Relative degradation of nuclear and mitochondrial DNA: an experimental approach

Single copy nuclear loci often cannot be amplified from degraded remains, necessitating the analysis of mitochondrial DNA (mtDNA). The success in analyzing mtDNA is generally thought to result from its higher copy number in the cell; however, other factors, such as cellular location or molecular features, may be equally or more important in the superior preservation of mtDNA. To explore and compare mtDNA and nuclear DNA degradation, mouse tissues (muscle, liver, and brain) were allowed to degrade at different temperatures, and the relative degradation of a mitochondrial gene, a single copy nuclear gene, and a multi-copy nuclear gene was assayed using real-time polymerase chain reaction. The tissues were also homogenized, allowing the three loci to degrade in the same cellular environment. Gene copy number and cellular location both influence DNA recovery. In some instances, multi-copy loci could be recovered when the single copy locus could not; however, the pattern of relative DNA degradation changed between whole and homogenized tissues. The overall results indicate that DNA degradation is influenced by multiple factors-including cellular location, chromatin structure, and transcriptional activity-factors that could be used to exploit loci for more robust forensic analysis from degraded biological material.