Here, I have described different types of commercially available gel extraction kits for gel excision. These are listed below in a table summarizing the most important comparative information about different kits. These commercially available gel extraction kits can easily be utilized for DNA gel excision.
The basic principle is that the DNA fragment selectively binds to the spin column with a built-in silica membrane. Then centrifugal force allows the passage of solutions and other contaminants while retaining the DNA into the spin column. The spin column-bound DNA can be eluted with an elution buffer. Each gel extraction kits have its own protocol and components but their basic principles are the same.
Dissolve the piece of gel containing DNA in an appropriate binding buffer in a ratio of 1:3 or 1:4. Incubate the gel-binding buffer mixture in a water bath of 50- 60 °C for 10 minutes (Note-1). Load the mixture into the spin column with a built-in silica membrane followed by centrifugation. Please follow the manual provided in the kit box. During the centrifugation, DNA binds to the silica membrane, and the rest of the components pass through the membrane.
Wash the spin column-bound DNA with ethanol-containing wash buffer for up to two times. Washing further removes contaminants such as nucleotides, salts, and other impurities. After that, centrifuge the spin column with no wash buffer to ensure that the spin column is free of ethanol.
Finally, elute the DNA bound to the spin column in a clean Eppendorf tube using a pre-warmed elution buffer (Note-2). Thus eluted DNA sample is pure and ready to use in downstream applications or for sequencing.
Note-1: The binding buffer contains chaotropic agents and a color indicator to make sure that the mixture has an optimal pH for DNA binding. Chaotropic agents such as guanidinium chloride break the H-bonding between the agarose and water molecules. The yellow color of the binding buffer indicates the optimal pH for DNA binding.
If the color of the gel and binding buffer mixture is orange or violet, then add 10 µl of 3 M sodium acetate of pH 5.2 solution. This is to make sure that the mixture has an optimal pH for DNA binding as indicated by the yellow color.
Note-2: If the DNA fragment is higher than 10 kb, you need to pre-warm the elution buffer to 65 °C before eluting the column-bound DNA.
Use of the commercially available gel extraction kits
I have mentioned here some of the available gel extraction kits such as the QIAquick Gel Extraction Kit, GeneJET Gel Extraction Kit, and more. QIAquick Gel Extraction Kit comes with spin columns, buffers, and collection tubes. It gives up to 95 % recovery of ready-to-use DNA.
The silica-based spin column provided with QIAquick Gel Extraction Kit can accommodate up to 400 mg of gel slices and can purify 70 bp to 10 kb of DNA fragments with an elution volume of 30-50 µl. As with other kits, it is also an integrated pH indicator that allows us to determine the optimal pH for the DNA binding to the spin column.
GeneJET Gen Extraction Kit is another commercially available gel extraction kit developed by Thermo Scientific. It is designed for the purification of DNA fragments ranging from 25 bp to 20 kb with a recovery rate of up to 95%. The product comes with a binding buffer, wash buffer, elution buffer, and spin-column preassembled with wash tubes. The gel extraction using GeneJET Gel Extraction Kit takes 15 minutes and gives about ready-to-use DNA fragments for downstream applications. The rest of the kits are described in the table below with their comparative complete details.
A commercially available gel excision kit with detailed information is presented in this table.
| Name of the Kits | Range of DNA size | Binding capacity | Elution volume | % Recovery |
|---|---|---|---|---|
| Monarch® | 50 bp to 25 kb | Up to 5 µg | ≥ 6 µl | 50-90 % |
| GeneEluteTM | 50 bp to 10 kb | Up to 10 µg | ≤ 50 µl | Up to 80 % |
| E.Z.N.A.® | 70 bp to 20 kb | Up to 25 µg | 30-50 µl | Up to 85 % |
| ZymocleanTM | 50 bp to 23 kb | Up to 5 µg | ≥ 6 µl | 50-90 % |
| PureLink® | 40 bp to 10 kb | Up to 15 µg | ≤ 50 µl | Up to 95 % |
| GeneJET | 25 bp to 20 kb | Up to 25 µg | ≤ 50 µl | Up to 95 % |
| QIAquick | 70 bp to 10 kb | Up to 10 µg | 30-50 µl | Up to 95 % |
