The real cost of a DNA gel

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.

* Assumes 2 lanes containing DNA standards. The amount of standard required depends
on the staining method - EtBr, 5 uL; Pre-stain SYBR Green, 2.5 uL; all others, 1 uL.
** Stain solution is used twice.
It may come as a surprise to learn that the use of EtBr is NOT the cheapest method! The reason for this can be seen in the break-down into specific item costs: because the new generation of dyes are typically 5 - 10 times more sensitive than EtBr, the amount of DNA molecular weight markers required is correspondingly lower, resulting in savings of up 76 cents per gel. This more than off-sets the extra cost of the dye.

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.
Clare Chemical Research

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