Refining a DNA Fingerprinting Procedure
Sarah Beckman1, Bethanny Smith-Packard1, Dr. Jim Peploski2,
Dr. Matt Skeels3
Department of Bio-Molecular Science, Clarkson University
Forensics is the use of science and technology to investigate and establish facts in criminal or
civil courts of law. In the freshman forensics lab, this is exactly what students are trying to do, with the
help of DNA fingerprinting. The current project focuses on refining a procedure that can be used to
introduce first year students in forensic chemistry to the basic principles of DNA fingerprinting. The
previous procedure yielded little to no results in past years.
DNA fingerprinting is a form of identification based on sequencing specific non-coding portions
of DNA that are know to have a high degree of variability from person to person. These sections are
known as variable number tandem repeats, or VNTRs. The reason they have such variability is that when
the DNA is replicated in the early stages of development, there are often small mutations in these areas
that cause tandem repeats of the same section of DNA. Thus it is possible to use these areas of the DNA
as individual, specific markers or “fingerprints” based on the length of the VNTRs.
Denature
Anneal
Figure 1. The PCR Process
Extend
There are three steps in the DNA fingerprinting process. The first step is to isolate the DNA from
cells; in the case of this research either check cells, hair follicles, or blood cells. The next step is PCR,
Polymerase Chain Reaction. In this cycle, DNA is denatured, annealed and elongated. The last step is
electrophoresis where DNA is “run” on an agarose gel and separated according to the length of the
VNTRs. By looking at the number and size of the bands on the gel, it is possible to compare the suspect’s
DNA to the DNA from the crime scene.
Two DNA fingerprinting regions are under consideration for use in freshman forensic chemistry.
The first is APOC2 which is a gene located on the long arm of chromosome 19 that codes for
Apolipoprotein C2 and is involved in cholesterol transport in the blood. The VNTR of this region is two
base pairs long and is located in the third intron of the APOC2 gene. (An intron is a non-coding portion
of the gene.) There are eleven different possible alleles for this region and the longest VNTR is 30
dinucleotides long.
The second region is D1S80, which is located on the short arm of chromosome 1 and is not part
of any gene. This VNTR is sixteen nucleotides long and there are 28 possible alleles for this region. The
longest VNTR is 41 repeated units in length.
Initial attempts to fingerprint using the APOC2 region have been unsuccessful. Variation in
sample preparation and DNA source has failed to produce results. Precipitation of DNA by the addition
of isopropanol indicated that cell lysis was occurring properly. Problems must therefore reside in the PCR
amplification process. Unless better results are obtained, focus will be shifted to the D1S80 region.
References:
Campbell, Malcolm A., Diane Padula, Steve Sundby, and John Williamson; Use PCR & a Single Hair to
Produce a “DNA Fingerprint” The American Biology Teacher, Volume 59, NO. 3, March 1997.
Federation of American Societies for Experimental Biology. Federation of American Societies for
Experimental Biology. 15 July 2003 <http://www.faseb.org/opar/pcr.gif>.
Inman, Keith, and Norah Rudin. An Introduction to Forensic DNA Analysis. New York: CRC P LLC,
1997. 59-85.
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Class of 2007, Bio-Molecular Science, Clarkson University Honors Program, Oral Presentation
Assistant Professor of Chemistry, Clarkson University
Visiting Assistant Professor of Chemistry, Clarkson University