel size.

It is also possible to add the dye to the sample buffer before applying (sample prestaining) into the well (1 μl of a 100x dye per 10 μl of a sample). However such approach reduces the quality of the DNA fragments separation.

Electrophoresis gel staining with dsGreen

SYBR® is a registered trademark of Molecular Probes.