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We studied the interaction of infrared optical traps with controlled-pore glass (CPG) beads in aqueous medium. The lateral optical trapping force and stiffness were experimentally found considerably smaller than those of their solid counterparts. The simulation using an average refractive index revealed significant losses of effective trapping efficiency, which quantitatively agreed well with experimentally fitted curves. This effect was ascribed to the reduced relative refractive index of medium-filled CPG beads with respect to the medium. Combining optical trapping with mechanical confinements, we demonstrated a microfluidic platform allowing for the synthesis of multiple DNA oligonucleotide sequences on individual beads of interest.