The initial purchase cost of the new generation of DNA stains can seem a little high. However, it is important to realize that the costs of the other reagents involved in fractionating DNA by agarose gel electrophoresis are actually more significant.
Table 1 breaks down the dollar costs involved in running a typical agarose gel and using a variety of methods to detect the DNA. The various methods compared include:
- the traditional technique of staining the gel with EtBr after electrophoresis
- staining the DNA samples with SYBR Green prior to electrophoresis (pre-staining)
- staining the gel with SYBR Green dye after electrophoresis (post-staining)
- post-staining the gel with SYBR Gold dye.
on the staining method - EtBr, 5 uL; Pre-stain SYBR Green, 2.5 uL; all others, 1 uL.
** Stain solution is used twice.
The analysis in Table 1 does not take into account the additional cost of preparing DNA samples. Because the new dyes are so much more sensitive than EtBr, reaction volumes can be significantly reduced and material costs reduced accordingly. For example, consider the cost of a set of PCR reactions that are to be subsequently analyzed by gel electrophoresis. The cost of Taq DNA polymerase and dNTPs is about $1.13 for a typical 50 uL reaction. Reducing the reaction volume to 10 uL, results in savings of over $10 for a set of 12 reactions.
An additional cost factor not addressed in Table 1 is the time involved in preparing, running and staining a gel. By using either GelStar, SYBR Green or SYBR Safe as a 'pre-stain' or 'in-agarose' it is possible to obtain results in 40 min. rather than the 2+ hours required using post-staining.
