DNA Fingerprinting: Catching Criminals
by Jessica Martell
Also crediting the following websites:
http://www.umbi.umd.edu/education-outreach/scitech/dnaexplorationstudentpacket.pdf
http://en.wikipedia.org/wiki/Genetic_fingerprinting
http://en.wikipedia.org/wiki/DNA
Goals:
 Students will reinforce their understanding of DNA.
 Students learn about DNA Fingerprinting.
 Students will work in groups to solve the mystery of the in class activity on
DNA Fingerprinting.
Background Information:
Provided by: http://en.wikipedia.org/wiki/DNA & http://en.wikipedia.org/wiki/Genetic_fingerprinting
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions
used in the development and functioning of all known living organisms and some viruses. The
main role of DNA molecules is the long-term storage of information. DNA is often
compared to a set of blueprints or a recipe, or a code, since it contains the instructions
needed to construct other components of cells, such as proteins and RNA molecules. The
DNA segments that carry this genetic information are called genes, but other DNA
sequences have structural purposes, or are involved in regulating the use of this genetic
information.
Chemically, DNA consists of two long polymers of simple units called nucleotides, with
backbones made of sugars and phosphate groups joined by ester bonds. These two strands
run in opposite directions to each other and are therefore anti-parallel. Attached to each
sugar is one of four types of molecules called bases. It is the sequence of these four
bases along the backbone that encodes information. This information is read using the
genetic code, which specifies the sequence of the amino acids within proteins. The code is
read by copying stretches of DNA into the related nucleic acid RNA, in a process called
transcription.
Within cells, DNA is organized into structures called chromosomes. These chromosomes
are duplicated before cells divide, in a process called DNA replication. Eukaryotic
organisms (animals, plants, fungi, and protists) store their DNA inside the cell nucleus,
while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the
chromosomes, chromatin proteins such as histones compact and organize DNA. These
compact structures guide the interactions between DNA and other proteins, helping
control which parts of the DNA are transcribed.
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Base pairing
Each type of base on one strand forms a bond with just one type of base on the other
strand. This is called complementary base pairing. Here, purines form hydrogen bonds to
pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two
nucleotides binding together across the double helix is called a base pair. As hydrogen
bonds are not covalent, they can be broken and rejoined relatively easily. The two strands
of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical
force or high temperature.[12] As a result of this complementarity, all the information in
the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in
DNA replication. Indeed, this reversible and specific interaction between complementary
base pairs is critical for all the functions of DNA in living organisms.[1]
The two types of base pairs form different numbers of hydrogen bonds, AT forming two
hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). DNA with high
GC-content is more stable than DNA with low GC-content, but contrary to popular belief,
this is not due to the extra hydrogen bond of a GC base pair but rather the contribution
of stacking interactions (hydrogen bonding merely provides specificity of the pairing, not
stability).[13] As a result, it is both the percentage of GC base pairs and the overall length
of a DNA double helix that determine the strength of the association between the two
strands of DNA. Long DNA helices with a high GC content have stronger-interacting
strands, while short helices with high AT content have weaker-interacting strands.[14] In
biology, parts of the DNA double helix that need to separate easily, such as the TATAAT
Pribnow box in some promoters tend to have a high AT content, making the strands easier
to pull apart.[15] In the laboratory, the strength of this interaction can be measured by
finding the temperature required to break the hydrogen bonds, their melting temperature
(also called Tm value). When all the base pairs in a DNA double helix melt, the strands
separate and exist in solution as two entirely independent molecules. These singlestranded DNA molecules have no single common shape, but some conformations are more
stable than others.[16]
DNA profiling (also called DNA testing, DNA typing, or genetic fingerprinting) is a
technique employed by forensic scientists to assist in the identification of individuals on
the basis of their respective DNA profiles.
Although 99.9% of human DNA sequences are the same in every person, enough of the
DNA is different to distinguish one individual from another. DNA profiling uses repetitive
("repeat") sequences that vary a lot, called variable number tande repeats (VNTR). VNTRs
loci are very similar between closely related humans, but so variable that unrelated
individuals are extremely unlikely to have the same VNTRs.
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The DNA profiling technique was first reported in 1985 by Sir Alec Jeffreys at the
University of Leicester in England,[1] and is now the basis of several national DNA
databases.
DNA profiling process
Genetics with the extraction of an individual's DNA (typically called a "reference sample").
The most desirable method of collecting a reference sample is the use of a buccal swab, as
this reduces the possibility of contamination. When this is not available (eg because a
court order may be needed and not obtainable) other methods may need to be used to
collect a sample of blood, saliva, semen, or other appropriate fluid or tissue from personal
items (e.g. toothbrush, razor, etc) or from stored samples (e.g. banked sperm or biopsy
tissue). Samples obtained from blood relatives (biological relative) can provide an
indication of an individual's profile, as could human remains which had been previously
profiled.
A reference sample is then analyzed to create the individual's DNA profile using one of a
number of techniques, discussed below. The DNA profile is then compared against another
sample to determine whether there is a genetic match.
RFLP analysis
The first methods for finding out genetics used for DNA profiling involved restriction
enzyme digestion, followed by Southern blot analysis. Although polymorphisms can exist in
the restriction enzyme cleavage sites, more commonly the enzymes and DNA probes were
used to analyze VNTR loci. However, the Southern blot technique is laborious, and requires
large amounts of undegraded sample DNA. Also, Karl Brown's original technique looked at
many minisatellite loci at the same time, increasing the observed variability, but making it
hard to discern individual alleles (and thereby precluding parental testing). These early
techniques have been supplanted by PCR-based assays.
PCR analysis
With the invention of the polymerase chain reaction (PCR) technique, DNA profiling took
huge strides forward in both discriminating power and the ability to recover information
from very small (or degraded) starting samples. PCR greatly amplifies the amounts of a
specific region of DNA, using oligo nucleotide primers and a thermostable DNA polymerase.
Early assays such as the HLA-DQ alpha reverse dot blot strips grew to be very popular
due to their ease of use, and the speed with which a result could be obtained. However
they were not as discriminating as RFLP. It was also difficult to determine a DNA profile
for mixed samples, such as a vaginal swab from a sexual assault victim.
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Fortunately, the PCR method is readily adaptable for analyzing VNTR loci. In the United
States the FBI has standardized a set of 13 VNTR assays for DNA typing, and has
organized the CODIS database for forensic identification in criminal cases. Similar assays
and databases have been set up in other countries. Also, commercial kits are available that
analyze single nucleotide polymorphisms (SNPs). These kits use PCR to amplify specific
regions with known variations and hybridize them to probes anchored on cards, which
results in a colored spot corresponding to the particular sequence variation.
STR analysis
The method of DNA profiling used today is based on PCR and uses short tandem repeats
(STR). This method uses highly polymorphic regions that have short repeated sequences of
DNA (the most common is 4 bases repeated, but there are other lengths in use, including 3
and 5 bases). Because different unrelated people have different numbers of repeat units,
these regions of DNA can be used to discriminate between unrelated individuals. These
STR loci (locations) are targeted with sequence-specific primers and are amplified using
PCR. The DNA fragments that result are then separated and detected using
electrophoresis. There are two common methods of separation and detection, capillary
electrophoresis (CE) and gel electrophoresis.
The polymorphisms displayed at each STR region are by themselves very common, typically
each polymorphism will be shared by around 5 - 20% of individuals. When looking at
multiple loci, it is the unique combination of these polymorphisms to an individual that
makes this method discriminating as an identification tool. The more STR regions that are
tested in an individual the more discriminating the test becomes.
From country to country, different STR-based DNA-profiling systems are in use. In North
America systems which amplify the CODIS 13 core loci are almost universal, while in the
UK the SGM+ system, which is compatible with The National DNA Database in use.
Whichever system is used, many of the STR regions under test are the same. These DNAprofiling systems are based around multiplex reactions, whereby many STR regions will be
under test at the same time.
Capillary electrophoresis works by electro kinetically (movement through the application of
an electric field) injecting the DNA fragments into a thin glass tube (the capillary) filled
with polymer. The DNA is pulled through the tube by the application of an electric field,
separating the fragments such that the smaller fragments travel faster through the
capillary. The fragments are then detected using fluorescent dyes that were attached to
the primers used in PCR. This allows multiple fragments to be amplified and run
simultaneously, a procedure known as multiplexing. Sizes are assigned using labeled DNA
size standards that are added to each sample, and the number of repeats are determined
by comparing the size to an allelic ladder, a sample that contains all of the common
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possible repeat sizes. Although this method is expensive, larger capacity machines with
higher throughput are being used to lower the cost/sample and reduce backlogs that exist
in many government crime facilities.
Gel electrophoresis acts using similar principles as CE, but instead of using a capillary, a
large polyacrylamide gel is used to separate the DNA fragments. An electric field is
applied, as in CE, but instead of running all of the samples by a detector, the smallest
fragments are run close to the bottom of the gel and the entire gel is scanned into a
computer. This produces an image showing all of the bands corresponding to different
repeat sizes and the allelic ladder. This approach does not require the use of size
standards, since the allelic ladder is run alongside the samples and serves this purpose.
Visualization can either be through the use of fluorescently tagged dyes in the primers or
by silver staining the gel prior to scanning. Although it is cost-effective and can be rather
high throughput, silver staining kits for STRs are being discontinued. In addition, many
labs are phasing out gels in favor of CE as the cost of machines becomes more manageable.
The true power of STR analysis is in its statistical power of discrimination. In the US,
there are 13 core loci (DNA locations) that are currently used for discrimination in CODIS.
Because these loci are independently assorted (having a certain number of repeats at one
locus doesn't change the likelihood of having any number of repeats at any other locus),
the product rule for probabilities can be applied. This means that if someone has the DNA
type of ABC, where the three loci were independent, we can say that the probability of
having that DNA type is the probability of having type A times the probability of having
type B times the probability of having type C. This has resulted in the ability to generate
match probabilities of 1 in a quintillion (1 with 18 zeros after it) or more. However, since
there are about 12 million monozygotic twins on Earth, that theoretical probability is
useless. For example, the actual probability that 2 random persons have the same DNA is
only 1 in 3 trillion.
DNA data bases
There are now several DNA databases in existence around the world. Some are private,
but most of the largest databases are government controlled. The United States maintains
the largest DNA database, with the Combined DNA Index System, holding over 5 million
records as of 2007[2]. The United Kingdom maintains the National DNA Database
(NDNAD), which is of similar size. The size of this database, and its rate of growth, is
giving concern to civil liberties groups in the UK, where police have wide-ranging powers to
take samples and retain them even in the event of acquittal.[3]
The U.S. Patriot Act of the United States provides a means for the U.S. government to
get DNA samples from other countries if they are either a division of, or head office of, a
company operating in the U.S. Under the act, the American offices of the company can't
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divulge to their subsidiaries/offices in other countries the reasons that these DNA
samples are sought or by whom.
When a match is made from a National DNA Databank to link a crime scene to an offender
who has provided a DNA Sample to a databank that link is often referred to as a cold hit.
A cold hit is of value in referring the police agency to a specific suspect but is of less
evidential value than a DNA match made from outside the DNA Databank.[4].
Evidence of genetic relationship
It's also possible to use DNA profiling as evidence of genetic relationship, but testing that
shows no relationship isn't absolutely certain. While almost all individuals have a single and
distinct set of genes, rare individuals, known as "chimeras", have at least two different
sets of genes. There have been several cases of DNA profiling that falsely "proved" that a
mother was unrelated to her children.[7]
Benchmark(s) Addressed:
Grade 6:
 6.1 Structure and Function: Living and non-living systems are organized
groups of related parts that function together and have characteristic
properties.
 6.1. LS.1. Describe the function and relative complexity of cells, tissues,
organs, and organ systems in organisms and explain that different body
tissues and organs are made up of different kinds of cells. Explain that the
way in which cells function is similar in all living organisms and compare and
contrast the types and components of cells.
 6.2 Interaction and Change: The related parts within a system interact and
change.
 6.2. LS.1 Describe the interactions between and among cells, tissues, organs
and organ systems.
 6.3 Scientific Inquiry: Scientific inquiry is the investigation of the natural
world based on observation and prior science knowledge. The investigation
includes proposing hypotheses, developing the procedures for questioning,
collecting, analyzing, and interpreting accurate and relevant data to produce
justifiable evidence-based explanations.
 6.3.1. Based on observation, and scientific concepts and knowledge, propose
hypotheses that can be examined through scientific investigation. Design
and conduct an investigation that uses appropriate tools and techniques to
collect relevant data.
 6.3.2 Organize and display relevant data, construct an evidence-based
explanation of the results of an investigation, and communicate the
conclusions.
6
 6.3.3 Explain why if more than one variable changes at the same time in an
investigation, the outcome of the investigation may not be clearly
attributable to any one variable.
Grade 7:
 7.1 Structure and Function: Living and non-living systems are composed of
component parts which are responsible for the defining characteristics and
traits of the system.
 7.1. LS.2 Distinguish between inherited and learned traits, explain how
inherited traits are passed from generation to generation, and describe the
relationships among phenotype, genotype, chromosomes, and genes.
 7.3 Scientific Inquiry: Scientific inquiry is the investigation of the natural
world based on observation and prior science knowledge. The investigation
includes proposing hypotheses, designing the procedures for questioning,
collecting, analyzing, and interpreting multiple forms of accurate and
relevant data to produce justifiable evidence-based explanations.
 7.3.1. Based on observations, and scientific concepts and knowledge, propose
hypotheses that can be examined through scientific investigation. Design
and conduct a scientific investigation that uses appropriate tools and
techniques to collect relevant data.
 7.3.2 Organize, display, and analyze relevant data, construct an evidencebased explanation of the results of an investigation, and communicate the
conclusions including possible sources of error.
 7.3.3 Evaluate the validity of claims, based on the amount and quality of the
evidence cited.
Grade 8:
 8.1 Structure and Function: Systems function through interactions of
component parts via mechanisms with various levels of complexity.
 8.1. LS.1 Explain how organisms from both the past and the present are
classified based on their genetics and their internal and external structures.
Describe how scientists use classification systems to show relationships
among organisms.
 8.2. LS.3 Explain how organelles within a cell perform cellular processes and
how cells obtain the raw materials for those processes.
 8.3 Scientific Inquiry: Scientific inquiry is the investigation of the natural
world through observations and prior science knowledge. The investigation
includes proposing hypotheses, designing procedures for questioning,
collecting, analyzing, and interpreting multiple forms of accurate and
relevant data to produce justifiable evidence-based explanations and new
explorations.
 8.3.1. Based on observations, and scientific concepts and knowledge, propose
hypotheses that can be examined through scientific investigation. Design
and conduct a scientific investigation that uses appropriate tools,
7
techniques, independent and dependent variables and controls to collect
relevant data.
 8.3.2 Organize, display, and analyze relevant data, construct an evidencebased explanation of the results of a scientific investigation, and
communicate the conclusions including possible sources of error. Suggest
new investigations based on analysis of results.
 8.3.3 Explain how scientific explanations and theories evolve as new
information becomes available.
Materials and Costs:
List the supplies and equipment needed for initial set up.
 PowerPoint program, computer and projector .........................................$ 0
(Available through school district)
 Scissor ($1..69 pack of 2 x 15) .................................................................... $25.35
 Copy of the “Final Report” per student .....................................................$ 0
(School copier)
 Copy of the ”DNA Evidence Evaluation” per group ................................$ 0
(School copier)
Estimated total, one-time, start-up cost ........................................................ $25.35
List the consumable supplies and estimated cost for presenting to a class of 30
students
 Copy of the “Final Report” per student ....................................................... $0
(School copier)
 Copy of the ”DNA Evidence Evaluation” per group .................................. $0
(School copier)
Estimated total cost each year ............................................................................. $0
Time:
Initial prep time: 60-120 minutes
Preparation time: 20 minutes
Instruction time: 60 minutes for presentation, 60-90 minutes for activity
Clean-up time: 15 minutes
Assessment:
 Each student should have filled out their own “Final Report.” Have every
student turn this in for you to evaluate their understanding.
 Have a class discussion about the activity once it is over, so students can not
only share their views, but you can asses the class overall on their
understanding of the material that was presented.
 The older the student the more detail you can require:
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 Have each student write a reflection page(s) about what they learned
from this lesson/activity. (What you require could be dependant on age.)
 EX: 6th grade… general overview with a few key points.
 EX: 7th grade… “…” with more key points and what they learned and
found interesting in this lab activity.
 EX: 8th grade… “…” and now have the students write about how this
is relevant in the real world.
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CITY POLICE DEPARTMENT
FINAL REPORT
Identify the members of your Forensic Team:
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Were there any suspects’ DNA found at the crime scene? If so, who?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
After processing the evidence, explain how your group made their conclusion.
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
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DNA EVIDENCE EVALUATION
WORK ONLY ON YOUR DNA SAMPLE
1. Each team member should have one DNA sequence strip. Use your scissors
(restriction enzymes) to cut your DNA samples only where you see this base pattern:
Cut between the
C and G as
CUT
CUT
shown in this
TACC l GGTAATTCATCC l GGTCAATTCTAGCGTAC
CCGG
ATGG
l
CCATTAAGTAGG
l
CCAGTTAAGATCGCATG
GGCC
example:
TACC
ATGG
GGTAATTCATCC
CCATTAAGTAGG
GGTCAATTCTAGCGTAC
CCAGTTAAGATCGCATG
Keep all the DNA fragments you cut from one sample together.
Do not mix up with other sample fragments.
2. Count the number of base pairs (bp) in each fragment of DNA that you have cut.
A base pair consists of two complementary bases.
3. Record the number of base pairs in each piece on the backside of the DNA
fragment.
1 2 3 4 5 6 7 8 9 10 11 12
GCTAATTCATCC
CGATTAAGTAGG
Base side
12 base pairs
Backside
4. Tape your DNA sequences on the chart according to the number of base pairs.
5. Be sure to put all the fragments from your sample in the proper column.
6. Analyze the DNA fragments.
7. Look at the number of fragments and sizes for all suspect and crime scene samples.
8. Are there any suspects that match the crime scene DNA?
9. Begin to fill out the Final Report sheet with your conclusions.
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Crime DNA
SUSPECT 1
SUSPECT 2
SUSPECT 3
SUSPECT 4
12 bp
# of Base
Pairs (bp)
34
33
32
31
30
29
28
27
26
27
25
24
23
22
21
20
19
18
17
16
15
14
13
12
11
10
9
8
7
6
5
4
3
2
1
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Crime DNA Crime DNA Crime DNA Crime DNA Crime DNA Crime DNA
GTCGACCGGTGACCGTGCGTACACAGTGCTCCGGATAGCTGATAGCTCCGGTG
CAGCTGGCCACTGGCACGCATGTGTCACGAGGCCTATCGACTATCGAGGCCAC
Suspect 1 DNA Suspect 1 DNA Suspect 1 DNA Suspect 1 DNA Suspect
GTCCCAGCCGGACCGTACCGGTAGATCAGCCGGTAGATTGATAGCGTGATGTG
CAGGGTCGGCCTGGCATGGCCATCTAGTCGGCCATCTAACTATCGCACTACAC
Suspect 2 DNA Suspect 2 DNA Suspect 2 DNA Suspect 2 DNA Suspect
GTCTACGTAATCGTAGCCATCCGGACAGTGTGCACGATCGTACATGCTACGTG
CAGATGCATTAGCATCGGTAGGCCTGTCACACGTGCTAGCATGTACGATGCAC
Suspect 3 DNA Suspect 3 DNA Suspect 3 DNA Suspect 3 DNA Suspect
GTCGACCGGTGACCGTGCGTACACAGTGCTCCGGATAGCTGATAGCTCCGGTG
CAGCTGGCCACTGGCACGCATGTGTCACGAGGCCTATCGACTATCGAGGCCAC
Suspect 4 DNA Suspect 4 DNA Suspect 4 DNA Suspect 4 DNA Suspect
GTCTCCATCCGGACTACCATACATCTGGTGTACCCGGTGATATCGTCCGGGTG
CAGAGGTAGGCCTGATGGTATGTAGACCACATGGGCCACTATAGCAGGCCCAC
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