I am planning to run some of the PCR products on a gel to identify the products of interest, perform a gel extraction, My products of interest will be approximately around 2300bp in size. In order to get a band with a good resolution I have decided to use TAE and 1% of agarose. I'd also like to know the optimum voltage and time to separate my products (2300 bp) in either 0,8 % or 1% agarose gel. Please assist with the numbers.
How to determine the optimum voltage and time for a better separation in gel electrophoresis?
There is no exact time in DNA separation using agarose gel electroporesis since we should observe the loading dye we mixed with PCR product to reach the agarose gel edge. You can use 5V/cm of gel long. If your gel is 12 cm long then it should be 60 V. Lower concentration of agarose gel is prefer for separating higher kb of PCR product. Optimal condition depends on your PCR product (single or multiple band) to visualize, staining skill and instrument.
1 to 1.5% agarose 70V should be suffice for most electrophoresis application. just monitor your loading dye migration. check your loading dye info. It will tell you what color correspond to what bp size so you can guess the location of your product in the gel.
To decrease the run time you could increase the voltage up to 10V/cm electrode distance.
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