The ABI 3130 and 3130xl Genetic Analyzers are the newest in a range of analyzers produced by ABI. These machines use capillary electrophoresis, which is a significant advantage over slab-gel based technologies. Rather than risking inconsistency as a result of pouring slab-gels, a simple capillary array is fit into the slots available. In addition, the arrays are guaranteed for 100 runs (rather than one slab per run) and there is no sample loss (unlike a slab-gel). The fragments of DNA (and all other negatively charged molecules) are attracted to the platinum cathode electrode attached to the end of the capillary (16 capillaries in all), which is open and filled with Performance Optimized Polymer (POP). When current is applied, the DNA fragments are attracted to the capillary and travel through the polymer to the detection window and array housing. As the fragments pass through a clear area in the capillary, the fluorophores are excited by a laser and emission is detected and recorded by a CCD camera (the 3130 series can detect up to five fluorophores). The ability to detect multiple fluorophores enables detection of a larger number of similar size DNA fragments.
The ABI 3130xl Genetic Analyzer is the new model, which is intended to replace the ABI 3100. Transition from the 3100 to the 3130xl should be simple as they are almost identical with ABI selling system upgrades from the 3100 avante and 3100 to the 3130xl model. Both the 3130 and the 3130xl support the loading of two 96-well or 384-well plates simultaneously, allowing for effective time management. For those with high-throughput applications or limited to 96-well plates, four slots would have been ideal for overnight analysis, but two is quite effective at cutting time requirements.
The 3130 Genetic Analyzer is similar to the 3100avante as it uses a 4 capillary array (i.e. you can process 4 samples at one time), while the 3130xl uses a 16 capillary array. To put this into perspective, the 3130 using the RapidSeq36_POP6 module for DNA sequencing (approximately a 500bp read length) will have a 24 hr throughput of 96 samples. The 3130xl with its extra 12 capillaries has a 24 hr throughput of 384 samples. In human identification, there is always a need for rapid throughput. Using the HID Fragment analysis 36_POP4 module, the 3130 would process only 2,560 samples in 24 hr while the 3130xl would process 10,240 samples in the same amount of time. In addition to optimizing the hardware, ABI has developed a new Performance Optimized Polymer (POP) that saves set-up time, actual polymer usage and prevents accidents with expensive arrays. All in all, it makes running various modules on the one machine more user-friendly.
Deciding between the two machines is dependant on your current and future throughput demands, as well as, your budget. Fortunately, upgrade options currently available address future needs. I’ve only used the 3130xl for fragment analysis and found it very easy to work with. You denature PCR products in ABI’s Hi-Di Formamide, heat to 95C and then place on ice. The data collection software is user friendly; all you have to do is enter the sample identifiers, choose the module for your application and then run in the self-contained system. The results I obtained were high quality and very consistant, while the system was easy to optimize for my personal requirements. As with all of ABI’s capillary-based genetic analyzers, increased use results in fewer problems related to resolution, injection and electrophoresis. ABI suggest continuous use of the machine or regular flushing with fresh polymer. Cleaning is also much easier as the process is now fully automated. The only drawback is that the process uses a LOT of polymer. Previously we had experienced problems with bubbles being trapped in the lines in the older 3100 series. In the event that bubbles do form, you have to manually push the syringe to flush them out of the polymer lines. However the 3130 series uses an automated system, which is usually very effective.
David Fegredo
Medical Scientist
PathWest
Australia