Agarose Gel is a porous matrix that acts as a sieve through which negatively charged linear DNA fragments migrate under an electric field and are separated based on their size. The agarose concentration in agarose gel determines the porosity and sieving properties of gel which in turn has an effect on the migration rate and separation of DNA fragments. By altering the agarose concentration in agarose gel we can optimize the separation of different size-range DNA fragments. Generally, higher concentration of agarose gel is used for efficient separation of low molecular weight DNA fragments and lower concentration for high molecular weight DNA. The following table suggests suitable agarose gel percentage for efficient separation of different size-range of DNA fragments.
| DNA fragment size range (base pair) | Percentage agarose gel |
| 0.10 – 2.0 kb | 2.0 % |
| 0.2 – 5.0 kb | 1.5 % |
| 0.4 – 10.0 kb | 1.0 % |
| 0.5 – 12.0 kb | 0.8 % |
| 1.0 – 30.0 kb | 0.5 % |
| DNA fragments ranging from 20 – 500 base pairs can be best resolved by polyacrylamide gel electrophoresis. Use pulse field gel electrophoresis to resolve the DNA fragments larger than 30 kb. | |
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