An acetylation step where a chemical cap is placed on active sites which have not received an amidite group. This terminates incomplete chains and prevents deletions in the final product. An oxidation step which forms an oxygen double bond, converting the newly formed phosphite bond into a more stable phosphate bond. These four steps are cycled for each subsequent addition of base to grow the oligonucleotide chain. Other intermediate steps of the protocol include washing and draining and are employed so as to insure as optimal a synthesis as possible.
Performance is monitored during operation by on-screen indicators .
Detailed machine operation is controlled by tables of operating parameters which are set during initial calibration and then typically not subsequently changed. The setup and operation of the machine typically requires only the importing of the files containing the prescribed oligonucleotide sequences and restocking of the reagents used in the operation. The tubing and jets which deliver the reagents to the 96-well plate are automatically primed with the reagents under computer control at the beginning of each run. At the end of each run the lines are purged of the synthesizing reagents. By purging with a neutral flushing agent, buildup of deposits or clogging of lines is prevented.