An Investigation of the Effect of DNA Degradation and Inhibition on PCR Amplification of Single Source and Mixed Forensic Samples

• NCJ Number: 236692
• Author(s): Bruce McCord; Kerry Opel; Maribel Funes; Silvia Zoppis; Lee Meadows Jantz
• Date Published: 2011
• Length: 66 pages
• Grant Number(s): 2006-DN-BX-K006
• Agencies: NIJ-Sponsored
• Publication Type: Report (Study/Research)
• Award: An Investigation of the Effect of DNA Degradation and Inhibition on PCR Amplification of Single Source and Mixed Forensic Samples

Annotation

This research examined the mechanisms for PCR inhibition and degradation as well as their effects on forensic DNA typing, which could lead to the development of more sensitive and robust analytical protocols.

Abstract

Based on the results, the researchers conclude that environmental damage to DNA in tissue samples occurs rapidly in reaching the state in which DNA becomes nearly unrecoverable. The template in such samples breaks down to small pieces in as little as 3 weeks. The effects of oxidative damage on such samples, however, was minimal. No oxidation of DNA bases was found for environmentally degraded DNA, although it was present in saliva samples. The study found that the combination of real-time PCR and DNA melt curves is an effective tool for the detection of PCR inhibition and permits classification of various inhibitors based on their behavior. In addition, the research found that the effects of DNA binding appear to be sequence-specific and/or length-specific PCR inhibitors that mainly affect Taq tend to inhibit DNA by influencing the largest alleles first, and inhibitors that bind DNA may affect smaller alleles as well as larger ones. Further, it has been widely reported that MiniSTRs improve resistance to PCR inhibition. Based on the findings of the current research, however, a caveat should be that such improvements may depend on the type of inhibition. Sequence-specific inhibition may still cause problems even with reduced sized amplicons. Regarding methodology, the researchers performed controlled studies in order to clarify the mechanisms of environmental and chemical degradation and PCR inhibition on single-source samples and mixtures. This was done by using real-time PCR and HPLC/EC in order to evaluate the mechanisms of DNA degradation, oxidative damage, and PCR inhibition on the recovery of STR profiles. Both degraded and pristine DNA were examined. 2 tables, 6 figures, and 32 references