Fluorescent DNA Stain for Gels

Charlotte K. Omoto
School of Biological Sciences
Washington State University
omoto@wsu.edu

There are safety concerns with the standard method for visualizing DNA in agarose gels. Ethidium bromide is a known carcinogen, and one must have eye protection when using a UV transilluminator. An alternative using fluorescent stain and viewing with Dark Reader makes DNA electrophoresisis safer for classroom use.

Procedure: The fluorescent stain that I use is Sybr Green I. It comes as a 10,000X concentrated stock. I dilute it 1:100 with good quality DMSO; the important point of good quality is that it does not have trace aqueous contamination. The fluorescent stain is unstable in aqueous solution. Then I use 1 µl of the diluted stain for each 10 µl of sample. I do this on a piece of parafilm, and then load it onto the gel. After the gel is run, I place the gel on Dark Reader. This is a visible light source using two colored filters. That's it!

Sources: Flourescent stain and Dark Reader can be obtained from Clare Chemical. The stain is also available from variety of other companies including Molecular Probes. Other fluorescent stains also work with Dark Reader.

Additional advantages:
• sensitivity -- at least 10X more sensitive than ethidium bromide
• cost -- Dark Reader is significantly less expensive than a UV transilluminator
• no DNA damage -- because UV is not used, there is no danger of UV damage of the DNA. This is especially nice for further use or manipulation of DNA.

The only drawback to the above procedure is when one runs the gel for longer than 2-3 hours. The Sybr Green stain diffuses with longer electrophoresis run. When running a gel for longer, you can stain with Sybr Gold after running the gel and still use Dark Reader for visualization.

Sample gel:

This 1% agarose gel is of
minipreps with lambda
HindIII fragments; on the
left side is a 1kb ladder.