What Makes a DNA Fingerprint Unique?
|Areas of Science||
|Time Required||Very Short (≤ 1 day)|
|Material Availability||Readily available|
|Cost||Very Low (under $20)|
AbstractDo you like solving mysteries? In this experiment, you can find out how a DNA fingerprint can help you figure out whodunit. The answer might just be in the "sequence" of events!
ObjectiveIn this experiment you will test if unique DNA sequences can create individual fingerprints that are also unique.
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Last edit date: 2020-01-12
All living things come with a set of instructions stored in their DNA, short for deoxyribonucleic acid. Whether you are a human, rat, tomato, or bacteria, each cell will have DNA inside of it. DNA is the blueprint for everything that happens inside the cell of an organism, and each cell has an entire copy of the same set of instructions. The entire set of instructions is called the genome and the information is stored in a code of nucleotides (A, T, C, and G) called bases. Figure 1 shows an example of a DNA sequence that is 12 base pairs long:
Figure 1. DNA Sequence.
Every individual has its own DNA code, but how can a code with only four letters be unique? It is hard to imagine how a code with so few parts can hold so much information. The key is that the longer the code is, the more unique sequences there can be. Table 1 is showing how many unique sequences are possible for a piece of DNA of a certain length in base pairs (bp):
|DNA Length (bp)||How Many Unique DNA Sequences are Possible?|
|1 bp||4 = 4|
|2 bp||4 × 4 = 16|
|3 bp||4 × 4 × 4 = 64|
|4 bp||4 × 4 × 4 × 4 = 256|
|5 bp||4 × 4 × 4 × 4 × 4 = 1,024|
|6 bp||4 × 4 × 4 × 4 × 4 × 4 = 4,096|
|7 bp||4 × 4 × 4 × 4 × 4 × 4 × 4 = 16,384|
|8 bp||4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 = 65,536|
|9 bp||4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 = 262,144|
|10 bp||4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 × 4 = 1,048,576|
For example, a two base pair long DNA sequence can be one of sixteen different sequences: AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, or GG. Longer sequences have even more possibilities. The 12 base pair sequence shown above is only one of 16,777,216 different DNA sequences that are possible for a piece of DNA that size! Considering that the entire human genome is 3 billion DNA bases long, the number of possible combinations is practically infinite. But the truth is, most of the DNA from person to person is the same. Because we are of the same species, our DNA is about 99.9% identical to each other. Even the DNA of a chimpanzee is 99% identical to our DNA.
With all of the similarities in the DNA sequences of humans, why does DNA fingerprinting still work? In this experiment you will investigate whether or not unique DNA sequences will generate unique DNA fingerprints. You will use an online random sequence generator to "make" pieces of DNA. Then you will use another online program to make a DNA fingerprint of each piece of randomly generated DNA. Will fingerprints with different DNA sequences look different or the same?
Terms and Concepts
To do this type of experiment you should know what the following terms mean. Have an adult help you search the Internet, or take you to your local library to find out more!
- DNA sequence
- Nucleotides (A, T, C, G)
- Base pairs
- Restriction enzyme
- DNA gel
- DNA fingerprinting
- What does a DNA sequence look like?
- What does a DNA fingerprint look like?
- What makes DNA fingerprints look unique? Is it the DNA sequence?
BibliographyHere are two great tutorials to learn about DNA fingerprinting and its applications:
- National Academy of Sciences. (2007). Putting DNA to Work - DNA and Criminal Justice - How DNA Determines Guilt or Innocence Marian Koshland Science Museum, National Academy of Sciences (NAS), Washington, D.C. Retrieved April 12, 2013 from https://koshland-science-museum.org/sites/all/exhibits/exhibitdna/crim01.jsp
- Cold Spring Harbor Laboratory. (2003). DNA Interactive: Applications. Dolan DNA Learning Center, Cold Spring Harbor Laboratory, NY. Retrieved March 6, 2007 from http://www.dnai.org/d/index.html
- Maduro, M. (n.d.) Random DNA Sequence Generator. Department of Biology, University of California, Riverside. Retrieved March 6, 2007 from http://www.faculty.ucr.edu/~mmaduro/random.htm
- UMass Medical School (2015). BioTools @ UMass Medical School. Retrieved October 8, 2015 from http://biotools.umassmed.edu/tacg4/
- Kimball, J. (2003). Restriction Enzymes. Andover, MA: Kimball's Biology Pages. Retrieved March 6, 2007 from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/RestrictionEnzymes.html
- Wikipedia contributors. (2013, April 3). Restriction enzyme. Wikipedia, The Free Encyclopedia. Retrieved April 12, 2013 from http://en.wikipedia.org/w/index.php?title=Restriction_enzyme&oldid=548484614
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Materials and Equipment
- A computer with Internet connection
- Java-based web browser
- Lab notebook and pencil
- The first step is to make a piece of DNA using the Random DNA Sequence Generator shown in Figure 2.
- Enter "1000" in the box for the Size of DNA in bp, and leave the setting for the GC content at 0.50 (which will give you half G+C and half A+T).
- Click the generate button and you will get a random piece of DNA shown in the text box:
A random DNA sequence generator hosted on ucr.edu. This generator allows you to set variables such as the number of base pairs and how often G and C will show up in the end result.
Figure 2. Screenshot of the Random DNA Sequence Generator tool.
- Print this page, cut it out, and paste it into your lab notebook for your records. Choose a name for this piece of DNA and write the name in your lab notebook ("Suspect #1" for example).
- Double-click in the text box to select your DNA sequence, then copy it to the clipboard by selecting "Edit" and then "Copy" from your file menu.
- The next step is to "Cut" your piece of DNA and run it through a gel matrix to make a fingerprint by using this Biotool site from UMass Medical School.
- The site has several sections. In the top section that says "Sequence Entry," shown in Figure 3, click inside the text box and paste your DNA sequence from the clipboard by selecting "Edit" and "Paste" from the file menu.
umassmed.edu hosts a TCAG restriction mapping program that creates a report based on DNA sequences that you upload or paste into the box.
Figure 3. Screenshot of the "Sequence Entry" section where you enter your generated DNA sequence.
- In the following section, "SubSequence Selection and Numbering Options" (Figure 4), leave all of the settings to the default settings.
SubSequence Selection and Numbering Options in the TCAG restriction mapping program. Default options are selected under Sequence should be analyzed from bases (end), and the sequence should be analyzed as (linear).
Figure 4. Screenshot of the "SubSequence Selection and Numbering Options." Leave all the settings as they are.
- Figure 5 shows the section titled "Restriction Enzyme Selection." You will use the right panel, "Select Explicitly," to select which enzymes you want the program to use for the digest. Check the box that says "Simulate multiple digestion" and then choose the following enzymes: BamHI, EcorI, HindIII, SmaI, SpeI, XbaI and XhoI. You can select multiple enzymes by keeping your control (Microsoft) or command (Mac) key pressed while clicking on the different enzymes. Once you have selected all enzymes, move to the next step.
Screenshot of the "Restriction Enzyme Selection" section. "Select Explicitly" selects which enzymes you want the program to use for the digest. "Simulate multiple digestion" will allow multiple enzymes to be selected including: BamHI, EcorI, HindIII, SmaI, SpeI, XbaI and XhoI. On this screen, you can also filter selections using a REBASE file.
Figure 5. Screenshot of the "Restriction Enzyme Selection" section where you select your desired enzymes.
- In the "Output Format" section (Figure 6), you do not need to make any changes. Leave all the default settings.
Screenshot of Output section with default values selected (Sort output by number of hits/names , and Show me errors from TACG).
Figure 6. Screenshot of the "Output Format" section. Leave all the settings as they are.
- In the "Analyses" section, which is shown in Figure 7, uncheck all boxes except the box for "Pseudo Gel Map." This one you do check. Keep the default settings for the cutoffs.
Screenshot of analysis section with "Pseudo Gel Map" selected, and a range of 100 to 1000 base pairs.
Figure 7. Screenshot of the "Analyses" section. Only check the "Pseudo Gel Map" box.
- Once you have done this, you click the "Submit Sequence to WWWtacg" button and you will get a page showing your piece of DNA after it has been "Cut" up by your selected restriction enzymes. This is called a DNA gel (this is the section of your output file that is called "Pseudo-Gel Map of Digestions"). Each line (called a "band") is a separate, small piece of cut-up DNA. The pieces of DNA are sorted by size from 100 to 1000 base pairs (bp), with bigger pieces on the right and smaller pieces on the left side. The output file will only show you the bands for enzymes that did cut the DNA (all the other enzymes should show only one uncut band at the 1000 bp mark because you generated a DNA piece that is 1000 base pairs (bp) in size). Figure 8 shows the DNA gel for a digested piece of random DNA generated. You can see that only the HindIII, the SmaI, and the XbaI enzyme cut the DNA because these columns have more than one band (fragment):
The pseudo gel map shows any restriction enzyme that did manage to cut the DNA, in this example the only successful enzymes were HindIII, SmaI, and XbaI. The lines in the middle of the graph are called bands and where they are on the graph determines how long the segment cut was in terms of base pairs.
Figure 8. Pseudo gel map.
- Print this page, cut it out, and paste it into your lab notebook for your records. Be sure you label the fingerprint with the name of your DNA (Suspect #1) and that you know the top from the bottom!
- Now you are ready to make a new "Suspect" DNA sequence.
- Repeat steps 1–13 with a new DNA sequence. Just go back to the Random DNA Sequence Generator and start over. This time name your DNA sequence something new (like "Suspect #2" for example).
- Repeat this experiment at least five different times. Each time you will make one new piece of "Suspect" DNA and make a new DNA fingerprint.
- Compare all of your sequences and fingerprints. Look at the pattern of bands. Do they match or are they different? Do unique sequences of DNA result in similar or different DNA fingerprints?
If you like this project, you might enjoy exploring these related careers:
- In this experiment, you are making a new, randomly generated sequence of DNA each time. In reality, our DNA changes very little from person to person. Can small changes in DNA sequences also result in unique DNA fingerprints? To test this, start with one piece of randomly generated DNA and make a fingerprint. Then, instead of making a new DNA sequence from scratch, only change a few nucleotides (letters) of the first sequence. For example, change the middle 10 letters to something new, but leave the rest of the sequence the same. What happens if you make these small changes in different places of the sequence?
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