I did gel electrophoresis for my PCR product. The size for the amplification was inconsistent but still in the targeted range. Then, I proceeded with purification but the end result obtained was increased in size (100+ bp) than the targeted and previous result. why?
Could be microhomologies are causing incompletely extended product strands to self prime resulting in catenation.
It's very unlikely that a purification would cause any change in PCR product size. My bet is that your previous gel was a bit "messy" and after the cleanup you got a nice single band.
Also, double-check that you used the same DNA ladder in both gels. There are many that are similar.
If your purification method involved a high salt step and salt was carried through with the purified dna then it would run slowly (larger)
What are the sizes? Is it from 500 bp to 600 bp, or 5000 bp to 5100 bp?
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