Date of Award

1-2026

Access Control

Campus-Only Access

Degree Name

Master of Science (MS)

Department

Chemistry

Advisor

M. Scott Goodman

Department Home page

Forensic Science

First Reader

M. Scott Goodman

Second Reader

Sujit Suwal

Third Reader

Drew Barber

Abstract

Polymerase chain reaction (PCR) is a cornerstone technique in forensic DNA analysis, enabling the amplification of minute quantities of genetic material. The presence of PCR inhibitors can significantly compromise amplification efficiency and accuracy. This study investigates the inhibitory effects of coffee – a commonly encountered contaminant at crime scenes – on the PCR amplification of human DNA. Various concentrations of coffee were introduced into PCR reactions to evaluate their impact on DNA yield, purity, and amplification success. Quantitative and qualitative analyses were performed using spectrophotometry, agarose gel electrophoresis, capillary electrophoresis, and quantitative PCR (qPCR). The results indicate a concentration-dependent inhibition of PCR, with significant amplification failure observed at higher concentrations of coffee. Polyphenolic compounds such as chlorogenic acid and tannins were suspected as key contributors to PCR inhibition, likely through direct interaction with DNA polymerase or by binding to DNA, thereby reducing its accessibility. These findings highlight the importance of recognizing environmental inhibitors such as polyphenols in forensic casework and stress the need for effective DNA purification strategies to ensure accurate amplification.

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