probe amplification in MLPA
I work for MRC-Holland, the developer of MLPA, and what Kacper explains is indeed the case. Any RPO (right probe oligo) that is not ligated is also amplified in the MLPA reaction, as the reverse primer can bind to the primer binding site of the RPO. HOWEVER, since this unligated RPO oligo LACKS the binding site for the (fluoresently labelled) forward primer, the amplification ends here. LIGATED probes, in contrast, contain the binding site for BOTH primers, and hence are amplified exponentially. Furthermore, the fluorescent label is only incorporated in the amplicons that results from ligated probes.