All no-DNA MLPA reactions will show four Q-fragments at 64, 70, 76, and 82 nt. Amplification of the Q-fragments is not dependent on sample DNA or ligation efficiency. The presence of Q-fragments in a no-DNA reaction indicates that the PCR reaction was carried out properly.
You may also see some additional peaks in your no-DNA reactions as MLPA no-DNA control reactions are more prone to non-specific peak formation than reactions that contain DNA. These non-specific peaks should not influence MLPA results when sufficient sample DNA is used, as they should be outcompeted by the amplification products of MLPA probes. At MRC Holland, we only approve probemixes that show non-specific peaks in the no-DNA reaction if they are below 25% of the median signal of the Q-fragments.
Detailed information can be found in the quality control section of the (MS-)MLPA General Protocol.
If you see a large number of peaks resembling a full peak pattern in your no-DNA control reaction, this is an indication of contamination.
The information provided in this material is correct for the majority of our products. However, for certain applications, the instructions for use may differ. In the event of conflicting information, the relevant instructions for use take precedence.