Since samples of environmentally degraded and inhibited DNA produce a variety of interpretational problems, such as allele imbalance, allele dropout, and sequence specific inhibition, the current project attempted to develop methods for improving the recovery of this type of evidence by applying magnetic bead hybridization to extract and preconcentrate DNA sequences containing short tandem repeat (STR) alleles of interest.
In this work, genomic DNA was fragmented by heating, and sequences associated with STR alleles were selectively hybridized to allele-specific biotinylated probes. Each particular biotinylated probe-DNA complex was bound to streptavidin-coated magnetic beads using enabling enrichment of target DNA sequences. Experiments conducted using degraded DNA samples, as well as samples containing a large concentration of inhibitory substances, showed good specificity and recovery of missing alleles. Based on the favorable results obtained with these specific probes, this method should prove useful as a tool to improve the recovery of alleles from degraded and inhibited DNA samples. (publisher abstract modified)