Capillary array as a carrier for polymers, the separation media, is critical for peak separation in Sanger sequencing and fragment analysis. Each capillary array costs several thousands of dollars; taking good care of the capillary array goes a long way for saving money and reducing operation cost.

Capillary array is a consumable and will need to be replaced eventually

However, capillary array is a consumable and at some point, after many runs, it will reach the end of life and need to be replaced no matter what you do. At the end of the array life, it will not generate well-separated peaks.

Should I replace my array now? Wait!

Before you throw out the array and purchase a new one, you want to make sure if the array can be saved by cleaning. It is normal that the array gets dirty after hundreds of runs and can’t perform optimally. At this time, if the array is cleaned or regenerated, it may still restore the optimal performance. In fact, if you can clean or regenerate the array in time, it can be cleaned multiple times before replaced.

What suboptimal results do I expect from a dirty array?

Dirty array leads to peak broadening (“fat peaks”), peak delay and therefore peak space changes. As a result, peak reading accuracy and reading length is reduced. The dirty array is caused by accumulated polymer debris and proteins from sample preparation. These contaminants can slow down the peak migration and result in above low-quality separation results.

Can I monitor the capillary array so I can clean it before it gets really dirty?

It takes hundreds of runs before the dirty debris and proteins accumulate in the capillary array and cause bad separation. It is important to monitor this process so you know when you can plan the cleaning before it generates suboptimal results. The most important thing is to monitor the EP current during the pre-run procedures and compare it with the EP current value when a new array is installed. After many runs, you will notice that the EP current starts to increase as the array is getting dirtier.

Another thing is to check the sequencing results itself. Paying attention to the peak space is a good practice. Note the peak space when a fresh array is used and maybe calculate the average space from multiple sample runs. If you start to notice that the space has increased significantly, maybe it is time to clean the array.

What other factors to consider besides a dirty array?

Suboptimal sequencing results mentioned above can be caused by a dirty array, it could be due to the usage of a bad/aged polymer or aged running buffer as well. Because sequencers are normally placed at room temperature, both polymers and sequencing buffer only have a short life at room temperature and need to be replaced according to the instruction from the manufacture. You may intend to use the buffer and polymer for a longer period because the current polymer and running buffer installed on the instrument has not been used that much lately. But the expired polymer and running buffer can contribute to poor separation and even make the capillary array dirty, thereby shortening the array cleaning interval.

How often do I need to clean the array? how many times can I clean my array before getting a new one?

These are most frequently asked questions. The frequency for cleaning the array depends on several factors including the quality of the polymer and running buffer used, the sample quality (does the sample contains a lot of proteins?), and the frequency that the instruments are used. We recommend you clean the capillary array after an average of 500 runs using the ADS capillary regeneration kit for either 3130 or 3730 series.

It is hard to say how many times can you clean the array before getting a new array because all the factors mentioned above and the frequency you clean the array will contribute to the array’s lifespan. We recommend you change the array when you do not see restoration of the optimal performance after cleaning, assuming you are using clean samples, fresh polymers and running buffer.

Why do you want to clean the capillary array with an inline regeneration kit?

Cleaning the array using an inline regeneration kit like ours has a few advantages:

  • Saving time: it takes a few hours rather than a few days if you choose to send it out to a third party to clean.
  • Saving money: it costs much less as no labor and shipping fee is involved.
  • No damage risk: there is no need to disassemble or reassemble the array.
  • No recalibration needed: there is no need for spectral and spatial calibration after array cleaning.