These days, electronic instruments are all around us – at home and at work – and it takes time to learn to operate and subsequently master all their different features. Operating manuals always provide critical support; it is, however, even more helpful if they do not need to be consulted all the time. As such, intuitive operation of an instrument is a basic hallmark of user-friendliness and thus plays an important role in saving time on an ongoing basis during routine applications. A touch screen enables direct interaction with the instrument, thus facilitating quick operation, as long as information is organized in an intuitive manner and the user interface is optimized for this purpose. In the case of a thermocycler, new protocols must often be generated quickly, and it will definitely be beneficial to have different PCR methods handy for use as possible templates. At the same time, it is necessary to adapt protocols for more specific applications through flexible programming. Easy copying of methods and transfer between cyclers (for example, via USB) adds to overall convenience.
One further point on the list of ways to reduce expenditure is the elimination of entire PCR runs. How is this possible? Consider the following two scenarios: on the one hand, routine runs of established protocols are carried out, and on the other hand, new experiments are developed. The latter often require optimization in order to achieve accurate and reliable results – a process that can easily necessitate a large number of different reactions. It is the aim of PCR to obtain large yields of the desired band(s) without generating unwanted products. To achieve this goal, the optimal annealing temperature must be applied, which, in turn, depends on a number of factors including the primer sequence, the buffer and the PCR reagent – as well as the heating properties of the cycler. For this reason, the annealing temperature must be determined empirically by sequentially testing different temperatures. While there are formulas to help calculate the annealing temperature based on the primer sequences and their melting temperatures, respectively, these methods are generally considered to be merely a first approximation and the basis upon which to build optimization runs. This procedure was considerably simplified by the first thermocycler with gradient technology (Mastercycler® gradient), launched by Eppendorf in 1997. This allows the design of a temperature gradient (across 12 columns) during one temperature step, through separate control of the Peltier elements present within the block. In this way, different annealing temperatures can be tested simultaneously in one run (figure 2).