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Gel Electrophoresis and PCR

Today we performed a gel electrophoresis (at 1% agarose) of our PCR products from the last lab session. The electrophoresis revealed that we obtained some positive results from our experimental temperatures and also from our positive controls, but the experimental samples also exhibited a large concentration of fragments smaller than our target gene. The experimental sample ran at 52.1 C (our highest temperature) yielded the highest concentration of DNA (judged by brightness of bands). Using this information, we decided to proceed to another PCR using higher temperatures, with 52 C as our control sample. We obtained a false positive from our negative plasmid control sample in our PCR so we opted to not use this as a control in following PCRs. For a control, we opted to continue to use the D5/TPOX control obtained from a faculty member (Dr. T. Spradling). This subsequent PCR was ran at 52, 54.1, 55.6, and 58 C.