If you analyze your competitive PCR products on non-denaturing gels you
have the possiblity of seeing heteroduplexes that have formed between your
target and your competitor. Since this heteroduplex formation could be
sample-dependent you must either (1) maximize heteroduplex formation and
correct for this effect when analyzing your data (heat denature and
re-anneal your PCR products prior to running them on your agarose gel) or
(2) analyze your PCR products with denaturing PAGE (I run my reactions on 8M
urea, 1X TBE, 5% polyacrylamide gels)
A good reference for quantitative competitive PCR: Becker-Andre M.
Absolute leves of mRNA by polymerase chain reaction-aided transcript
titration assay. Methods Enzymol 1993; 218:420-445.
Laboratories for Reproductive Biology
University of North Carolina at Chapel Hill