25 September 2023 2 5K Report

Recently carried out PCR in order to amplify MMP9 Product from A431 Cells in order to prove its presence in the cancer cell. However, when Electrophoresis was carried out post-PCR here was the result:

*Image attached below*

(Left to Right: 100bp DNA Ladder, Non-Template Control, Wild Type A431, Positive Control, Negative Control, MMP9(1) & MMP9(2))

Bands were formed at ~500bp instead of the expected 106bp. In fact, ZERO product was formed at 106bp. The ideal was for bands to form at ONLY 106bp for each well apart from the NTC, yet there was only one single incorrect band. (-ve Control yielded no result from this PCR likely due to human error) This result is unacceptable as the primers used were specific for MMP9 product and was ordered from a locally renowned Biotech Company, with reference to research papers and was tested again Primer-Blast.

Does anyone have experience with PCR to identify this band?

(Can MMP9 specific primers possibly amplify non-targeted DNA during PCR?)

Is it possibly somehow MMP9 related?

(Does DNA form Pentamers of sorts in excess?)

This PCR-Electrophoresis was conducted several times and this was one of the better results. I've also attached the Temperature Gradient PCR for reference.

Thanks in advance!

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