I am observing a smear for qPCR amplified cDNA from miRNA. What is the most likely cause? Is it the voltage I'm using for the run, or is it something to do with the gel itself?
Smearing of amplified dna is often caused by over amplification when the amplimer is annealing with other amplimer molecules and amplifying longer pcr products. This is very often caused by pcr product contamination. Are your no template controls showing zero product as they should do?
Not letting the gel solidify and cool completely can have this effect as can running the gel at too high a voltage when the gel gets too hot and the ladder and samples run badly. If the buffer is hot to touch at the end of the gel run then this may be the case