A PCR-laboratory must be divided into three areas, according to the number of technological operations:
- Sample preparation area;
- Reaction mix preparation area (the clean area);
- Detection area.
All the three areas must be in isolated rooms equipped with sealed entry chambers. It is also important to have air filters. If there are special cabinets available, the first and the second areas can be merged in which case a separate room must be allocated for performing the amplification reaction. The location of the detection area depends on the method of detection used. If the detection method involves the opening of the test tubes enriched with amplification products (detection by electrophoresis or hybridization analysis), then the detection area must be placed as far as possible from the other two areas (another floor, a different building) and must have its own ventilation system that has no links to the ventilation systems of the other areas. This is a key design requirement for a PCR laboratory.
In addition to that, it is also advisable to have separate rooms for changing and storing outerwear, eating, and a general storage room for laboratory materials. All rooms must be equipped with short wave ultraviolet lamps. Laminar air flow safety cabinets must be installed for the treatment of clinical samples. These ensure the safety of personnel working with infected material; their internal surfaces must be pretreated with ultraviolet light for prolonged periods of time. The reaction mix must be prepared in a PCR cabinet equipped with AC power outlets, fluorescent and ultraviolet lamps. The entire operation space must have necessary equipment and expendables, including smocks and spare footwear, with each set assigned to specific rooms. All test tubes, supports etc. shall be permitted only to move from the clean area to the sample preparation and detection areas. Clinical samples that arrive at the laboratory must be treated as soon as possible (DNA and RNA must be isolated) in the sample preparation area. Amplification test tubes prepared in the clean area must have DNA samples put in inside the sample preparation area and then moved to the amplification area. Test tubes with positive controls or clinical samples must never be taken into the PCR box for the preparation of the reaction mix (the clean area) whether prior to or after treatment. After the thermocycling has been completed the test tubes must be carried into the detection area without their caps being opened. A separate laboratory assistant must be assigned if gel-electrophoresis is used as the detection method. If fluorescent probe hybridization during amplification is used as the detection method there is no need to open the test tube after completing PCR; this eliminates the danger of a large number of amplicons getting out into the external environment, consequently, the probability of contamination is significantly reduced. In this case there is no need to have a separate detection room with