EDVOTEK Workshops offered at the 2024 NJ Science Convention. Tuesday & Wednesday October 15th and 16th. 1. Left at the Scene of the Crime:High School Forensics 2. Sweet Science: Exploring Complex Mixtures with Biotechnology
EDVOTEK WORKSHOPS • 2024 NJ Science Convention
TABLE OF CONTENTS
WORKSHOP
PAGE
01 Left at the Scene of the Crime: Introduction to Forensic Science 02 Sweet Science: Exploring Complex Mixtures with Biotechnology
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01 - Left at the Scene of the Crime: Intro to Forensic Science
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Introduction There’s a break-in at the lab! Your students become crime scene investiga- tors as they inspect evidence and use forensic tools like DNA fingerprinting to catch a criminal. This exciting workshop will help you incorporate bio- technology and electrophoresis into your classroom. Left at the Scene of the Crime Late one night Dr. Elektra Phoresis worked on an important biotechnology experiment in the laboratory. She was very close to creating a groundbreak- ing vaccine that could save many lives. After working in the lab all day, Ele- ktra decided to go home to eat dinner and get a good night’s rest. The next morning the lab was in shambles. The scientist found that many important pages were ripped from her lab notebook. Furthermore, security footage showed that someone had stolen some critical reagents from the labora- tory. A ransom note was left behind, demanding money in exchange for the lab notebook pages. Upon investigating the crime scene, Officer Evie Dence identified a broken window in the laboratory as a potential entry point by the suspect. The forensic scientists believe the perpetrator may have been cut on the broken glass, as several blood-like samples were found around the crime scene. The potential biological samples were collected as evidence to be analyzed. Using handwriting analysis, the ransom note will also be examined as evi- dence. Background Information Excerpts from EDVO-Kits 190 & 130 An abundance of material evidence can be left behind at the scene of a crime. This evidence can include blood on clothing, walls or floors, or even on the potential murder weapon. In some cases a few cells caught under the victim’s nails during a struggle can provide a wealth of information. Evidence can be obtained based on microscopic examination and biotech- nological analysis, and then compared to a sample obtained from a person of interest who may have been at the site of the crime. Advances in molecular biology and genetics over the past 30 years have produced a variety of applications that have forever changed forensic sci- ence. Human tissues and hair are made up of cells that contain DNA, which can be collected from evidence. When combined with the polymerase chain
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01 - Left at the Scene of the Crime: Intro to Forensic Science
reaction (PCR) and DNA fingerprinting a very small amount of DNA from a biological sample can be analyzed. In many cases the crime can only be solved, and the criminals brought to justice, through the meticulous work of forensic scientists. DETECTION OF BLOOD SPATTERS
Often trace amounts of blood cannot be detected by the naked eye, however it can easily be en- hanced and made visible by spraying the area with certain chemical enhancers such as Leucocrystal violet. This reagent will react with blood to generate a purple/violet color. In this experiment, students
will use Leucocrystal Violet to differentiate between trace blood samples and on different objects simulating materials recovered from a crime scene. DNA FINGERPRINTING In humans, DNA is packaged into 23 pairs of chromosomes that are inher- ited from an individual’s biological parents. Although most of this genetic material is identical in every person, small differences, or “polymorphisms”, in the DNA sequence occur throughout the genome. For example, the simplest difference is a Single Nucleotide Polymorphism (or SNP). Changes in the number and location of restriction enzyme sites result in Restriction Fragment Length Polymorphisms (or RFLPs). Short repetitive stretches of DNA at specific locations in the genome can vary in number to produce STRs (Short Tandem Repeats) and VNTRs (Variable Number of Tandem Re- peats). Although most polymorphisms occur in non-coding regions of DNA, those that disrupt a gene can result in disease. Medical diagnostic tests can identify specific polymorphisms associated with disease. Analyzing several different polymorphisms within a person’s genome gener - ates a unique DNA “fingerprint”. DNA fingerprints can allow us to distinguish one individual from another. Because polymorphisms are inherited, DNA fingerprints can also be used to determine paternity/maternity (and other familial relationships). The best-known application of DNA fingerprinting is in forensic science. DNA fingerprinting techniques are utilized to interpret blood, tissue, or fluid evidence collected at accidents and crime scenes. After DNA is extracted from these samples, forensic scientists can develop a DNA fingerprint. The DNA fingerprint from a crime scene can then be compared to the DNA fingerprints of different suspects. A match provides strong evidence that the suspect was present at the crime scene.
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Early fingerprinting analysis involved restriction digestion of the isolated DNA. Following electrophoresis of the digested sample, the DNA is trans- ferred to a nylon membrane during a process known as Southern blotting. Sequence-specific DNA probes are used to visualize the membrane-bound DNA. If the DNA is not digested by the restriction enzyme, the probes will only hybridize to a single DNA segment. If a restriction site occurs within this sequence, the probe will hybridize with multiple bands of DNA. VNTRs are identified when a probe labels DNA at a dissimilar molecular weight. Although RFLP analysis is very precise, it is time-consuming and requires large amounts of DNA. To address these problems, forensic scientists use the polymerase chain reaction (PCR) to produce DNA fingerprints. PCR al - lows researchers to quickly create many copies of a specific region of DNA in vitro (summarized in Figure 1-1). This technique requires 500-fold less DNA than traditional RFLP analysis and it can be performed in an afternoon. To perform PCR, purified double-stranded DNA is mixed with primers (short synthetic DNA molecules that target DNA for amplification), a thermostable DNA polymerase (Taq) and nucleotides. The mixture is heated to 94°C to denature the DNA duplex (i.e., unzip it into single strands). Next, the sample is then cooled to 45° C - 60° C, allowing the primers to base pair with the target DNA sequence (called “annealing”). Lastly, the temperature is raised to 72°C, the optimal temperature at which Taq polymerase will extend the primer to synthesize a new strand of DNA. Each “PCR cycle” (denaturation, annealing, extension) doubles the amount of the target DNA in less than five minutes. In order to produce enough DNA for analysis, twenty to forty cycles may be required. To simplify this process, a specialized machine, called a “thermal cycler” or a “PCR machine”, was created to rapidly heat and cool the samples.
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Figure 1-1: Polymerase Chain Reaction
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Experiment Procedures: Agarose Gel Electrophoresis
Concentrated buffer
Distilled water
Agarose
60°C
Flask
Caution! Flask will be HOT!
WAIT
POUR
60°C
ADD SYBR Safe
60°C
CASTING THE AGAROSE GEL 1. DILUTE concentrated (50X) buffer with distilled water to create 1X buffer (see Table A). 2. MIX agarose powder with 1X buffer in a 250 mL flask (see Table A). 3. DISSOLVE agarose powder by boiling the solution. MICROWAVE the solution on high for 1 minute. Carefully REMOVE the flask from the microwave and MIX by swirling the flask. Continue to HEAT the solution in 15-second bursts until the agarose is completely dissolved (the solution should be clear like water). 4. COOL agarose to 60°C with careful swirling to promote even dissipation of heat. 5. While agarose is cooling, SEAL the ends of the gel-casting tray with the rubber end caps. PLACE the well template (comb) in the appropriate notch. 6. Before casting the gel, ADD diluted SYBR ® Safe to the molten agarose and swirl to mix (see Table A). 7. POUR the cooled agarose solution into the prepared gel-casting tray. The gel should thoroughly solidify within 20 minutes. The gel will stiffen and become less transparent as it solidifies. 8. REMOVE end caps and comb. Take particular care when removing the comb to prevent damage to the wells.
Individual 0.8% UltraSpec-Agarose™ with SYBR ® Stain
7 x 7 cm
0.6 mL
29.4 mL
0.23 g
30 mL
30 µL
10 x 7 cm*
1.0 mL
49.0 mL
0.39 g
50 mL
50 µL
14 x 7 cm
1.2 mL
58.8 mL
0.46 g
60 mL
60 µL
* Recommended gel volume for the EDGE™ Integrated Electrophoresis System.
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Experiment Procedures: Agarose Gel Electrophoresis
9. PLACE gel (on the tray) into electrophoresis chamber. COVER the gel with 1X electrophoresis buffer (See Table B for recommended volumes). The gel should be completely submerged. 10. LOAD 25 µL of each QuickStrip™ sample into the well in the order indicated by Table D. 11. PLACE safety cover. CHECK that the gel is properly orient-
Reminder: Before loading the samples, make sure the gel is properly oriented in the ap- paratus chamber.
ed. Remember, the DNA samples will migrate toward the positive (red) electrode. source and PERFORM electropho- resis (See Table C for time and volt- age guidelines). 13. After electrophoresis is complete, REMOVE the gel and casting tray from the electrophoresis chamber. 12. CONNECT leads to the power
LANE LABEL
SAMPLE NAME
1 2 3 4 5 6
A B C D E --
DNA Standard Marker Crime Scene PCR reaction Suspect 1 PCR reaction Suspect 2 PCR reaction Suspect 3 PCR reaction
------
Time and Voltage Guidelines (0.8% Agarose Gel)
1x Electrophoresis Buffer (Chamber Buffer)
EDGE™
M12 & M36
Volts
Min/Max (minutes)
Min/Max (minutes)
EDGE™
150 mL
3 mL
147 mL
150 125 100
10/20
20/35 30/45 40/60
M12
400 mL
8 mL
392 mL
N/A
M36
1000 mL
20 mL
980 mL
15/25
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Experiment Procedures: Agarose Gel Electrophoresis
dH 2 O
VISUALIZING THE SYBR ® GEL 14. SLIDE gel off the casting tray onto the viewing surface of the transilluminator and turn the unit on. DNA should appear as bright green bands on a dark background. 15. PHOTOGRAPH results. 16. REMOVE and DISPOSE of the gel and CLEAN the transil- luminator surfaces with distilled water.
Be sure to wear UV goggles if using a UV transilluminator.
Related Product: Cat. #608 SYBR® Safe DNA Stain
Save time, money, the environment...and get better gel results! SYBR Safe® is a DNA stain that fluoresces with a bright green color when excited with blue light. Like Ethidium Bromide, SYBR Safe® binds specifically to the DNA double helix. Howev - er, unlike Ethidium Bromide, SYBR Safe® has been engineered to be less mutagenic then Ethidium Bromide, making it much safer to use, particularly in the classroom.
• SAFE for the Biotechnology Classroom • More sensitive than ethidium bromide • Non-mutagenic • 10,000 X Concentrate for 750 mL • Volume: 80 µL
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Experiment Procedures: Blood Splatter Analysis 1. Work with one item at a time to avoid cross contamination or sample mix-up. EXAMINE the object for the visible red-brown staining and general characteris- tics. 2. PLACE the item on a flat, clean surface. 3. Use the fine-mist sprayer to gently SPRAY the targeted area on the object with the Leucocrystal Violet (LCV) solution from a distance of about 2-3 inches. 4. ALLOW the samples to sit for 30 seconds before analyzing. LCV generates a purple/violet color and indicates the presence of blood. 5. RECORD your sample ID and observations in the Table, below:
Leucocrystal Violet +/-
Sample ID Crime scene #1
Crime scene #2
Crime scene #3
Crime scene #4
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Experimental Results and Analysis
AGAROSE GEL ELECTROPHORESIS
Lane
Tube
1 2 3 4
A B C D E
DNA Standard marker Crime scene PCR reaction Suspect 1 PCR reaction Suspect 2 PCR reaction
5 Suspect 3 PCR reaction The DNA standards in Lane 1 make it possible to measure the DNA bands obtained from the PCR reactions. The results of this analysis indicates an identical pattern in Lanes 2 and 4. This is strong evidence that the crime scene DNA and Suspect 2 match. In criminal investigations, several known variable regions in DNA are ana- lyzed to match crime scene and suspect DNAs.
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01 - Left at the Scene of the Crime: Intro to Forensic Science
Related Products FEATURED KIT: DNA Fingerprinting by PCR Amplification For 8 gels. Forensic DNA fingerprinting has become a universally accepted crime-fighting tool. Recent advances use the polymerase chain reaction (PCR) to amplify human DNA obtained from crime scenes. This experiment, based on a crime scene scenario, has an inquiry-based component. Cat. #130 (Features FlashBlue™ Stain) Cat. #130-S (Features SYBR® Safe DNA Stain) NEW: Forensic Escape Room: Design Your Own Biotech Adventure For 10 groups. Explore the world of forensic science with this fun and exciting crime scene escape room! In this investigation, students decipher clues, solve puzzles, and unravel the evidence to free the innocent. Hands-on techniques include forensic blood detection, blood typing, and DNA fingerprinting. Compre - hensive instructions on how to set up an escape room are included. Cat. #190 Forensics Enhancement Techniques For 10 groups. Trace amounts of blood are often sufficient to identify the individual responsible for any number of crimes, including murder, burglary, or assault. Enhancement procedures can make a small stain of body fluid or tissue visible to the naked eye. In this experiment, students will act as detec- tives following the aftermath of a drug bust involving gang warfare over territory. Reagents that are routinely used as a first screen will be utilized to detect simulated blood and DNA. In addition, biological materials will be recovered from splatters, blood trajectory, and small droplets of simulated human materials. Cat. #194 Forensic Toxicology For 10 groups. In today’s forensic science laboratory, toxicologists identify drugs and toxins in samples collected from crime scenes, victims, and potential suspects. If present, the toxicolo- gist also determines whether the drug or toxin contributed to a person’s behavioral changes or death. In this forensic science experiment, students will use the Enzyme Linked Immunosorbent Assay (ELISA) to analyze simulated crime scene samples for the presence of drugs. Cat. #195
Whose Fingerprints Were Left Behind? For 10 groups. After a crime has been committed, the evidence left behind can identify a potential culprit, although a single piece of evidence is not usually enough to convict someone. Even in this age of DNA, fingerprints and blood stains are still important at helping to identify a criminal. In this experiment your students will learn to detect and analyze fingerprints and then use these techniques to solve a classroom crime . Cat. #S-91
Details for all these products and MORE can be found on our website!
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01 - Left at the Scene of the Crime: Intro to Forensic Science
RELATED PRODUCTS
EDGE™ Integrated Electrophoresis System Runs one 10 x 7 cm gel Cat# 500
M12 Complete™ Electrophoresis Package For 1 or 2 Lab Groups Cat# 502-504
DuoSource™ 100/150 V, for 1 or 2 Units Cat# 509
QuadraSource™ 10-300 V, for 1 or 4 Units Cat# 5010-Q
White Light LED Transilluminator Cat# 552
EDVOTEK® Variable Micropipette 5-50 µL Micropipette Cat. # 590
TruBlu™ Jr Blue Light Transilluminator Cat# 555
Long Wave UV Light Cat# 969
Fixed Volume MiniPipette™ 35 µL MiniPipet™ Cat. # 587-2
Details for all these products and MORE can be found on our website!
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Introduction
In this experiment, students will investigate how gel electrophoresis unlocks the color code by investigating food dyes used to make colorful candies.
Background Information Color is an integral aspect of our culture. Companies have long been using color additives in a variety of products, including candies, shampoos, perfumes, drinks, etc. All the colors that we see are a mixture of the three primary colors: red, green, and blue. That these three simple colors can be combined to form the myriad of colors that we see everyday makes them a great example of how complex things, such as colors, can be broken down into their individual components. In the classroom, a great way to break down colors is by examining color additives in food. The color of food has always been important for us. The early Romans believed that people not only eat with their palate, but also “eat with their eyes”. For centuring, humans have used dyes from natural ingredients to add color to food, drink, clothing, and other products. These days, manufacturers add colors to food to offset color loss due to product exposure to various environmental conditions and to make them look more attractive to consumers. As the use of color additives to food continues to grow, concerns regarding the addition of food colors to products also emerge. The seven more commonly used food dyes in the United States are shown in Table 2-1. However, the FDA and independent scientists are looking into whether or not certain dyes, such as yellow 5 and red 40, are linked to hyperactivity or allergic reactions.
Figure 2-1: Example of Candy Ingredient Label
AGAROSE GEL ELECTROPHORESIS
Agarose gel electrophoresis is widely used to separate molecules based upon charge, size and shape. It is particularly useful in separating charged biomolecules such as DNA, RNA and pro- teins. Agarose gel electrophoresis possesses great resolving power, yet is relatively simple and straightforward to perform. The gel is made by dissolving agarose powder in the electropho- resis buffer. The solution is boiled to dissolve the agarose and then cooled to approximately 60º C and poured into a gel tray where it solidifies. The tray is submerged in a buffer-filled electrophoresis apparatus, which contains electrodes. Samples are prepared for electrophoresis by mixing them with glycerol or sucrose to give the mixture higher density. This makes the samples denser than the electrophoresis buffer. These
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
samples can then be loaded with a micropipet or transfer pipet into wells that were created in the gel by a template during casting. The dense samples sink through the buffer and remain in the wells. A direct current power supply is connected to the electrophoresis apparatus and current is applied. Charged molecules in the sample enter the gel matrix. Molecules having a net negative charge migrate towards the positive electrode (anode) while net positively charged molecules migrate towards the negative electrode (cathode). Within a range, the higher the applied voltage, the faster the samples migrate. The buffer serves as a conductor of electricity and to control the pH. The pH is important to the charge and stability of biological molecules. Agarose is a polysaccharide derived from agar. In this experiment, UltraSpec-Agarose™, a mixture of agarose and hydrocolloids which renders the gel to be both clear and resilient, is used. At first glance, an agarose gel appears to be a solid at room temperature. However, on the molecular level, the gel contains microscopic pores which act as a molecular sieve, allowing the different molecules to pass through. Food dyes are composed of ions. When these charged ions are subjected to an electric field, the molecules will migrate toward the electrode of opposite charge. Positively charged mol- ecules will migrate toward the negative electrode, while those with a negative charge will move toward the positive electrode. Small dye fragments move through these holes easily, but large dye fragments have a more difficult time squeezing through the tunnels. Factors such as charge, size and shape, together with buffer conditions, gel concentrations and voltage, affects the mobility of molecules in gels. Because molecules with dissimilar sizes travel at different speeds, they become separated and form discrete “bands” within the gel. After the current is stopped, the bands can be visualized (Figure 2-2). In this experiment, students will extract several different dyes from food source. The dyes will then be analyzed using agarose gel electrophoresis and their rate of migration will be observed and measured.
( - )
Figure 2-2: Overview of agarose gel electrophoresis.
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TABLE 2-1 – SEVEN ARTIFICIAL COLORS APPROVED BY THE FDA FOR COLORING FOOD
Abbreviation
Name
Shade
Structure
Brilliant Blue
Blue
Blue 1
Blue 2
Indigotine
Indigo
Green 3
Fast Green
Turquoise
Red 3
Erythrosine
Pink
Red 40
Allura Red
Red
Yellow 5
Tartazine
Yellow
Yellow 6
Sunset Yellow
Orange
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Experiment Overview
1 Prepare dye samples by extracting food dyes from candies
2
Prepare agarose gel in casting tray.
3
Remove end caps & comb, then submerge gel under buffer in electrophoresis chamber.
4
Load each dye sample in consecutive wells.
5
Attach safety cover & connect leads to power source to conduct electrophoresis.
After electrophoresis, transfer gel for visualization.
( - )
6
Analysis on white light source.
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Module I: Extraction of Food Dyes from Candy
T.C. yell
250 µL Dye Extraction Buffer
T.C. blue
T.C. red
T.C.
T.C. pur
T.C. gre
SWIRL
RINSE your cup. REPEAT steps 2-6.
T.C. yell
T.C. red
T.C. pur
T.C. red
T.C. gre
T.C. blue
T.C.
We recommend using brightly-colored candies M&M’s®, Skittles®, jelly beans, & gum balls. 1. LABEL five microcentrifuge tubes with your initials and the colors of the candy you will be investigating. 2. LABEL the provided cup with your initials. ADD one candy to the cup 3. ADD 250 µL of Dye Extraction Buffer to the cup containing the candy. 4. SWIRL the candy gently in the Dye Extraction Buffer to dissolve the color coating until the white layer of the candy is exposed. 5. REMOVE the candy from the cup. 6. TRANSFER the dissolved color solution into the appropriately labeled microcentri- fuge tube. 7. RINSE the cup. REPEAT steps 2-6 with the remaining 4 candies. 8. PLACE the tubes on lab bench. PROCEED to Module II: Separation of Food Dyes by Agarose Gel Electrophoresis. OPTIONAL STOPPING POINT Dye samples may be stored in the refrigerator for up to 24 hours before performing electrophoresis.
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Module II: Agarose Gel Electrophoresis
Concentrated buffer
Distilled water
Agarose
60°C
Flask
Caution! Flask will be HOT!
WAIT
POUR
60°C
CASTING THE AGAROSE GEL 1. DILUTE concentrated 50X Electrophoresis buffer with distilled water (refer to Table A for correct volumes depending on the size of your gel casting tray). 2. MIX agarose powder with buffer solution in a 250 mL flask (refer to Table A). 3. DISSOLVE agarose powder by boiling the solution. MICROWAVE the solution on high for 1 minute. Carefully REMOVE the flask from the microwave and MIX by swirling the flask. Continue to HEAT the solution in 15-second bursts until the agarose is completely dissolved (the solution should be clear like water). 4. COOL agarose to 60°C with careful swirling to promote even dissipation of heat. 5. While agarose is cooling, SEAL the ends of the gel-casting tray with the rubber end caps. PLACE the well template (comb) in the appropriate notch. 6. POUR the cooled agarose solution into the prepared gel-casting tray. The gel should thoroughly solidify within 20 minutes. The gel will stiffen and become less transpar - ent as it solidifies. 7. REMOVE end caps and comb. Take particular care when removing the comb to pre- vent damage to the wells.
Individual 0.8% UltraSpec-Agarose™ Gels
7 x 7 cm
0.6 mL
29.4 mL
0.24 g
30 mL
*Recommended gel volume for the EDGE™ Integrated Electrophoresis System (Cat. #500).
10 x 7 cm*
0.9 mL
44.1 mL
0.36 g
45 mL
14 x 7 cm
1.2 mL
58.8 mL
0.48 g
60 mL
* Recommended gel volume for the EDGE™ Integrated Electrophoresis System.
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Module II: Agarose Gel Electrophoresis, continued
RUNNING THE GEL 8. PLACE the gel (still on the tray) into the electrophoresis chamber. COVER the gel with 1X Electrophoresis Buffer (See Table B for recommended volumes). The gel should be completely submerged. 9. PUNCTURE the foil overlay of the Quick-
TABLE 2: GEL LOADING
Strip™ with a pipet tip. LOAD the entire sample (35 µL) into the well in the order indicated by Table 2, at right. 10. PLACE safety cover on the unit. CHECK that the gel is properly oriented. Re- member, the DNA samples will migrate toward the positive (red) electrode. 11. CONNECT leads to the power source and PERFORM electrophoresis (See
Candy Color
Lane
Standard Dye Marker
1 2 3 4 5 6
Table C for time and voltage guidelines). Allow the tracking dye to migrate at least 3 cm from the wells. 12. After electrophoresis is complete, RE- MOVE the gel and casting tray from the electrophoresis chamber and VISUALIZE the results. No staining is necessary.
Time and Voltage Guidelines (0.8% Agarose Gel)
1x Electrophoresis Buffer (Chamber Buffer)
EDGE™
M12 & M36
Volts
Min/Max (minutes)
Min/Max (minutes)
EDGE™
150 mL
3 mL
147 mL
150 125 100
10/20
20/35 30/45 40/60
M12
400 mL
8 mL
392 mL
N/A
M36
1000 mL
20 mL
980 mL
15/25
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Module III: STEM-Based Data Analysis of Food Dyes Using a Standard Curve
Agarose gel electrophoresis separates biomolecules into discrete bands, each comprising molecules of the same size. How can these results be used to deter- mine the lengths of different fragments? Remember, as the length of a biomolecule increases, the distance to which the molecule can migrate decreases because large molecules cannot pass through the channels in the gel with ease. Therefore, the mi- gration rate is inversely proportional to the length of the molecules—more specifi - cally, to the log 10 of molecule's size. To illustrate this, we ran a sample that contains bands of known lengths called a “standard”. We will measure the distance that each of these bands traveled to create a graph, known as a “standard curve”, which can then be used to extrapolate the size of unknown molecule(s). 1. Measure and Record Migration Distances Measure the distance traveled by each Standard Dye Molecule from the lower edge of the sample well to the lower end of each band. Record the distance in centime- ters (to the nearest millimeter) in your notebook. Repeat this for each dye fragment in the standard. Measure and record the migration distances of each of the fragments in the un- known samples in the same way you measured the standard bands.
A B C
Figure 2-3: Measure distance
migrated from the lower edge of the well to the lower edge of each band.
2. Generate a Standard Curve. Because migration rate is inversely proportional to the log 10 of band length, plotting the data as a semi-log plot will produce a straight line and allow us to analyze an exponential range of fragment sizes. You will notice that the vertical axis of the semi-log plot appears atypical at first; the distance between numbers shrinks as the axis progresses from 1 to 9. This is because the axis represents a loga- rithmic scale. The first cycle on the y-axis corresponds to lengths from 100-1,000 base pairs, the second cycle measures 1,000-10,000 base pairs, and so on. To create a standard curve on the semi-log paper, plot the distance each Standard Dye Molecule migrated on the x-axis (in mm) versus its size on the y-axis (in base pairs). Be sure to label the axes!
QUICK REFERENCE: The Standard dyes have the fol- lowing base pair equivalents.
Blue Red
5000 3000 1000
Purple Orange
500
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
8,000 10,000 9,000
7,000 6,000 5,000 4,000
3,000
2,000
1,000
800 700 600 500 400 900
300
200
100
80 70 60 50 40 90
30
20
10
3 cm
2 cm
4 cm
5 cm
1 cm
6 cm
X-axis: Migration distance (cm)
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Experimental Results and Analysis
1 2 3 4 5 6
1 2 3 4 5 6
NOTE: In the idealized schematic, the relative posi- tions of dye fragments are shown but are not depicted to scale. No positively charged dyes are shown.
Lane
Sample
1 2 3 4 5 6
Standard Dye Marker
Dye extracted from Candy #1 Dye extracted from Candy #2 Dye extracted from Candy #3 Dye extracted from Candy #4 Dye extracted from Candy #5
QUICK REFERENCE: Standard Dye marker sizes - length is expressed in base pairs.
5000, 3000, 1000, 500
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02 - Sweet Science: Exploring Complex Mixtures with Biotechnology
Related Products
M12 Complete™ Electrophoresis Package For 1 or 2 Lab Groups Cat# 502-504
M36 HexaGel™ For 1 to 6 Lab Groups Cat# 515
QuadraSource™ 10-300 V, for 1 or 4 Units Cat# 5010-Q
DuoSource™ 100/150 V, for 1 or 2 Units Cat# 509
White Light LED Transilluminator Cat# 552
Fixed Volume MiniPipet™ 35 µL MiniPipet™ Cat. # 587-2
EDVOTEK® Variable Micropipette 5-50 µL Micropipette Cat. # 590
For 10 Groups. NGSS-aligned with MS-PS1. Investigate how agarose gel electrophoresis unlocks the color code used by food scientists to make colorful candies. Students will extract color activities from common candies and separate the dyes on agarose gel electrophoresis. A fun lab exten- sion involves the use of candy to build a DNA model. Cat. #S-47 Linking Food Science to Biotechnology: Unlock the Color of Candies
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