I used the Intact Genomics FastAmp® Plant Direct PCR kit and when seeding the gel with the PCR product there was a lot of DTT smell. After running the gel, partially degraded dna was observed, even in the molecular weight marker. Could it be possible that DTT diffuses into the gel and degrades the DNA?
DTT has a beneficial effect stabilising enzymes and can break rna secondary structure so is possibly good for end point pcr and helps rtpcr but can interract with fluorophores to spoil quantitative pcr but the amounts in your kit will be very small and possibly too low to smell. It may be that some H2S producing organism is growing in your electrophoresis buffer and it is this that infiltrates yor gel or produces nucleases that permeate the gel and degrade you dna and this may happen on a scale that allows you to smell the H2S
DDT is commonly used during DNA extraction and does not affect DNA stability. However, it may affect the function of enzymes such as DNA polymerase. But since the marker is also affected I don't think DDT has anything with it. I suggest to check the buffer and gel. By the way, the SDS states that the product should be odorless. This suggests that the odor should not be from the kit product!
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