*Analytical Chemistry - Advancement, Perspectives and Applications*

EtBr appear. This fume will be hazardous when incorporated through the respira-

To avoid such hazardous fumes, a freeze-and-thaw of used agarose gel is very effective for removing toxic EtBr from the gel [17]. By repeating freeze-and-thaw, the EtBr concentration of used agarose gel dramatically reduces to as much as a negligible

Agarose is hydrolyzed in acidic condition. Therefore, repeating the boiling and melting step in acidic condition might degrade the polymer structure of the agarose. The freeze-and-thaw method mentioned above is free from such a degradation.

The most standard buffer for agarose gel electrophoresis is TAE buffer (tris, acetic acid, EDTA). TBE (tris, boric acid, EDTA) is the second major buffer. It is said that TBE has an advantage to fractionate small length DNA; in an old sequence analysis, a combination of acrylamide gel and TBE buffer was a standard condition. When TAE is compared with TBE, the cost of TBE is higher than TAE. This is

For RNA electrophoresis, MOPS buffer (MOPS, sodium acetate and EDTA) is another standard, although this buffer is much expensive. Anyhow, daily agarose

Yet another electrophoresis buffer is SB buffer, which is obtained from sodium borate. The vast majority of SB buffer is the cost, 1/4 of TAE and 1/10 of TBE [18]. In my experience, DNA is well migrated and fractionated in the agarose gel electrophoresis with SB buffer, although small but many air cavities appeared after finishing the electrophoresis. The cavities do not exist when starting the electrophoresis, but they do appear several ten minutes after switching on and/or staining

It is a very simple and effective idea of cost-saving that dilution of the buffer is available or not. If 1/2 dilution is available, the cost also will be 1/2. In my experi-

because of the difference of the price of acetic acid and boric acid.

gel electrophoresis is achieved in a condition of using TAE in standard.

level. The result of electrophoresis by recycled agarose is shown in **Figure 5**.

*Cost-Effective Technical Tips for Agarose Gel Electrophoresis of Deoxyribonucleic Acid*

tory system.

**3. Electrophoresis buffer**

*DOI: http://dx.doi.org/10.5772/intechopen.93439*

the gel after electrophoresis (**Figure 6**).

ence, 0.5 TAE buffer works fine (**Figure 7**).

*SB buffer resulted in small but many air cavities in the gel.*

**3.1 Concentration of buffer**

**Figure 6.**

**175**

#### **Figure 4.**

*Scheme for staining and visualizing of DNA in agarose gel electrophoresis.*

electrophoresis, and (c) soak the gel in the reagent buffer after electrophoresis (**Figure 4**). In (a) and (b), a photograph of the gel can be taken with a gel tray, when the tray is clear. In such a situation, a low gel strength does not disturb electrophoresis and DNA visualization. Based on these reasons, a low gel strength seems not a too much annoying point when simply doing electrophoresis and taking photographs.

#### **2.2 Recycling and reusing of agarose**

It is known that used agarose gel is reusable again and again. Recycling of agarose after electrophoresis is very effective for cost-saving. Several reports are published [13, 14], in which used agarose gels are simply boiled and poured to a gel tray. After cooling to make the recycle gel solid, the recycled gel is enough for applying another electrophoresis. On the other hand, the DNA staining reagent (such as EtBr) still remains in the used agarose gel. EtBr is well known as toxic mutagen [15, 16], so when used and stained gel is boiled, toxic fumes containing

**Figure 5.** *Recycled gel (1% weight per volume) was applied to the electrophoresis.*

*Cost-Effective Technical Tips for Agarose Gel Electrophoresis of Deoxyribonucleic Acid DOI: http://dx.doi.org/10.5772/intechopen.93439*

EtBr appear. This fume will be hazardous when incorporated through the respiratory system.

To avoid such hazardous fumes, a freeze-and-thaw of used agarose gel is very effective for removing toxic EtBr from the gel [17]. By repeating freeze-and-thaw, the EtBr concentration of used agarose gel dramatically reduces to as much as a negligible level. The result of electrophoresis by recycled agarose is shown in **Figure 5**.

Agarose is hydrolyzed in acidic condition. Therefore, repeating the boiling and melting step in acidic condition might degrade the polymer structure of the agarose. The freeze-and-thaw method mentioned above is free from such a degradation.
