The melt peak is not single. But I run the qPCR products on an agarose gel and I observed amplicons of the same size.
Since qPCR is much more sensitive you might have additional peaks and still see only one band on your agarose gel.
Can you upload an image of your melting curves? This would facilitate the interpretation of your data.
1. If you are not getting a single peak, is the other peak smaller. It could be the melting curve of the primers that you are also seeing. As Sabine mentioned, it would be best if you could upload the image of the melting curve.
2. Since most qPCR amplicons are rather small it might be that you need to increase the percent agarose in your gel and run it at a low voltage for an extended period of time to see the separation between the bands.
Instead of agarose gel try an 6% PAGE. You might see a double band there.
If you have a sequence variation, heating/cooling before running the gel may show two bands (homo- and heteroduplex). In this case, heating/cooling should also influence the melting peaks.
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