Titel der Masterarbeit: Primer design for PCR-based ancient DNA analysis — Examination of the suitability of different primer design strategies
The polymerase chain reaction (PCR) is nowadays one of the most important techniques in molecular biology and allows to amplify small amounts of specific DNA. Since its development in the 1980s, the PCR was swiftly expanded to different scientific research areas, such as the analysis of DNA from archaeological material. This ancient DNA can be preserved for long time periods and therefore allows a genetic access to the past. However, ancient DNA retrieved from archaeological material is usually present only in small amounts and various states of degradation, which impedes the analysis.
Primers, small single stranded nucleotide sequences, are one of the key components of the PCR. They flank the region of the DNA that should be amplified and serve as initiation site for the DNA-polymerase, the enzyme responsible for the DNA-replication. Primers are usually up to 25 bp in length and uniquely bind to one specific DNA region to avoid the amplification of unspecific sequences. To select primers, various literature and software tools are available. However, since ancient DNA exhibits unique properties, common primer design strategies may not yield well suited primers for PCR-based ancient DNA analysis.
The aim of my thesis is to compare different primer design strategies regarding their suitability for PCR-based ancient DNA analysis. Therefore, primer pairs for identical genetic markers are designed via different primer design strategies. Primers will be designed according to literature on primer design as well as with the help of software tools. Additionally, theoretical considerations on how primer design could be adapted specifically for ancient DNA analysis will be developed and tested. Comparison of the results should reveal whether primer design has an influence on the success of the analysis and which primer design strategies are suitable for the analysis of ancient DNA.