The ancient DNA clean room (commissioned in June 2006) is two purpose outfitted rooms dedicated to the extraction of low copy number DNA from "old" samples (bone, sediments and coprolites). The rooms have a number of safeguards (both equipment and procedural) which aim to reduce contamination of "ancient" specimens with modern DNA and/or previously amplified PCR products. However, processing a sample in a clean room will not guarantee a contamination "free" DNA extract as the sample may of been contaminated prior to arrival in the lab (for example bones washed and handled at an excavation site). In essence the goal of the clean room is to minimise further contamination.
A movie which takes a quick tour into the aDNA lab will be downloadable from this page will soon be available.
Personal wishing to enter the clean room must not of entered a post-PCR area that day - the aim of this procedural restriction is to minimise the possibility of physically carrying PCR products into the lab. DNA is everywhere - while this is is beneficial for forensic purposes it is detrimental to aDNA analyses. When you handle a sample (without gloves) or breath on it you are depositing your DNA on that sample. Entrance into the aDNA clean room is through a staging room where researchers get suited up (bodysuits, gloves, boots, face masks - pictured). The storage room also functions as a storeroom for lab supplies. Air filtering devices containing UV lights are in constant operation in this area.
This clean room is under positive air pressure. The air handelling unit mounted on the wall (pictured) is HEPA filtered, ensuring clean air circulates through the clean room and into the staging room. The airflow then exits the lab and ensures a constant pressure gradient always exists. The clean room is equipped with two glove boxes (pictured) which are regularly treated with UV lights. One glove box is used for DNA extractions and aliquoting DNA , the other for reagent handling (no DNA). Other equipment include UV lighting, centrifuges with aerosol control and a ductless cabinet for dealing with toxic chemicals. Work surfaces, reagents and equipment is also routinely irradiated or cleaned with bleach to remove any DNA.
The clean room environment plays a key role in minimising contamination - so do do procedures used in DNA extraction and PCR set-up. These procedures include:
- Multiple DNA extraction and PCR controls
- Using reagents/labwear suitable for use in a DNA clean room (e.g. Filter tips)
- Changing gloves often
- Processing only single samples or small batches
- common sense approaches to minimise handling and potential of cross contamination