Primer dimers or contamination?
I am trying to reamplify some microsatellite fragments that I have previously amplified about a year ago. When amplifying them now though I find bands of around the same size are produced in all reactions (including negative controls). This suggests that they might be primer dimers. However the size of these bands is also the size of the microsatellite that I am trying to amplify in the reaction which has also lead me to suspect that it may be contamination.
I have therefore changed over all of my reagents to overcome any possible contamination and have also found a second stock of the primers. However I am still getting bands in the negative control.
I have checked over the gel pictures from last year when I previously amplified these samples and there is no indication of dimers being produced. I have also performed fragment analysis using these microsatellites with no indication of primer dimers.
I would welcome any suggestions as to how I could overcome this problem.
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