NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 1 of 7 Kelly Tommasino
UNIT 5: DNA isolation and fingerprinting
Unit Plan: DNA isolation and fingerprinting
Concepts: DNA is the universal method of continuity. DNA is able to be isolated, amplified, and analyzed
for numerous purposes (criminals, crops, etc.). Restriction enzymes are used to cut DNA during gel
electrophoresis.
Scientific Inquiry
ƒ Use of experimental controls
ƒ Interpretation of experimental results
ƒ Use of DNA evidence in court
ƒ Creation and use of standard curves
Genetics
ƒ Restriction fragment length polymorphisms (RFLP analysis)
ƒ Genetic engineering techniques
ƒ Mendelian inheritance
ƒ
Time Frame: The unit will take approximately 8 days total (50 min class periods). It will be broken
up into three segments. First the students will demonstrate safe procedures using the gel
electrophoresis equipment. The second part will be isolating DNA from the strawberry, and the final
section will be to apply their prior knowledge and run a DNA electrophoresis gel to identify the
“suspect”
ƒ
Prior knowledge: The students will have learned about DNA’s structure complete with the history
of finding the structure of the DNA strand, and current technological advances dealing with DNA.
The students will also be able to synthesize the replication of a complimentary strand of DNA with a
parental strand. The students will have researched some famous cases of DNA fingerprinting, and
how it is used in identifying suspects. At the beginning of this unit, the class will discuss restriction
enzymes and how they work.
Unit Overview:
Lesson 1: The students will demonstrate correct usage of electrophoresis equipment
Lesson 2: The students will isolate DNA from a strawberry and analyze lengths of the
samples
Lesson 3: The students will conduct a DNA fingerprinting lab and construct an argument
to support or reject the identification of a possible suspect
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 2 of 7 Lesson 1: 1st activity of the unit:
Time required: ~two 50 minute periods
Prior Knowledge: The structure of the DNA molecule, specifically it is a negatively charged molecule.
Opposite charges attract.
General Concepts: Gel electrophoresis is a tool used by scientists to separate DNA into different sized
fragments. Because DNA is a negatively charged molecule, the fragments will move toward the positive
electrode (opposite charges attract). Fragments travel through the agarose gel according to their molecular
weight with the smallest fragments moving the greatest distance.
National Science Education Standards:
Content Standard A: Science as Inquiry
Abilities Necessary to do Inquiry
“Identify questions and concepts that guide scientific investigations” NSES p.175
“Design and conduct Scientific investigations” NSES p.175
Arizona State Standards:
Science Standards
Strand 1: Concept 2: PO 1.
Referenced Misconceptions:
“Though students are usually familiar with the base pairs, they often do not understand the antiparallel
orientations of the DNA strands and usually have not thought about the fact that 5’ and 3’ ends of the
strands are different….”(Kreuzer, pg.118).
Essential questions:
1. What is the correct way to use a micropipette?
2. How will the positive and negative charges in the electrophoresis power supply influence the
direction the dyes will run?
3. Which dye should go the farthest? Why?
Behavioral Objectives:
1. Students will be able to correctly use a micropipette.
2. Students will be able to correctly set up an electrophoresis rig.
3. Students will be able to correctly load the gel wells.
Inquiry Level: 2- Structured inquiry (Students are following a specific protocol and aren’t asking their own
questions).
Materials:
P-20 micropipettes and tips
Gel electrophoresis chambers and power supplies
P-1000 micropipettes and tips
Safety Concerns:
Always be sure the lab area is dry and free of water when using any electrical equipment. The
days could stain your skin and clothing. Keep dyes away from the face.
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 3 of 7 Assessment:
Assessment is performance based.
Real world connection: Gel electrophoresis is a tool used by scientists to separate DNA into different sized
fragments.
Description of Lab:
1. Micropipette lab- the students will have the instructor sign off on correctly using a micropipette
2. Gel electrophoresis: The students will run a gel using a charged dye. They will measure the
length the dye ran, and the class will construct a data table. We will discuss as a class why there
were any discrepancies (if any) with the results.
3. The students will do the DNA goes to the races activity (paper and pencil)
(Kreuzer, pgs 195-203.
Lesson 2: 2nd activity of the unit:
Time required: ~three 50 minute periods
Prior Knowledge: Students must have knowledge of cell structure as well as the structure of DNA.
General Concepts: Cells are surrounded by a plasma membrane consisting of a phospholipid bilayer and
sometimes a cell wall. DNA is found in the nucleus of eukaryotic organisms. DNA is a negatively charged
molecule that is closely associated with proteins.
National Science Education Standards:
Content Standard A: Science as Inquiry
Abilities Necessary to do Inquiry
“Identify questions and concepts that guide scientific investigations” NSES p.175
“Design and conduct scientific investigations” NSES p.175
“Use technology and mathematics to improve investigations and communications” NSES
p.175
Arizona state standards:
Science Standards
Strand 1: Concept 2: PO 1, PO 4 & PO 5.
Referenced Misconceptions:
“Pupils seem to suffer from interference between the concepts of ‘cell’ and ‘molecule’. It seemed that pupils
confined the concept ‘molecules’ to things encountered in physics and chemistry.” (Driver et al. pg 25)
Essential questions:
1. Does a strawberry have DNA?
2. How will a restriction enzyme facilitate the isolation of DNA?
3. How did the class data compare to your results?
Behavioral Objectives:
1. Students will extract DNA from strawberries.
2. Students will explain the role of restriction enzymes in the isolation of DNA.
3. Students will communicate their results to the class.
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 4 of 7 Description of Lab:
Students will isolate DNA from strawberries. Prior to the lab, a class discussion will illicit DNA differences
and similarities among species. The extracted DNA will be used to run a gel electrophoresis and the results
communicated to the class.
Inquiry level: 2- structured inquiry (Students are following a specific protocol and aren’t asking their own
questions.)
Materials:
Bio-Rad “DNA Fingerprinting Kit #166-0007EDU. NOTE. Some items contained in the kit need to be
chilled or frozen upon arrival. 30-60 minutes of preparation are required before the lab period.
P-20 micropipettes and tips
Gel electrophoresis chambers and power supplies
P-1000 micropipettes and tips
DI water
Microwave or hot plate
Permanent markers
Overhead sheets
250 mL and 500 mL Erlenmeyer flasks
Ice bucket and ice
Laboratory tape
Strawberries
Ethanol
Dish detergent
Ziploc bags
Saline solution
Meat tenderizer
Safety Concerns: Gloves, goggles and aprons should be worn at all times during this lab.
Assessment:
The assessment is both performance-based and qualitative. Did the students follow the procedures to obtain
DNA, set up and run the electrophoresis correctly? Secondly, how well did they communicate their results
to the class?
Activities:
1. The students will isolate the DNA from a strawberry. (Anderson, N.)
2. The isolated DNA will be subjected to restriction enzymes, and the class will have a discussion
about what a restriction enzyme is, and what is does.
3. The students will perform the DNA scissors activity (paper and pencil) (Kreuzer et al. pg. 190)
4. The class will discuss PCR and how it works. The students will then perform the PCR simulation
activity (paper and pencil) (Kreuzer et al. pg. 249)
5. The students will then run their samples, and collect class data with the size of their fragments.
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 5 of 7 Lesson 3: 3rd activity of the unit:
Time required: three 50 minute periods
Prior Knowledge:
Cells are surrounded by a plasma membrane consisting of a phospholipid bilayer and sometimes a cell wall.
DNA is found in the nucleus of eukaryotic organisms. DNA is a negatively charged molecule that is closely
associated with proteins. Restriction enzymes are proteins that cut DNA at a specific recognition sequence.
The number of DNA fragments formed after digestion by an enzyme depends on the number of times the
particular sequence of bases which the enzyme acts on is present.
General Concepts: DNA fingerprinting can be used to support or reject the identification of a possible
suspect
National Science Education Standards:
Content Standard C: Life Science
The Molecular Basis of Heredity
“In all organisms, the instructions for specifying the characteristics of the organism are carried in
DNA. The chemical and structural properties of DNA explain how the genetic information that
underlies heredity is both encoded in genes and replicated. Each DNA molecule in a cell forms a
single chromosome.” NSES p.185
Arizona state standards:
Science Standards
Strand 4: Concept 2: PO 1 & PO 2.
Referenced Misconceptions: The following misconceptions come from Making Sense of Secondary
Science. The common misconception is about the size of bacteria. Most students do not comprehend the
small size, their growth rate and how they reproduce. (pg 57)
As far as the DNA experiments goes, some misconceptions are: (pg 50-51)
1. Nature makes offspring, not genetics
2. Students know little of the nature or the function of genes and chromosomes. They do not
understand these structures have a chemical basis to them.
3. The students do not know why genes are responsible for inheritance from their parents.
4. They can rarely apply the concept of chance and probability to inheritance and evolution
Essential Questions:
1. What is a DNA fingerprint?
2. What information can the DNA fingerprint give detectives?
3. What are some of the possible ethical issues associated with fingerprinting an individuals
DNA?
4. The class will research court cases where DNA fingerprinting was used
Behavioral Objectives:
1. Students will perform the DNA fingerprinting investigation.
2. Students will predict the outcome and analyze their data.
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 6 of 7 Inquiry level- 2 structured inquiry (Students have the ability to run the lab but do have a chance to support
their explanations of the results on their own.)
Activities:
1. The class will research court cases where DNA fingerprinting was used
2. The class will discuss the ethical issues associated with DNA fingerprinting (including
case studies from Tgen)
3. Subjecting the given DNA to restriction enzymes (Bio-Rad fingerprinting kit)
4. Running the DNA fragments in a gel electrophoresis
5. Staining the gel
6. Analyzing the results of the gel.
Materials: (per class)
DNA fingerprinting kit (Bio-rad)
Micropipettes and tips
Agarose gel
Electrophoresis power supply (Bio-rad system)
Gloves
Strawberries
DNA samples (Bio-rad)
Loading dye (Bio rad)
DNA marker (Bio-rad)
Quick stain (Bio-rad)
Paper lab packets
Safety Considerations:
Other than basic laboratory safety (examples, No eating or drinking, proper cleanup), the students
will need to be aware of how to use the micropipettes correctly, and need to use gloves and
goggles.
Assessment:
All labs will require a formal lab write-up, complete with an analysis section. The students will be required
to explain their results using charts, graphs, and descriptions. They will also be required to explain why the
results were not what they were expecting if they were not. The pen and paper labs will be turned in to be
graded, and the class results for the gels will be collected, and the class will analyze them together.
Throughout the sections, the class will have discussions regarding the information and essential questions,
and student questions will be addressed. There will be a test over the unit at the end.
Real world connection:
DNA is a tool for forensic identification and for determining paternity or genetic relatedness. Scientists
extract DNA from samples and use the unique genetic “fingerprint” of DNA to confirm or reject the
identification of an individual.
After the lesson: When the lesson is finished, we will be discussing genetically modified organisms. We
will be conducting the pGLO experiment, and relating it to the medical field with advances in medicine. We
will also be doing a unit on ethical issues of GMO in Arizona, the US, and around the world.
NAU BIOTECH © 2009 Kelly Tommasino NAU BIOTECH Unit 5 of 12: DNA isolation and fingerprinting Page 7 of 7 Field Trip: Students will be exploring how to transcribe a gene into a protein via the web site
http://learn.genetics.utah.edu/units/basics/transcribe/.
Lessons: Objectives
Identify the correct RNA molecules that correspond to DNA
Describe the process for transcription
Identify the correct Amino Acids that correspond the RNA
Describe the process for translation
Build a protein
Computer simulation in which students get to explore the concepts surrounding
transcription and translation.
NAU and classroom experiences: We used the pGLO transformation lab multiple times at NAU as
well as have discussed how bacterial cells will automatically uptake DNA from their surroundings.
References:
The University of Utah. (2009). Transcribe and translate a gene. Retrieved May 8th, 2009 from:
http://learn.genetics.utah.edu/units/basics/transcribe/.
Anderson, N. (2002). The University of Arizona Biotech Project: Mobile biotechnology for the
classroom, from http://biotech.biology.arizona.edu/labs/labs.html
Driver, R., Squires, A., Rushworth, P., Wood-Robinson, V. (2006). Making Sense of Secondary
Science - Research into Children’s Ideas, New York: RoutledgeFalmer.
Kreuzer. H, Massey.A. (2001). 2nd Edition, Recombinant DNA and Biotechnology - A Guide for
Teachers, Washington DC: ASM Press.
National Research Council. (1996). National Science Education Standards.
Washington DC:
National Academy Press.
The University of Utah. (2009). Transcribe and translate a gene. Retrieved May 8th, 2009 from:
http://learn.genetics.utah.edu/units/basics/transcribe/.
Kits:
DNA Fingerprinting Lab,
http://www.biorad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=@@@@0246598331.1241474269@
@@@&BV_EngineID=ccceadehehfdjkhcfngcfkmdhkkdfll.0&divName=Life+Science+Education&
categoryPath=%2fCatalogs%2fLife+Science+Education%2fClassroom+Kits%2fForensic+DNA+Fin
gerprinting+Kit&loggedIn=false&lang=English&catLevel=4&country=HQ&catOID=18877&isPA=false&serviceLevel=Lit+Request
pGLO Transformation Lab,
http://www.biorad.com/B2B/BioRad/product/br_category.jsp?BV_SessionID=@@@@0246598331.1241474269@
@@@&BV_EngineID=ccceadehehfdjkhcfngcfkmdhkkdfll.0&divName=Life+Science+Education&
categoryPath=%2fCatalogs%2fLife+Science+Education%2fClassroom+Kits%2fpGLO+Bacterial+T
ransformation+Kit&loggedIn=false&lang=English&catLevel=4&country=HQ&catOID=18873&isPA=false&serviceLevel=Lit+Request
NAU BIOTECH © 2009 Kelly Tommasino