The Eppendorf Mastercycler EP is a modular PCR system that can be used either as a single standard PCR machine or as a computer-controlled, run-recording, GLP compliant PCR network. We considered this as a future-proofing advantage when purchasing the instrument – even though we do not require GLP compliance at present, we may in the future. Operation is via an optional, removable control panel (which can enable multi-unit networking) or an IBM-compatible computer, which can then regulate an entire network. This way, should we require further PCR machines, we can purchase them as the machine only, without the extra controllers. The single control panel allows the user to multi-task the control and reporting functions of all networked units using a simple LCD interface that is intuitive and easy to control (using a standard PS2 or serial mouse). Alphanumeric data is entered using a keypad or, alternatively, using the mouse. However, we found the mouse to be too sensitive for practical use. A feature that we required in our recent purchase decisions has been the ability to produce hard-copy output of procedures. In contrast to the limitations of other instruments, hard-copy output is available via the serial or centronics printer connections and all data is recorded in real-time. This feature enables us to print-out values for variables such as temperature and time for each step of the run, verifying the entire process and recording data for GLP compliance. The machine can store more than 700 separate programs internally, while also being compatible with MultiMedia and SecureDigital cards. Using this system, there is an infinite capacity for storage of programs and results. This has been a problem with many of our older machines that have limited storage capactity – much of the equipment in our department is shared, and program space can run out quickly.
The Mastercycler EP can be used in a fully-automated setup based on the selection of the motorized lid. Although the heating element is typically motorized, Eppendorf offers the option of a mechanically-operated lid (upon request). However, we do not use our PCR machines in conjunction with liquid handling robots, so it was conventient discount on the price as this feature was not required. On all machines, the lid is heated prior to contact with the tubes, which prevents sample exposure before cycling has begun. The heating element is adjusted automatically based on tube heights determined as it is lowered into place. Across our department, many different tube types are used by different groups. We found that the automatically adjusting lid, rather than a fixed-height lid, was useful in this instance as the consideration for tube type is no longer required.
The Eppendorf Mastercycler EP is a fan and peltier cooled unit and we have found this to be very quiet during cooling and heating stages, in comparison to liquid cooled, and even many other peltier cooled systems. Because we purchased this unit as a shared machine, and as a general-purpose machine for many different PCR reaction types, we required a versatile block format. The blocks available for this machine accommodate 96 reactions in 0.2mL PCR tubes, PCR strips or PCR trays. Unlike our other machines, however, they do not accommodate 0.5mL tubes. The blocks are capable of gradient operation with a temperature variance of 20oC and we have found this very useful for fast optimisation of annealing temperature, although the range of 20oC is rarely used. A silver block is now available that will allow ultra-fast ramping speeds (up to 6oC per sec), significantly decreasing the run time (up to 50%). However, during the amplification from bacterial genomic DNA, using mid-sized products (typically 1-5kb), we have noticed a reduced yield when using the fast ramping programs. The ramp rate is fully adjustable, however, and can be programmed to simulate the ramping characteristics of standard PCR machines. We have found the fast ramping speed to be advantageous in reactions where the yield is not critical; checking for the presence of a particular sequence, confirmation of mutant constructs and so forth.
Scott Coutts
Graduate Student
Bacterial Pathogenesis Group
Monash University
Australia