Purpose and Scope
Purpose
The 392 / 394 DNA / RNA Synthesizer uses Teflon tubing to conduct reagents from bottles to the reaction columns and then on to waste. The tubing tends to build up material on the inside over time. The tubing that is especially prone to building up material is the tubing that channels several different reagents and most especially the Pre Column Tubing. After some time, the Pre Column Tubing builds up so much material that it starts to impede the reagent flow. The reagent that is most sensitive to this build up of material is Deblock. Acetonitrile may flow at a normal rate but when Deblock hits the tubing, it just stops or goes very slow. This document tells you how to clean the instrument and how to keep it clean.
Scope
The scope of this document covers the cleaning process for the ABI 392/394. This cleaning process should be performed frequently to receive good quality oligo synthesis.
Definitions
- ACN: Acetonitrile
Procedure
For the ABI 392 / 394 we recommend that customers run the End Cycle every 2 ΓÇô 4 weeks (depending on usage) to clean the system. The End Cycle will keep the system clean and running well if it is performed regularly. However if it has been a long time between cleanings, the point restrictors may plug due to material breaking off the wall of the tubing and getting stuck in the very small passage through the point restrictors.
If it has been a long time since the End Cycle was run, we recommend the following:
- Replace the point restrictors with a tool that is available from Biolytic Lab Performance, Inc. (Part Number: 522-103147-4, Link to website). This tool has the same outside dimensions as the point restrictor, but it has a larger hole through the center. This means that material that is removed from the inside wall of the tubing during the cleaning process will not get stuck and plug the system.
- Repeat the End Cycle 3 times using the tool in place of the point restrictor.
- Reinstall the point restrictors and remove the tool.
- Perform the End Cycle one more time.
1. End Cycle Procedure
- Enter a 1 base sequence. Any base is fine
- Install a collect vial on the collect port for each column.
- Install a dummy column for each column position.
- Put fresh Ammonium Hydroxide in Bottle 10. Make sure that Bottle 18 also has ACN in it.
- Setup a synthesis on all 4 columns using the 1 base sequence.
- Use any protocol you like because the protocol will not actually run.
- No need to do the Begin Cycle (Prime).
- When you come to the screen that says Manual, change that to Auto. This means to automatically cleave the oligo.
- Select DMT ON for each column.
- Select the 0.2um CE End Cycle.
- Then start the run.
- Ammonium Hydroxide should go through each column 4 times. The run takes about 1.5 hours.
- All 4 collect vials should end up with about the same volume of Ammonium Hydroxide at the end of the run.
- When the run is complete, remove and empty the collect vials.
