POP-6™ Polymer for the 310 Genetic Analyzer - FAQs

How often should I change my polymer and buffer?

Polymer in the syringe should be changed every three days. Do not return unused polymer to the bottle.

Buffer and water should be changed every 48 hours or, if the run lasts for more than 48 hours, after the run is complete.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

How often do I really need to clean the pump block?

The pump block needs to be cleaned when:

Installing a syringe.

Switching applications (i.e., from sequencing to fragment analysis).

Shutting down the instrument for a long period of time.

If the instrument has run for more than 4 days without any of the above occurring.

Appearance of unusual spikes in the electropherogram.

If the syringe containing the polymer has been on the instrument for more than a week, it is important to clean the syringe and the block, and to change the polymer. At room temperature, enough urea decomposition can occur in one week to cause transient current increases during electrophoreses. If polymer is allowed to dry in the pump block channel, the pump block may be ruined.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

What happens to the 310 Genetic Analyzer if it runs out of polymer during the run?

A message will appear at the start of the run telling you if you have enough polymer to complete the run. If you should continue without adding more polymer, then the run will be cancelled at the injection where it ran out and an entry will be made into the run log that there is no polymer. The following injections will appear to run for 1–2 minutes each and will be recorded into the run log. No data will be collected for these injections.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

How do you do a Test CCD 4-color?

The Test CCD 4-color module is used to make sure that the capillary window is aligned properly within the detection cell and that the baseline is below 2,000 rfu so that the data is not compromised. Before running the module, make sure that there is polymer in the capillary and that there is sufficient buffer in the buffer vial in position one of the autosampler.

To perform the Test CCD 4-color:

(1) After starting the instrument, open the 310 Data Collection Software.

(2) Prepare a sample sheet and create a new injection list for your run (an old sample sheet can also be used to perform this test).

(3) From within the new injection list, select a sample sheet.

(4) Under Inj.#, click on 1 (first line) and select Insert under the Edit pull-down menu to insert a blank line at the position 1.

(5) Configure the first injection to be the Test CCD 4-color Module

1. Choose any sample name from the pull-down menu in the Inj. Tube & Sample Name column.
2. Choose the Test CCD 4-color module in the Inj #1 Module column.

My baseline is too high (too low). How can I fix this?

Clean the capillary window on the capillary using a lint-free tissue (or use Kimwipe®: tissue) to remove all particulates. After cleaning, perform the Test CCD 4-Color test. This is a 5-minute module and should give you 4 lines in the scan window while the module is running. You should expect to see the lines in the following ranges on a scale of 2,000 on the y-axis: Red and Yellow – 700–1,600 and the Green and Blue – 300–1,000 range.

If your results are not close to these ranges, clean the capillary window again. If that fails, then clean the syringe with warm distilled water and change the polymer using a fresh, unexpired bottle. Replace the polymer in the capillary by using the Seq Fill Capillary module and discard the waste water and replace with fresh water.

If all of the above fails, the problem may be hardware related. Please contact Thermo Fisher Scientific Support to initiate a service call.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

My base spacing is too high/low. What does this mean and what can I do about it?

Base spacing is roughly defined as the number of scans per base. This value is directly related to the speed at which your samples are traveling through your polymer. The base spacing number will vary depending on the sample quality, capillary length, run module settings, polymer type, how long the polymer was on the system, electrophoresis buffer age, and environment. When you first start running samples, check the spacing to see what the average values are.

If the software is unable to determine the base spacing, it will give a best guess that will appear in red in the base spacing column. Usually this is either due to the data quality or a problem with the sample migration. If you notice the numbers fluctuating, check the following:

-Polymer expiration—if the polymer has expired, wash the block, syringe, and water/waste containers and replace.

-Polymer time on the system—the polymer should be in the syringe on the system for no more than a week. Polymer kept on the system longer than that may compromise the length of read and overall data quality.

-Electrophoresis buffer—the buffer is sold as a 10X concentrate and should be diluted to 1X prior to use. The 1X buffer is good for 1 month.

-Environment conditions—the instrument should be run at ambient temperature. Air flow can also affect migration. Make sure there are no fans, wind from an open window, or air vents blowing directly on the system.

-Sample quality—quantitate the template DNA prior to sequencing. After the sequencing reaction is done, clean the samples using one of the recommended procedures in the BigDye Terminator User Guide. If you are still getting poor results, run the Sequencing Standard as a sample to narrow the focus of your troubleshooting efforts. If the standard looks good, focus on the template and clean up procedures. If the standard looks bad, focus on the system.

If all of the above fail, please contact Thermo Fisher Scientific Technical Support for further assistance.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.