Hi,

I am currently working with PCR of bacterial communities and would like to be able to differentiate PCR-products with small differences in base pair length. However, when I am running the products on electrophoresis, I get very varied quality on the gels.

I am using 1,5 % agarose gel, 1µL ladder, and 1µL loading dye combined with 1,5-5 µL sample (have tried different volumes depending on the DNA concentration in the sample), 120V run for 90 minutes. As you can see on the picture, the bands are wavy and the ladders on each side are unequal (even though it is the same loading volume). What can be the reason for this?

I have rinsed the combs, changed buffer, made new gels, mixed the GelRed into the agarose very well, tried with different sizes on the combs, and run on different voltages but none of these adjustments have resulted in improved results. What else can I try to make my gels look better and to make it easier to read exact band size? I am very thankful for all tips!