I am trying to amplify by PCR a fragment (2kb) from a DNA template which is the product of MDA reaction. This MDA reaction is previousliy performed with plasmids as template and all of them include the sequence of the oligos I am using for the PCR. The MDA reaction is performed with hexamers (Repli-g mini kit from qiagen) and the PCR polymerase I am using is PFU ultra II HS. I am getting multiple bands (both larger and smaller than the 2kb expected) from the PCR. Primers work great when PCR template is the plasmid. Although, I tried different annealing temperatures, 2% of DMSO in PCR reaction to "relax" DNA. Still multiple bands.

Is this normal? Should I expect this king of PCR result due to the branched structure of the MDA product? If so, any idea to "push" the PCR when template is MDA product to prefer my fragment?

Thanks a lot in advance.