The synthesis of oligonucleotide probes on in situ synthesized arrays, such as by photolithography, can result in a population of incomplete or “truncated” probe sequences which accompany the probe sequences synthesized at the full desired or intended length (“full-length” probe sequences). The presence of truncated probe sequences can have a detrimental effect on array performance, especially in assays requiring enzymatically addressing the free probe terminus (e.g., polymerase extension reactions, ligation reactions).
In contrast, oligonucleotide probes immobilized on bead arrays (e.g., Illumina) and other spotted arrays may be attached to their substrates via an amine or other functional group synthetically attached to the 5′-end of the probe. In this way, only full-length sequences may be immobilized, and truncations or other defects associated with an exposed free 3′-end may be reduced or virtually eliminated.