title: Are we fishing or catching? Evaluating the efficiency of bait capture of CODIS fragments.
abstract: This study sought to document the efficiency of DNA bait capture (i.e., "fishing") methods by two measures: (1) its ability to retain targeted DNA molecules, and (2) its ability to remove non-target DNA molecules from a pool containing both. DNA bait capture uses synthetic biotinylated DNA primers to bind target DNA, which are then immobilized onto streptavidin coated magnetic beads and drawn to a magnet. Bound DNA should, therefore, be isolated from non-target DNA and impurities (e.g., PCR inhibitors) and can be later eluted from the beads for downstream applications. Efficiencies were estimated by comparing the number of "copies in" to "copies out" with quantitative polymerase chain reaction (qPCR). Retention of target DNA molecules, ranging from 109 to 288 base pairs (bps) in length, averaged just 9.06-3.53% (i.e., loss of 90.94-96.47%) using the fishing protocol as originally described. Some improvement was achieved by employing a modified protocol (i.e., with a shortened hybridization time, use of twice the amount of M-270 streptavidin-coated beads, and modified bead washing), resulting in average retention of 31.41-12.08% of the same set of targeted molecules. Noted was the lack of efficacy in removing non-target DNA molecules as opposed to targeted molecules. It was also observed that most of the molecules (61.35-69.49%) are "lost" during the essential hybridization step of the fishing protocol, suggesting its suitability for high copy number samples only. While the bait capture method may be useful in the study of polymerase chain reaction (PCR) inhibited DNA samples as previously suggested, it is necessary to carefully weigh this possible advantage against the degree of expected DNA loss and the non-selectivity of the method for targeted over non-targeted DNA.
authors.affiliation: Department of Anthropology, Washington State University, Pullman, WA 99164-4236, United States; School of Biological Sciences, Washington State University, Pullman, WA 99164-4910, United States.
authors.forename: Misa
authors.initials: M
authors.lastname: Winters
authors.affiliation: Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK 73019, United States.
authors.forename: Cara
authors.initials: C
authors.lastname: Monroe
authors.affiliation: Department of Biological and Health Sciences, Madonna University, Livonia, MI 48150, United States.
authors.forename: Jodi Lynn
authors.initials: JL
authors.lastname: Barta
authors.affiliation: Department of Anthropology, University of Oklahoma, Norman, OK 73019, United States. Electronic address: bmkemp@ou.edu.
authors.forename: Brian M
authors.initials: BM
authors.lastname: Kemp
mesh_terms: D004247:DNA / Q000302:isolation & purification*; D053836:DNA Degradation, Necrotic; D017931:DNA Primers; D006801:Humans; D008280:Magnetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction; D019809:Streptavidin / Q000737:chemistry
chemical_list: D017931:DNA Primers; D004247:DNA; D019809:Streptavidin
keywords: DNA capture; Degraded DNA; LCN DNA; qPCR