Date of Award

January 2016

Degree Type

Open Access Thesis

Document Type

Master Thesis

Degree Name

Master of Science (MS)



First Advisor

Jamie D. Fredericks

Department Affiliation


Second Advisor

Judith L. Jenkins

Department Affiliation


Third Advisor

David D. Cunningham

Department Affiliation



Analysis of polymorphisms in nucleic acid sequences provides the basis for identification of individuals and their genetic deficiencies. Currently, the accepted method of analysis for profiling is Short Tandem Repeat (STR) profiling. This is a lengthy process, typically taking up to 3 days. The time necessary to generate an STR profile, along with the ever-increasing reliance on DNA to solve crimes, has led to a large DNA sample backlog, with violent crime turnaround taking an average of 103 days. The time and resource investment required for STR analysis is significant, and not all samples generate useful profiles.

The current methods for use of STR technologies require an isolated template sample. This isolation typically requires hours of extractions and incubations, followed by still more time for analysis. The considerable length of time necessary for this process makes it inherently expensive, while also increasing the backlog. A universal protocol allowing amplification from various, frequently used samples would allow extremely rapid sampling and results. Further, these templates are faster and easier to amplify than standard STRs, which reduces the risk of resources and time on a sample which may not amplify.

Common forensic samples include blood, hair, saliva, and buccal swabs. Using a single, universal protocol to prepare these samples for analysis without extensive isolation allows the simultaneous preparation of multiple samples. Accordingly, this work explores the development of a preparatory method for multiple forensic samples coupled with the optimization of polymerase chain reaction conditions to facilitate the real-time monitoring of the interaction of molecular beacons (MBs) with the template. These MBs can then be used to identify the presence or absence of specific nucleotide polymorphisms. This increase in throughput has extensive application in forensic and medical applications.