Simulation of DNA Replication Using PCR
The enzyme that you will be using today in this simulation is Hae III, which slices the
DNA between the C and G in the sequence CCGG. This allows the DNA strand to be
observed in smaller portions instead of the extremely long strand.
As a forensic investigator, you will look at DNA left at a crime scene and determine
if it matches any of the suspects. The victim’s blood has already been ruled out as a
possibility.
Materials:
Scrap paper
Highlighter
Glue
Six simulated DNA samples from suspects
One simulated DNA sample from the crime scene
Procedure:
You have “DNA” samples from the six people who submitted blood samples and who are
suspected to be involved in a crime. You also have the “DNA” from the crime scene.
1.
2.
3.
4.
5.
Begin by making copies of the crime scene DNA using a PCR-like technique.
Cut out the crime scene DNA and tape the ends together to make one long strip.
Make a complementary strand by writing the appropriate base below the original.
Simulate the denaturing or “unzipping” of the DNA by cutting it into two long pieces.
Add the primer, AT, to begin the process and continue adding the complementary
base pairs until you have two new strands of DNA. Do this along both strips.
6. Repeat until you have eight copies of the original crime scene DNA. Label the back
of each strip.
7. Cut the strip of DNA for each person and tape the ends together so that you have one
long strip for each person.
8. Mark the position of the restriction enzyme recognition site with your pencil for each
suspect and the crime scene. Remember that Hae III cuts between the C and G of the
CCGG sequence only. Cut the strands at this point.
9. Now it’s time to run your fingerprints. Make a column for each person and the crime
scene. Place each person’s DNA fragments in order of size from top to bottom. The
longest pieces should be the closest to the top, and the shortest should be farthest
away. Try to equally space the fragments in six rows.
10. Glue or tape these fragments to the scrap paper.
11. In order to see the DNA, you must use a probe or marker to show where it is;
otherwise the DNA molecule will be invisible. The probe that you are using is a GTA
probe. Match the probe with its complementary strand on the DNA by coloring it
with a highlighter. (Don’t highlight GTA; highlight its complement!)
12. Repeat this for each person and the crime scene DNA.
13. Make a chart for the DNA fingerprint. Use six rows (numbered 1 through 6) and
seven columns (one per sample). Draw a line in each of the rows where you find a
marker. (it will look like a gel electrophoresis)
14. Can you tell if one of the suspects left the blood at the scene of the crime?
Sample Data Table:
Crime
Scene
Matt
Tommy
Cindy
Mike
Katie
Nathan
1
2
3
4
5
6
Questions
1.
What are the four steps of DNA fingerprinting?
2.
If everyone has A, T, G, and C as the base pairs for their DNA, then how is it different in each person?
3.
What is the complementary sequence for these probes:
 GTAAG

CCGTA
4.
What is the function of the probe?
5.
Which suspect left blood at the scene of the crime? How can you tell?
6.
After two cycles, how many copies of the original DNA do you have? After four cycles? After 10
cycles? After 20 cycles? Show your work.
7.
Extra Credit: Using the CCGTA probe, identify the complementary sequences on the DNA strands,
using a different color. What can you say about the probability of your suspect identification?
Matt:
AACTGTTGGCAGGCATTACCGGTTCACTGCTAGCCATGGTAATCCGGACTACGCTATACCGGATCA
CTATCCGGGCATATCCGGCAT
Tommy:
CGTAGGTCATTGCAATGACTTATCCGGTACCTAGCATTAATGTCCGGCATTCAGTTAGCCGGCAAC
TAGTCCGGCTTAGACCGGATA
Cindy:
GCTATTACATTCAATAGGTATGTCCGGCAGGTATCGCTCCGGTCGCTATACGTAATGACCGGATCA
GCTACCGGAGTAGCCGGCTC
Mike:
ATAGCGTTAGTTACCATATGTTACCGGATTAGCATTAATGGATCCGGTACTGATAGTACCGGTAGC
ATACCGGTCTACTCCGGCAT
Katie:
TTAGCAGGTATTCGGTAATGCTACCGGATCTATGTTCGATCAGCCGGTAGCTTAGATACCGGCATC
TAAGCCGGTGCATACCGGCAT
Nathan:
ATTGGGATAGCTATCGAGGTTAGCCGGCTAAGCTTACCATGATCCGGTAGCATATGATCCGGATCA
TATGCCGGTCATTACCGGTAA
DNA from the crime scene:
TACTGTAGGCAGGCATTGCCGGTACACCGCTAGCATTGGTTATCCGGACAACGCTATACCGGATCA
CTATCCGGGCATATCCGGCAT