Use Of Small Amplicons To Improve Amplification Success On Highly Degraded Samples

As noted in Chapter 7 when encountering highly degraded DNA samples where the molecules have been fragmented to small sizes, the use of smaller sized PCR products improves recovery of information from the original DNA template. This is also the case with mitochondrial DNA and 'mini-primer sets' have been developed to amplify smaller portions of HV1 and HV2 (Gabriel et al. 2001a, Edson et al. 2004). The bottom portion of Figure 10.3 shows the relative position and PCR product sizes for eight mini-products ranging in size from 126 bp to 170 bp.

The use of these mini-amplicons that overlap one another is sometimes referred to as an 'ancient DNA' approach and is capable of recovering abundant DNA in a sample that might otherwise fail to produce results with a standard protocol (Gabriel et al. 2001a, Melton and Nelson 2001). This approach has been used to successfully recover information from Neanderthal bones that are thousands of years old (Krings et al. 1997, 1999).

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