Who are you? - Using DNA Profiling in Crime Scene Investigation

Introduction
a. Background- DNA profiling has many applications. Restriction Fragment Length Polymophism (RFLP) is a process of DNA profiling that provides a unique banding pattern based on the restriction sites present in an individuals DNA sequence. They do so by comparing band patterns produced by restriction enzyme cleavage of DNA samples when separated on an agarose gel and is compared to the patterns of potential suspects. Scientists do so by using restriction enzymes, which make cuts at specific sequence of base pairs that is recognizes within the phage DNA, and cut at that site. Bacteria protect their own restriction sites by adding a methyl group. The restriction enzyme sits on a DNA molecule and slides along the helix until it recognizes specific sequences of base pairs that signal the enzyme to stop sliding and cut the DNA molecule at that site. There are more than one restriction site on a DNA molecule and when the restriction enzyme cuts at both of those sites, the result is fragments of different lengths. DNA that has been cut with restriction enzymes can be separated using agarose gel electrophoresis, meaning a current is run through a loaded agarose gel slab. DNA is negatively charged so they are drawn towards the positive pole, so smaller DNA fragments can move through the gel more easily than the larger base pairs. This travel expresses the banding patten in the gel. DNA contains a specific nucleotide sequence, and a radioactive complementary DNA probe can be made that will recognize and bind to that sequence. These probes are used to locate, identify, and compare DNA of different individuals. It is the radioactive tag that allows for the banding pattern to be expressed. Restriction enzymes  are the "chemical scissors" that recognize a particular recognition sequence on DNA, and cut DNA at that point. Two commonly used enzymes are EcoRI and Pstl. Enzymes function best under specific buffer and temperature conditions. In order to make DNA visible, a bluish loading dye is added to the DNA samples. The loading dye does not stain DNA but makes it easier to load the samples and to monitor the progress of the DNA electrophoresis. Bromophenol blue, the "faster" dye, comigrates with DNA fragments 500 bp in a 1% agarose gel, while the xylene cyanol, the "slower" dye, comigrates with DNA fragments 4000 bp in a 1% agarose gel. When the gel is immersed in Fast Blast DNA stain, the stain molecules attract to the DNA trapped in the agarose gel. Two major factors affecting the reliability of DNA fingerprinting are population genetics and genetic statistics. Some segments will show more variation than others.
b. Purpose- DNA typing is used every day to show the relatedness or identity of individual humans, plants, or animals. It is used in industries such as forensics, anthropology, and conservation biology to determine relatedness and to determine teh identity of individuals. It has been used to free innocent suspects in crimes, used in food identification, the reunification of family members and in paternity tests, as well as in identifying human remains. In this particular situation, DNA typing is being used to test and match a suspect to a sample from a crime scene.
c. Summary- In this lab, we will be using restriction enzymes from bacteria to cut DNA at palindromes. It will cut in a specific, staggered way so that sticky ends are created to bind to DNA with an exact shape match. The DNA differences are fragments of different lengths  and then we pipet the DNA into wells in agarose gel. An electric current is run through the gel and the negatively charged DNA is attracted towards the positive end of the gel. It is easier for smaller pieces of DNA to move to the positive end quickly and each DNA sample will provide a specific banding pattern, created by its movement towards the positive end of the gel. We will compare the banding pattern of the crime scene sample to samples of potential suspects in order to narrow the suspects down to one criminal.
d. Hypothesis- I hypothesize that we will be able to match the sample from the crime scene to one of the suspects in order to catch the criminal.
Procedure
On Day One, we first placed the restriction enzyme on ice. We then put 10 micro liters of each DNA sample from the stock tubes and transferred it to the test tubes corresponding with each suspect. We then added 10 micro liters of the enzyme mix into each of the suspect tubes. We then placed the tubes in the centrifuge to mix and collect all the liquid in the bottom of the tube. We then placed the tubes in a water bath of 37 degrees Celsius overnight. The following day, we removed the DNA samples from the refrigerator and centrifuged the tubes again. We then added 5 micro liters of loading dye into each of the tubes and centrifuged it. We then loaded 20 micro liters of the crime scene sample and suspect samples into their respective lanes in the agarose gel. We put the lid on the electrophoresis chamber and turned on the power and ran our samples at 100 V for 3 minutes. When the electrophoresis was complete, we turned off the power and removed the top of the chamber. We then removed the gel and tray and added 120 ml of the 1x Fast Blast DNA stain to the staining tray. we let the gels stain overnight. We then poured out the stain and recorded our results.
Discussion
After examining our results, we determined that the suspect sample in lane 3 turned out to match the sample taken from the crime scene. The banding pattern of sample 3 matched the pattern of the sample from the crime scene. As it turns out, the criminal of the crime was our own lab partner Chloe. There were possible sources of error that could have changed the results of this lab. One possible source of error could have been caused by not using clean pipets when adding the enzyme mix to the samples. It the pipets were not uncontaminated, they could mix the various samples and change the results.