ENRICHED SCIENCE (CLUES) PROGRAM
Version B
DNA FINGERPRINTING ALLOWS SCIENTISTS TO COMPARE DNA FROM VARIOUS ORGANISMS AND IDENTIFY A PARTICULAR INDIVIDUAL.
DNA IS EXTRACTED AND CUT INTO FRAGMENTS. THE FRAGMENTS FORM A PATTERN ON AN ELECTROPHORESIS GEL. THAT PATTERN PROVIDES AN IDENTITY PROFILE.
IN THIS EXPERIMENT YOU WILL BE GIVEN A MYSTERY SAMPLE OF DNA. YOU WILL SEPARATE THE PIECES, PRODUCING A PATTERN ON A GEL, AND IDENTIFY YOUR DNA.
USES FOR DNA FINGERPRINTING
CRIME WORK: ASSAULT AND MURDER*
PATERNITY SUITS
MISSING PERSONS AND UNIDENTIFIED BODIES
IMMIGRATION DISPUTES
ANIMAL WORK
1. BREEDING COMMERCIAL SPECIES (HORSES,CATTLE,DOGS, CATS ETC.)
2. BREEDING ZOO ANIMALS
3. BREEDING ENDANGERED SPECIES
*DNA FINGER PRINTING IS PARTICULARLY IMPORTANT TO SOCIETY IN CRIMINAL CASES BECAUSE IT PROTECTS THE INNOCENT AND IMPROVES THE CONVICTION RATE OF THE GUILTY.
LAB UNIT 4: GEL ELECTROPHORESIS - Version B
OBJECTIVES:
1. To introduce students to agarose gel electrophoresis as a tool for separating DNA fragments
2. To introduce students to the concept of DNA fingerprinting
I. BACKGROUND
One of the most basic and frequently used tools of the molecular biologist is electrophoresis. In this experiment, you will be using agarose gel electrophoresis to separate DNA pieces of different sizes. Electrophoresis means "to carry with an electrical current". What you will observe is that different sized pieces of DNA will be carried different distances by an electric current as the pieces migrate through agarose, a Jell-O like substance derived from seaweed, which you will apply to a glass slide. The gel coated slide will be placed in a "gel box" where the gel serves as an "electrical bridge" between two electrodes submerged in a conducting solution. You will place your DNA samples into small wells cast at one end of the gel. Current supplied by electrodes at either end of the chamber creates an electric field across the gel. The DNA and other negatively charged ions will migrate through the pores in the agarose toward the positive end of gel. The diagrams below should prove helpful.
It is possible to do gel electrophoresis with DNA because the DNA molecule has an overall negative charge. The negative charge comes from the phosphate groups which alternate with the sugar, deoxyribose, to form the "rails" the "twisted ladder" of the double helix. The negatively charged DNA is attracted to the positively charged electrode when the current is turned on. The different sized DNA pieces separate because the smaller fragments will migrate farther than the larger. After the fragments are separated, you will turn off the current, remove the gel and stain it with methylene blue stain which will bind to the DNA pieces and allow them to become visible.
While electrophoresis has many applications in state-of-the-art molecular biology laboratories, one of its most interesting and important uses is in the courtroom using a technique called DNA fingerprinting. DNA fingerprinting can reveal a DNA pattern which is unique to an individual and hence can link a suspect to a particular piece of evidence with an extremely high degree of certainty. For example, a hair found at the scene of a crime and is taken to a forensic laboratory. There the DNA in cells in the root of the hair is extracted and then is cut into pieces by special bacterial enzymes called restriction enzymes. An individual's DNA is as distinctive as a fingerprint since restriction enzymes cut each person's DNA into different sized pieces. When the cut DNA is separated into its pieces by electrophoresis, the visible end result looks something like the bar code on a super market package. The DNA from the hair root cells can then be compared with the DNA obtained from one or more suspects.
The PRACTICE PAGE ( at end of module) exercises should help you understand DNA fingerprinting:
The practice examples are vastly over-simplified. In actual criminal cases, several restriction enzymes may be used resulting in complex patterns consisting of dozens of DNA bands. The probability of any two individuals having identical band patterns is then computed. Usually the probability of two individuals having the bands is approximately 1 in 1019 which is many times the world's population. It is important to note that this method will also free an innocent suspect.
OVERVIEW OF THE EXPERIMENT:
1. You will work in pairs; however, each of you will run a fingerprint on an "unknown" piece of DNA.
2. Following the directions on the next page, you and your partner will pour one agarose gel. The gel will have several wells so that each of you has a lane for your "unknown" DNA.
3. While your gel is hardening, you will each select one of the "unknown" DNAs from your teacher, and following the directions, you will add loading dye to your DNA.
4. After the gel has hardened, it will be placed in the solution in the gel box. The DNA samples of you and your partner will be placed in the wells on the gel and, and you will turn on the current as directed.
5. While the gel is running you will carefully examine the patterns of the possible "unknown" DNA's.
6. After fifteen minutes, you will turn off the current, remove your gel and stain the DNAs with methylene blue stain.
7. Finally you will figure out which "suspect" your DNA came from by comparing your gel pattern with the patterns provided.
Version B
Supplies for each lab station:
Test tube rack
Two 1.5ml test tubes
1.5ml test tube containing loading dye "L"
1 micropipettor and tips
10ml graduated pipette
Pipet-aid
3" X 2" glass slide
Plastic "comb"
Plastic staining tray
Transparent plastic ruler
Marking pen (Please use regular pen or pencil on paper.)
Known DNA pattern sheet
Small cup for used tips
Two lab stations will share:
Electrophoresis device ("gel box")
Four lab stations will share:
Power supply for gel boxes
Supplies at a central location for use by the whole class:
1.5ml test tubes with DNA unknowns
Micropipettor tips
60-70∞C water bath with flasks of melted agarose gel
Bottle of "electrophoresis solution"
Bottle of methylene blue stain
Bottle for "used methylene blue stain"
Transparent plastic sheets for tracing staining pattern
Gel viewers
Clock
Deionized water
Procedure for the Electrophoresis/DNA fingerprint lab
A pair of students should work at each lab station
Check the list of materials against supplies at your station
I. Preparing the gel
A. Set glass slide on a smooth level section of lab bench where comb can be positioned over it later.
B. Fit the pipet-aid to the 10ml pipette and go to the flask of melted agarose gel; obtain 8ml of melted agarose solution; return to your station and promptly spread 7ml of the warm solution on the glass slide; position the comb as has been demonstrated to you.
C. Allow the agarose solution to cool and solidify for at least 3-4 minutes.
Meanwhile...
II. Preparing the samples for electrophoresis
A. Each lab partner should label one of the 1.5ml test tubes with his or her initials.
B. Each member of the lab partner team will now get his or her sample of unknown DNA. Decide which of you is to go first. Set micropipette to 10ml and put on a tip. Take your micropipette and your tube to the location where your teacher is giving out the unknown DNA solutions.
1. Put a clean tip on your micropipette.
2. Check to see that the micropipette is set for 10ml.
3. Add10ml of DNA unknown solution to your tube.
4. Discard your pipette tip and get a new tip. Set your micropipette to 2ml.
5. Add 2ml of loading dye to the tube containing your DNA solution. Mix the contents well and discard the tip.
6. Give the micropipette to your partner.
7. Record the number of your DNA unknown solution on the answer sheet.
C. The second member of the team will now get his or her unknown DNA following Steps 1-5 and 7 in Part B.
III. Loading the gel
A. By now the gel should be solidified. It will appear cloudy. Press down on the gel and gently lift the comb. Return comb to your lab station kit.
B. Lift the slide with the gel and place onto the platform of the gel box with wells at the left end.
C. Check to see that the solution gives a smooth surface over the gel with no dents at the wells. Only if dents are present should you add more electrophoresis solution.
D. Decide which lab partner will load the gel first. Set the micropipette for 10 ml. Get a new tip. Transfer the contents of your DNA sample into one of the wells in the gel. The other member of the team will get a new micropipette tip and transfer his or her DNA into the other well. Record which well contains your sample and which contains your lab partner's.
IV. Running the gel (two groups share a power supply).
A. Close the lid of the gel box without disturbing the solution and sloshing the DNA samples.
B. Turn on the power supply. Adjust the power supply to be just under 200 volts. Record the time. You will stop the electrophoresis run in 15 minutes. Look to see if bubbles are being produced at the electrodes in the gel box and that the colored dyes in the loading dye are migrating. Ask for help if no bubbles are visible.
Go on to next instructions while you wait for the gel to run.
V. While you wait: Housekeeping and practice analysis
A. Label the top edge of the staining tray with your names.
B. Observe the patterns for samples of DNA that you have been given on page 9. Write a few sentences describing the distance and pattern of the bands for each DNA. Use the answer page (pg. 8).
Sample description:
The overall pattern, starting from the well, is of a space, then two bands close together, then a space equal to the first space, then two more bands close together.
C. After 15 minutes turn off the power supply. The bluish dyes in the loading dye will have migrated about 1/2 to 3/4 of the distance to the end of the gel. (These dyes are not DNA, but they help you tell at a glance if the electrophoresis has worked.)
D. Remove the lid of the power supply. Pick up the slide with the gel (be careful because the gel tends to slip off the slide) and then place the gel into the staining tray. Return the glass slide to your kit.
VI. Staining the DNA in the gel.
A. Add methylene blue dye until the gel is barely submerged. Note the time and begin rocking the tray. You will stain for 5 minutes.
B. After 5 minutes pour the stain back into the "used stain" bottle and rinse the gel once in deionized water (NOT TAP WATER!). Then add enough deionized water to submerge the gel. If you will not "read the gel" until later, place the labeled tray in the designated location in your lab.
C. After the gel has destained (at least 5 minutes, or the next day) rinse the gel once more (deionized water) and pour off the water. Place the transparency on top of the gel and trace the locations of the wells and the bands of stained DNA onto the transparency. Ignore the loading dye locations as you trace (loading dye is usually not "band-like"). Each lab partner should make his or her own transparency.
D. Use transparent tape to attach the transparency to your lab report sheet (pg. 8).
E. Discard or save the gel as instructed.
VI. Observations and conclusions.
A. Measure the distance that your stained DNA bands migrated in the gel and record on below.
B. Describe in a few sentences the pattern of the bands in your sample.
C. Compare your sample to the patterns on page 9 and give your conclusions about the identity of the person whose DNA was your "unknown." Explain how you made the determination.
