Apparatuses and methods for plate-based oligonucleotide synthesis are disclosed. In one embodiment a synthesis plate having wells and waste tips is coupled to a receiving plate having through holes corresponding to the pattern of wells. A press with a pressure plate applies a uniform downward force to the well synthesis plate such that each of the waste tips are driven through the corresponding through holes of the receiving plate thereby creating a secure mechanical coupling between the synthesis plate and the receiving plate. The coupled assembly may be positioned on top of a drain apparatus such that the through holes of the receiving plate are aligned with corresponding O-rings of the drain apparatus. A keeper may then be placed over the top of the coupled assembly to apply a downward force that forms a fluid-tight seal at each of the waste tips.