MLPA requires a capillary electrophoresis device that uses denaturing conditions. Devices that use non-denaturing conditions, such as the QIAGEN QIAxcel, the Agilent (formerly Advanced Analytical/AATI) Fragment Analyzer or the Caliper LabChip GX/GXII, are not suitable for MLPA.
The use of non-denaturing conditions can alter the relative mobility of the MLPA reaction products. As a result, the distance between some peaks may be larger or smaller than under denaturing conditions. In some cases, fragments may even swap positions in the electropherogram due to secondary structure formation.
At MRC-Holland the distance between each fragment is optimized based on denaturing electrophoresis conditions. Therefore, our products are not suitable for use with electrophoresis devices that use non-denaturing conditions.
For a list of supported capillary electrophoresis devices please refer to our current protocol.