DNA Fingerprinting Lesson Plan

DNA Analysis
DNA Analysis
Big Ideas
• The use of enzymes to cut DNA at specific patterns. ( Self-assembly. )
• Scientific procedures for "measuring" samples too small to be seen.
• Mechanisms of DNA replication in living cells and in the laboratory. ( Self-assembly. )
• Selection and amplification of specific sections of DNA for detailed analysis.
• The general mechanisms of RFLP, PCR, and STR DNA analysis techniques.
Additional Concepts
• 99.9% of all human DNA on the planet is identical - We are all much more alike than different.
• "DNA Fingerprinting" has nothing to do with fingerprints or even fingers.
• The power of exponential increase.
• The probability of multiple simultaneous events is much smaller than the probability of any
single event independent of the others.
• Mismatched DNA samples prove they came from different people, but matched samples only
have a VERY high probability of coming from the same person. The presence of someone's
DNA at a crime scene does not prove that they committed the crime or were ever even there.
Overview
Students will learn three important mechanisms used in the forensic analysis of DNA, and how selfassembly
plays an important role in those procedures. In particular they will learn about RFLP,
Restriction Fragment Length Polymorphism, in which enzymes are used to cut DNA into
measurable fragments, PCR, Polymerase Chain Reaction, responsible for DNA duplication in living
cells and used by scientists to selectively duplicate ( amplify ) selected sections of DNA, and STR,
Short Tandem Repeats, which is the primary method for DNA analysis used by forensic scientists
today. Along the way they will learn how self-assembly plays an important role in each of these
procedures, as well as some general information about the properties of DNA and scientific methods
and procedures.
Background Information
Human DNA contains about 3 billion base-pairs, 99.9% of which are identical among all humans on the
planet, and all of which are too small to be seen with even the most powerful microscopes. ( There are
microscopes that can see atomic-level details, but only for metals. ) So how can scientists compare the
DNA from two different samples when the material to be examined is both too small ( in physical size )
and too large ( in terms of number of base-pairs ) to be directly measured?
RFLP was one of the first DNA analysis tools developed and widely used. RFLP involves the use of
restriction enzymes to cut DNA into smaller fragments whose length can then be "measured" using
gel electrophoresis. ( see below. ) Restriction enzymes are naturally occurring biological molecules
that attach themselves onto DNA only at certain very specific sequences of nucleotides ( via selfassembly
), and cause the DNA strands to break at that point. Samples with different distributions of
fragment sizes definitely come from different individuals, and samples with identical distributions are
highly likely to come from the same individual. Unfortunately scientists have no control over the cut
points chosen by these naturally occurring enzymes, and so it is not always possible to distinguish
between two different individuals using RFLP analysis. ( There is a certain small probability chance
that two samples with matching RFLP patterns actually came from two different individuals. ) RFLP
analysis also takes up to a month to complete and requires a sample size at least as large as a quarter
to be effective.

DNA Analysis
Gel electrophoresis is a technique that scientists use to "measure" the size of DNA fragments. DNA
samples are first tagged with a dye, and then injected near one edge of an agarose gel. An electric
current is then applied, which pulls the DNA material through the gel. Smaller fragments travel farther
through the gel in a given time, which can then be detected thanks to the dye. A reference sample of
known material is always included, to set a scale for the results.
Figure 1 - Typical electrophoresis gel
Whenever a cell replicates itself, all of the contents of the cell must be duplicated, including the DNA
within the cell. The mechanism by which this happens starts with unwinding and then separating the
two strands of DNA from their initial double helix configuration. Each single strand then grows a
complementary mate through a polymerization reaction controlled by the biological chemical
polymerase. This polymerization reaction is termed the polymerase chain reaction, PCR. The
original strand serves as a template to ensure that only a specific matching strand of DNA gets created,
in an example of self-assembly.
Within the laboratory scientists can use the polymerase chain reaction in a slightly different form in
order to duplicate ( amplify ) a specifically chosen section of DNA for further analysis. First the DNA is
heated to completely unwind and separate the two strands. Then primers are added onto the DNA
strands in specific locations ( using self-assembly ) as starting points for the polymerization. Finally the
polymerase chain reaction is used to grow duplicate strands on each of the two original single strands.
This procedure is then repeated for 20 to 30 cycles, yielding millions to billions of copies through the
power of exponential increase. Careful selection of the original primers limits the duplication process to
only a short specific section of the original DNA. PCR can be applied to samples as small as a single
molecule, and even to degraded DNA that may have been broken down by time or harsh environments.
Short Tandem Repeats, STRs, are short sections of DNA which repeat themselves a certain number
of times. Where the repeat count differs among different individuals, it changes the length of the
encompassing DNA fragment, which can be isolated with PCR and analyzed with gel electrophoresis.
STR sections are frequently found within the 98% or so of "junk DNA" or "non-coding DNA" that does
not contain the codes for any known genetic traits. The probability of two random individuals having
identical STR counts at one particular DNA location ( loci ) is relatively large, but the chances of this
happening at thirteen different loci ( the number used in U.S. forensics ) are so vanishingly small as to
be nearly impossible. ( Identical twins, triplets, etc. have identical DNA, and the probability of
laboratory error is higher than the statistical probability of random DNA matching. )

DNA Analysis
Major Learning Goals
1. The student can explain the general mechanism of three important procedures in forensic DNA
analysis, and explain how self-assembly play a part in each one.
A. RFLP, cutting DNA into fragments with restriction enzymes.
B. PCR, selectively amplifying specific sections of DNA strands.
C. STR, analyzing fragment length differences due to variable numbers of short tandem
repeats.
2. The student can illustrate how DNA replication occurs in both a living cell and in the laboratory,
and can indicate which important steps involve self-assembly.
3. The student can explain how scientists "measure" the size of DNA fragments, which are both
too small ( in physical size ) and too large ( in numbers of base pairs ) to examine visually.
Secondary Learning Goals
1. The student understands that 99.9% of human DNA on the planet is identical.
2. The student understands the power of exponential growth ( amplification. )
3. The student learns that the chances of multiple events occurring simultaneously are much
smaller than the chances of each event happening independently.
4. The student understands that mismatching DNA results prove the samples came from two
different individuals, but that matching results only show an infinitesimally small chance that
they could have come from two different individuals, and that the presence of a suspect's DNA
at a crime scene does not prove that they committed the crime, or were ever even there.
Activities
Students will be presented with the information described above in a prepared PowerPoint
presentation. In addition, the students will participate in a number of interactive activities centered
about the motivating example of solving a crime mystery:
1. Visual examination of five strings of beads representing five samples of DNA. Students should
conclude that this would not be a practical method for analyzing DNA.
2. "Cutting" the DNA models into fragment lengths, using clothespins representing restriction
enzymes. At this point a visual examination should rule out one of the four suspects but be
unable to distinguish the other four DNA samples.
3. Simulating PCR amplification by duplicating a section of the DNA bead models into individual
bracelets. First one student makes a duplicate, then two students, then 4, 8, 16, etc to illustrate
the power of exponential growth. Each student gets to take their copy home as a souvenir.
4. Simulating STR analysis by very carefully measuring the lengths of DNA sections marked by
clothespins representing primers, and plotting their results on graph paper. Through this
analysis students can rule out all suspects except one, and solve the motivating crime.
References
1. http://en.wikipedia.org/wiki/Genetic_fingerprinting
2. http://en.wikipedia.org/wiki/Dna
3. http://en.wikipedia.org/wiki/Chromosome
4. http://en.wikipedia.org/wiki/Gene
5. http://workbench.concord.org/database/activities/260.html