Functionalization of oligonucleotides with fluorescent dyes, biotin, and other reporter and capture labels is efficient, reliable, and convenient on the ABI 3948. The entire process of sequence entry, oligonucleotide synthesis, cleavage, deprotection, purification, quantitation, and sample collection is automated. Up to 48 oligonucleotides can be produced during unattended operation. The OneStep columns are filled with a mixture of nucleoside-loaded and underivatized, high-cross link, non-swelling polystyrene beads to conduct both synthesis and purification. Real-time, quantitative PCR, FRET hybridization, sequencing and genetic analysis experiments show the positive performance effects of the combined synthesis and purification of fluorescent dye-labelled primers and probes.