DNA Fingerprinting

Short Tandem Repeats Each individual has unique DNA sequences making up about 1% of
their genome. Some of the unique sequences are called short tandem repeats. These are sets
of repeated, short sequences of bases that are tandemly arranged (one after the other) along the
length of a chromosome. For example, TTTTC or CGG could be a tandem repeat. The sequence
of nucleotides could then be repeated anywhere from 5 to 50 times. The number of short
tandem repeats differs from individual to individual.
TTTTCTTTTCTTTTCTTTTC

or

CGGCGGCGGCGGCGGCGG

Process PCR is used to amplify a region of a chromosome known to have tandem repeats.
Several regions are actually used. The size of PCR generated fragments differs among
individuals because the number of tandem repeats also differs among individuals. An individual
with only 5 repeats will generate short fragments while an individual with up to 50 repeats will
generate long fragments. The fragments are separated by gel electrophoresis and then
visualized using nucleic acid hybridization (Southern blotting).
Evaluating DNA Fingerprints Each individuals DNA is loaded in one well so that the bands in
the lane corresponding to that well are the fingerprint for that individual. In the example
below, Bob has 8 tandem repeats while Joe only has 2. When their DNA is amplified using PCR,
the fragments from Bob will be longer than those from Joe. When the DNA is run on a gel and
visualized with methylene blue, ethidium bromide, or nucleic acid hybridization, Bobs band of
longer fragments will migrate slower and thus be closer to the top of the gel than Joes.
Bob

Joe

The banding pattern is different for each individual. If only one area of tandem repeats
was tested then there would be a lot of similar DNA fingerprints. However several regions are
tested. If a least three regions are tested there would be a 1 in 1X10 18 chance of two people
having the same banding pattern (except for identical twins). 1X10 18 is far more than the
number of people on Earth

Crime Scene
Evaluate the following DNA fingerprint from a crime scene and answer the questions. (Actual
DNA fingerprint analysis contains more bands. This fingerprint is simplified for ease of use and
learning.)

Questions
1. Which suspects blood was found at the scene of the crime? (Compare the suspects
band pattern with blood found at the scene of the crime.)
2. Is the victims blood on the knife?
3. Who elses blood is on the knife?
4. What can be determined by the bands from blood on the knife?
5. Which suspect is guilty?
6. Can DNA fingerprinting be used to prove guilt? Explain.

Genetics and DNA Fingerprinting

Tandem repeats are inherited in a Mendelian fashion. Just as a gene can have different
alleles, the tandem repeats can have different numbers of times they are repeated. Each diploid
cell will have two tandem repeat patterns. Just as with genetic crosses the offspring inherit one
tandem repeat pattern from their father and one from their mother.
For example if a dad had a fingerprint consisting of bands of 800 and 400 base pairs, then
you could expect his offspring to have either the 800bp band (see child 1 and 3 in the figure) or
the 400 bp band (see child 2 and 4). The offspring would not get both bands because they will
only inherit one chromosome from the father (remember meiosis). If the mother had bands of
900 and 200 base pairs, then again the offspring would have one or the other band. The
offspring would have a band from the father and from the mother. Comparing offspring with
parents can demonstrate relatedness. The pictured gel is just a possible example, however
typical DNA fingerprints have many more bands and are much more complex, but they still show
this basic inheritance pattern.

Genetics and DNA Fingerprinting

Determine what possible tandem repeat patterns the offspring of this Dad and Mom could have.
Dad has repeat Q on one chromosome and repeat R on the other chromosome. The DNA
fragments from each chromosome could be generated using restriction enzymes as show with
the scissors or PCR. In either case many copies of the same two fragments for each parent
would be generated which would migrate at a specific speed through an agarose gel resulting in
a band each (see depiction of the gel electrophoreses below)
Dad

repeat
repeat

Q
R

Mom repeat
repeat

S
T

Treating each tandem repeat of the dad and mom like alleles in a genetic cross do the Punnett
square to show the possible combinations of tandem repeats the offspring could have. Child 1 is
done as an examplethey receive Q from dad and S from mom.
Mom Mom
S
T
Da
d
Q
Da
d
R

QS

Child
1

Child
2

Child
3

Child
4

On the gel below label the dads and the moms DNA bands (Q, R, S, and T) in the text boxes to
the left. Use the depicted length shown above. The longest fragments migrate the slowest, so
you can label the band that migrates the slowest with the letter designating the longest
fragment.
Based on the Punnett square, place the red bands on the DNA gel where the bands would be for
each possible offspring. Each square on the Punnett square is labeled child 1-4. The possible
offspring in square 1 becomes child 1 on the gel. Child 1 has been completed as an example.

Bands