An investigation into the protective capabilities of nucleosomes on forensic STRs

Abstract

Partial DNA profiles are often obtained from degraded forensic samples due to allelic and locus dropout, particularly at the high molecular weight loci. It is hypothesized that nucleosomes could offer protection to the bound DNA by limiting access to enzymes. Choosing and incorporating STRs that are protected into a “high nucleosome-binding” multiplex could mean that a better DNA profile could be obtained from degraded samples. 58 STRs were previously evaluated for their nucleosome-forming potential (NFP) using two computer programs – NXSensor and nuScore. Ten mini-STR primer sets for amplifying ten loci with varying nuScores were designed and optimized. They were used to amplify degraded saliva samples and simulated casework samples to determine if there was any correlation between nuScore and DNA survivability, indicated by DNA concentration. The effect of nucleosome protection was not observed for both sample types (ρ = −0.166, p = 0.647). High-nuScore loci did not perform better than low- or medium-nuScore loci. It was possible that nucleosome protection might only work in living cells and not in forensic stains, as histones could be removed during necrosis by lysosomal proteases, and subsequently DNA would be degraded by endo- and exonucleases. Other processes such as chromatin remodeling and DNA methylation could shift nucleosomes away from the predicted sites, thereby changing nuScores. It was concluded that nucleosome protection did not exist for degraded saliva samples, given that nuScores accurately represented the probability of finding a nucleosome.