Long-Term Capillary Array Storage on Parallel Capillary Electrophoresis Instruments

Answer

This Information Applies To: Agilent 5200/5300/5400 Fragment Analyzer, Femto Pulse, ZAG DNA Analyzer, and Oligo Pro II

Issue

Methods for storing capillary array when not in use for longer than two weeks. The array can either be stored installed in the instrument or in the external array docking station.

Items Required

• Capillary Storage Solution
  • For use with the Femto Pulse and Oligo Pro II system (p/n GP-435-0100)
  • For use with the Fragment Analyzer and ZAG DNA Analyzer systems (p/n GP-440-0100)
• Conditioning Solution

Steps to Follow

Before Storing the Array:

• 5200/5300/5400 Fragment Analyzer, Femto Pulse, ZAG DNA Analyzer: Perform a full conditioning.
• Oligo Pro II: Run a Step 3 for 15 minutes with gel only.

The capillary array must be stored with the capillary tips in fresh Capillary Storage Solution under the capillaries. 

Caution: The recommendations for the rows and drawers in this article apply to the default settings. If the configuration has been changed, use the updated rows and drawer.

• 5200 Fragment Analyzer, and Femto Pulse: Place 1.0 mL/well of Capillary Storage Solution into Row H of the buffer plate.
• 5300/5400 Fragment Analyzer, ZAG DNA Analyzer, and Oligo Pro II: Place 100 μL/well of Capillary Storage Solution in a fresh sample plate in drawer 3. For a 24 capillary array, fill rows A and B, for a 48 capillary array, fill rows A to D and for a 96 capillary array fill rows A to H.

The Capillary Storage Solution should be changed at least once every four weeks. However, it is recommended to change the Capillary Storage Solution every one to two weeks due to evaporation, especially in low humidity/high temperature environments. It is best practice to run a full conditioning run weekly.

The capillary can either be stored in the instrument or using the array docking station. The array will require some capillary array cleaning after prolonged downtime.

Storing the capillary array in the instrument

• After preparing a plate with Capillary Storage Solution:
  • Femto Pulse and 5200 Fragment Analyzer: place the storage plate in drawer B (top drawer).
  • Oligo Pro, 5300 and 5400 Fragment Analyzer: place the storage plate in sample draw 3 (sixth drawer from the top).
  • ZAG DNA Analyzer: place the storage plate in draw S (third drawer from top on right).
• Move the storage plate under the capillaries in the Fragment Analyzer, Femto Pulse, or ZAG DNA Analyzer controller software:
  • Select the Operation tab > click Store > in the Oligo Pro II controller software, select the Utilities tab > click Move Stage > Store (Figure 1).

Figure 1. Moving the stage in the Fragment Analyzer, Femto Pulse, and ZAG DNA Analyzer controller software (top), and Oligo Pro II software (bottom).

Using the Array Docking Station

Operation of the external docking station requires the array spindle accessory kit, part number A1300-910, which is shipped with all instruments.

1. Remove the array as described in chapter 9 of the Oligo Pro II user manual, and chapter 8 of the 5200, 5300, and 5400 Fragment Analyzer, Femto Pulse, and ZAG DNA Analyzer system manuals.
2. Place the tray base inside the array docking station (Figure 2).
   

   
   
   Figure 2. Array docking station with 96-deep well tray

3. Place a 96-deep well tray (Agilent part number P60-20 or Fisher Scientific part number 12-566-120) into the array docking station with tray base. Fill the required wells with 1.0 mL of Capillary Storage Solution (Figure 3)
   

         
    
   Figure 3. Array docking station with 96-deep well tray

4. Place capillary array into the array docking station using the four leg holes as guides. Ensure that the capillary tips are in the Capillary Storage Solution side of the tray, not left in open air.
    
5. To tighten the capillary array into place, insert the two white screws (Figure 4).
   

                
   
   Figure 4. Array docking station with capillary array installed, and held in place by the two white screws

6. Fill the provided glass vial with 20 mL of Capillary Storage Solution and place into the array spindle storage device (Figure 5). 
   

        
   
   Figure 5. Array spindle storage device, no Storage Solution in this example bottle
   
   

7. Slide the array spindle storage device onto the capillary array side arm, located to the left of the capillary array window, and screw the locking screw into place (Figure 6). 
   

       
   
   Figure 6. Array spindle storage device installation

8. Remove the capillary array outlet spindle from the black storage plug and place it into the array spindle storage device (Figure 7). 
   • Depending on the capillary array size, there are two different cap sizes for the glass vial on the array spindle storage device: the cap with a smaller opening is used for 12-capillary arrays, the cap with the larger opening is for the 48- or 96-capillary arrays.  
     

         
     
     Figure 7. Array docking station with array installed.

9. The Capillary Storage Solution should be changed at least every four weeks. However, it is recommended to change the Capillary Storage Solution every one to two weeks due to evaporation, especially in low humidity/high temperature environments.

Powering on System After Prolonged Downtime

After prolonged storage of the system, it is recommended to perform a Method B – Hot Water Soak of the capillaries followed by a Method C – 0.5N NaOH flush.

1. Power on the PC, instrument, and software.
2. Replace the Capillary Storage Solution.
3. Perform a Method B – Hot Water Soak as outlined in the appendix of the 5200, 5300, and 5400 Fragment Analyzer, Femto Pulse, and ZAG DNA Analyzer system manuals.*
4. Perform a Method C – 0.5N NaOH flush as outlined in the appendix of the 5200, 5300, and 5400 Fragment Analyzer, Femto Pulse, and ZAG DNA Analyzer system manuals.*
5. Prepare fresh Conditioning Solution and separation gel according to the Kit Guide or Quick Guide, update solution levels in the software and prime lines.

*The Oligo Pro II system does not have appendixes detailing the Method B or Method C flush. Instead of the flushes, place a buffer tray filled with 1.0 mL/well of hot water (150 to 200 °F, 66 to 93 °C) in the buffer position. Send to this location for 30 minutes.

For Research Use Only. Not for use in diagnostic procedures.

PR7001-0966

Learn how to effectively maintain and operate your parallel capillary electrophoresis instrument: 5200, 5300, and 5400 Fragment Analyzer system manual on Agilent.com Femto Pulse user manual on Agilent.com ZAG DNA Analyzer system manual on Agilent.com Oligo Pro II user manual on Agilent.com