Download Lab 8 DNA Fingerprinting

ONLINE LAB #8
BIO 101
PROF. SHIN
(adapted from HHMI Biointeractive: www.biointeractive.org)
Introduction:
DNA fingerprinting is a technique that is currently used to identify sources of DNA in a number
of contexts. Forensic scientists use this technique to identify the source of DNA at crime and
disaster scenes. DNA fingerprinting is also used in paternity cases as a means of definitively
identifying the father of a newborn child. Scientists also use DNA fingerprinting to determine
the degree of relatedness between different species in evolutionary studies. The uses for DNA
fingerprinting are widespread.
In this week’s lab, we will be utilizing a particular form of DNA fingerprinting, called STR analysis
in order to solve a crime!
Background:
While most of the genome is identical among individuals of the same species, differences do
exist. DNA profiling takes advantage of these differences. Variations occur throughout the
genome, and in particular, in regions of noncoding DNA, which is DNA that is not transcribed
and translated into a protein. Variations in noncoding regions are less likely to affect an
individual’s phenotype, and therefore changes in these regions are less likely to be eliminated
by natural selection. DNA profiling uses a category of DNA variations called short tandem
repeats. STRs are comprised of units of bases, typically two to five bases long, that repeat
multiple times. The repeat units are found at different locations, or loci, throughout the
genome. Every STR has multiple alleles, or variants, each defined by the number of repeat units
present or by the length of the sequence. They are surrounded by nonvariable segments of
DNA known as flanking regions. For example, the STR allele in Figure 1 could be designated as
“6” because the repeat unit (GATA) repeats six times, or as 70 bp (where bp stands for base
pairs) because it is 70 bp in length, including the flanking regions. A different allele of this same
STR would have a different number of GATA repeat units but the same flanking regions.
Flanking regions are important because knowing their sequences enables geneticists to isolate
the STR using polymerase chain reaction, or PCR, amplification.
Figure 1. Each one of the rectangles above represents a repeat unit. In this example, the STR is comprised of six
repeats of the four-base unit GATA. On either side of the STR is a flanking region of DNA. If you were to write out
the STR sequence in Figure 1, it would be GATAGATAGATAGATAGATAGATA. For STRs with many repeat units,
writing out the sequence can get very unwieldy, so geneticists use shorthand. The repeat unit is placed in brackets
with a subscript indicating the number of times it repeats. The shorthand for the STR in the example above would
be [GATA]6.
The difference STRs will differ slightly in length. These differences can be resolved using a
technique called gel electrophoresis. In this process, a sample containing mixed fragment sizes
of DNA is forced through a gel matrix that contains numerous molecular-sized pores. The gel
matrix is made from an extract from algae called agarose. Once DNA is loaded onto a gel, the
DNA must be forced to move. This is accomplished by the application of an electrical current to
the DNA. DNA, which is negatively charged (remember the negatively charged phosphate
groups on the nucleotides?), will move toward the positive node of the electrophoresis
chamber and away from the negative node of the electrophoresis chamber.
Once a mixture of differently sized DNA fragments begins moving through a gel matrix, the
smaller fragments travel more easily than the larger fragments through the pores of the gel.
This results in the smaller fragments moving faster than the larger ones, and separation of
these fragments is accomplished.
A quick video showing the process of gel electrophoresis can be found here.
Because individuals are so unique genetically, scientists are able to utilize the differences in our
DNA to create unique profiles, or DNA fingerprints. They can use these DNA fingerprints to
match crime scene samples with the individuals that left them!
Exercise:
(1) Download the student worksheet.
(2) Use the following link to launch the HHMI Biointeractive Exercise: CSI Wildlife.
https://media.hhmi.org/biointeractive/click/elephants/dna/
(3) Solve the crime!