In the simplified diagram of the lab design shown in Figure 1, you will notice that each of the main task in the PCR workflow is dedicated to one room and that the sample goes in an unidirectional flow. Starting with the sample processing/storage room, this is where you keep or perform a certain processing step on the raw sample that you have received. For example, in a GMO lab, here is where the foodstuff is processed into finer components before it is used for DNA extraction. The raw sample is then transferred to the next room – the Sample Preparation room for subsequent DNA/RNA extraction.
The extracted nucleic acid samples are then brought to the next room – the PCR Setup room. Here is where we put all the reaction components into a tube to form a PCR reaction mix. Once this reaction mix is setup, it will be transferred to another room called the PCR Amplification Room. This is the room where thermal cyclers are placed. The only thing that you should do in this room is to put the reaction tubes into the thermal cyclers and let them run. Nothing else is performed.
However, depending on the exact workflow and resources, it is usual to see different thermal cyclers dedicated for pre-PCR (e.g. cDNA synthesis), PCR and even post-PCR (sequencing). Sometimes, these cyclers are even separately placed in different rooms. In such cases, the PCR setup and PCR amplification rooms are usually combined for each of these prePCR, PCR, and post-PCR steps. The main point is on minimizing cross-contamination from one part of the workflow to the next. It is also easier to control, troubleshoot and eliminate any contamination that does occur this way.
The Electrophoresis room is the last room where you check the results of the reaction. The end product – that is, the PCR product – will be left here and should not be brought out of the room unless you intend to do some further experiments with the products.
To further avoid cross-contamination of aerosols from one room to another, the PCR setup room will have a slightly positive pressure so that there is a constant flow of air from the room to the outside environment. This will prevent the entry of aerosols. On the other hand, the Electrophoresis room will have a slightly negative pressure and this will draw a constant stream of air into the room, making sure no aerosols can escape the room. At the same time, the red dots in these rooms represent each room has its own exhaust system. This is installed in order to channel any aerosols out of each room individually to minimize crosscontamination. The air-conditioning system in each room should also be decentralized.
Of course, not everybody can afford the luxury of a huge lab with multiple rooms. With smaller labs, you make the best out of what you have by rearranging where and how each main function should be performed (Figure 2). In this setup, there should be a separate bench for each critical task along the PCR workflow – DNA extraction, RNA extraction, and PCR setup. Additionally, the electrophoresis area should at the very least be isolated by proper partition.