title: Optimization of STR locus enrichment for STR profiling of fragmented DNA.
abstract: DNA degradation is a major obstacle in gaining an accurate profile with standard DNA typing technology. Although alternative genotyping strategies such as mini-STRs and SNPs have proven to be more successful in profiling degraded DNA, these approaches also have limitations. Here, we show that locus enrichment by hybridization of degraded genomic DNA with an STR locus-specific biotinylated oligonucleotide is a powerful approach to overcome problems in STR typing of highly degraded DNA. An experimental investigation of factors affecting the efficiency of this method indicates that the choice of primer and molar ratio of primers to genomic DNA are critical factors in improving enrichment of the STR locus before genotyping with multiplex kits. In addition, we find that indirect capture rather than direct capture with magnetic beads yields better enrichment efficiency for STR locus enrichments. Using these strategies, we demonstrate an improvement in STR typing of DNA from cultured cells damaged by exposure to sunlight or UV. We suggest that this approach could be applied to highly degraded forensic samples alone or in combination with mini-STRs.
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea.
authors.forename: Seon-Kyu
authors.initials: SK
authors.lastname: Ham
authors.forename: Se-Yong
authors.initials: SY
authors.lastname: Kim
authors.forename: Jang-Won
authors.initials: JW
authors.lastname: Ahn
authors.forename: Bo Young
authors.initials: BY
authors.lastname: Seo
authors.forename: Kwang-Man
authors.initials: KM
authors.lastname: Woo
authors.forename: Cheol Yong
authors.initials: CY
authors.lastname: Choi
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Lee
mesh_terms: D004247:DNA / Q000032:analysis*; D016172:DNA Fingerprinting / Q000379:methods*; D053938:DNA Fragmentation; D053803:Forensic Genetics / Q000379:methods*; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D059346:Magnets; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D004247:DNA
keywords: Degraded DNA; Hybridization; Magnetic bead; STR locus enrichment