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Abstract

Since law enforcement first used DNA evidence to solve crimes in 1985, DNA typing and the comparison of STR (Short Tandem Repeat) profiles have become the accepted gold standard in forensic science for identification. Although common DNA extraction methods such as phenol-chloroform extraction and silica binding matrices are often effective, a small percentage of samples fail to yield a profile. Some types of samples, for example bones or bloodstains on concrete, are particularly challenging due to environmental degradation of the DNA and high concentrations of PCR inhibitors relative to the amount of available DNA. This ultimately makes obtaining a DNA profile very difficult and sometimes impossible for this class of samples. This thesis introduces SCODA (Synchronous Coefficient of Drag Alteration) as a novel electrophoretic nucleic acid clean-up method for purifying trace amounts of DNA from PCR inhibited forensic samples. Unlike other extraction techniques that rely on the chemical properties of DNA, SCODA takes advantage of the physical properties unique to long and charged molecules such as nucleic acids to selectively concentrate them in an agarose gel matrix. SCODA was compared to other extraction and purification methods to determine the best method for obtaining DNA profiles from difficult forensic samples. Samples that were examined included bones, bloodstains on concrete and two actual forensic exhibits. DNA yield and PCR inhibition were assessed by quantitative PCR and STR analysis was conducted to ensure that profiles could be obtained. In summary, it has been found that SCODA is optimal for highly inhibited samples that mask the presence of DNA, as in some cases of bone, and that specific protocols can be designed to further improve SCODA to outperform other extraction methods, which are more difficult to customize.