PLTW 12 Steps Gel Electrphoresis

Step 1: Define the Problem

Problem Statement:

Your police department has issued a task to build a Gel Electrophoresis in a limited time
and with very little funding. The finished design and model has to work and must be built with
plexiglass.To solve the crime of the stolen artwork in the museum, you must build a working
finished model to test the DNA and find out which of the suspects have done the crime.

Step 2: Brainstorm

Brainstorming

Questions and Topics to Research:
- What is optimal ratio of Gel to buffer
-Acrylic vs. Lexon Plexiglasss
- What is the Speed of the DNA moving through the GEL affected by
-What is the best adhesive to use with Plexiglass


What we already know:
- Banana plug size= .24 ( Hole must be .24 for allowance )
- DNA is Negatively charged
- The gel is made of Agarose
-DNA will move towards negatively charged Anode
-3.051sq.inches of Agarose

Step 3: Research and Generate Ideas

Research & Generate Ideas

- Lid will be placed on top of the lid for easy removal

Acrylic vs. Lexon Plexiglass
Acrylic Plexiglas is cheaper while still being very strong. It is also less likely to deform in
normal temperatures unlike lexon which bends easily in room temperature. Acrylic is also less
likely to scratch and polishing it will make it clear again if its gets dirty.

The Optimal Ratio of Gel to Buffer
Concerning how much buffer to put in the Gel Electrophoresis DNA Tester, the surface of the
buffer should be about 5 mm above the surface of the surface of the gel. Too much buffer will
slow down the migration of the DNA in the gel. Along with this, too much buffer will also cause
band distortion.

What Affects the Speed of the DNA moving through the Gel
Separation of the DNA molecules happen because some move slower through the GEL than
others. One main factor is the size of the molecule. DNA strands with alot of base pairs will
move slower than those with few. The shape of the DNA also plays a role in the speed it travels.
Spherical shaped DNA is more compact than a strand shape and this will allow it to travel faster
through the GEL. Also how strong its charge is also affects its speed because a DNA molecule
that is the same shape and
size as another but is more negatively charged will cause it to move through the GEL faster than
its same sized counterpart. Finally, how well the DNA molecules bind to the agarose is another
factor at how far and fast the DNA will travel in the agarose.

What is the Best Adhesive to use with Acrylic Plexiglas
Acrylic Weldon is by far the best adhesive to use for plexiglas. There are
many different varieties of it with multitude of different specializations. Also being designed for
use with Plexiglas ensures it will be of high quality and will adhere quickly to the plexiglass.

Research Paper:

The Gel Electrophoresis Project is a group activity to help with DNA recognition of
humans. The model will use the gel to contain the material to dismember the chromosomes
and give the DNA of that a person a graph. The project is to be done with the intentions of
helping a group of detectives and the police solve a crime of a stolen painting. The painting only
has a few traces of the DNA of the thief to test and find out who the criminal is. The project will
have to correctly draw out the DNA of someone in the correct order. A continuous DC electric
current will cause the the negatively charged DNA to migrate towards the positively charged
anode.

The Gel Electrophoresis consists of a box, chamber, comb, and a lid. The lid has two
holes with the diameter of .25 in. that will contain banana plugs with a diameter of .24 in. The
chamber will have an electrical current throughout the container. Two different substances will
be placed inside the unit, one being agarose and the other is buffer. Only 50 mL. of agarose and
150 mL. of buffer is given to the group. The buffer submerges the agarose and flows the current
through the gel (the agarose) causing the DNA to move through the gel.

There are certain factors to how the DNA moves through the gel. Factors like the shape,
size, its charge, and how well the pieces will adhere to the gel will influence how DNA moves.
Rod shaped DNA moves slower than spherical shaped DNA because the spherical DNAs
volume is more compact. The size of the DNA affects the speed at which it travels also. Larger
DNA molecules have a harder time going through the small pores of the agarose which slows it
down whereas small DNA molecules can easily move through the agarose. DNA gets its
negative charge from the phosphate backbone. Therefore a larger DNA molecule will also have
more of a negative charge thus causing it to move faster but it is not enough to counteract the
effort it will take for a larger molecule to go through the small pores. Finally if the DNA adheres
to the gel very well it will have a tough time moving through the agarose because it will be
sticking to the walls of the pores while it is trying to move through.

The Gel Electrophoresis is a project to help the group develop teamwork skills
and time management. All the classes that we have been taking inside the academy is all
incorporated inside this project to develop real life skills with what we have learned. The project
incorporates Biology for the ingredients inside the gel, Math for dimensioning, IED for the
electronic CAD drawings, and ITC for the actual solid build of the project. This project needs a
very accurate design to complete a working design that will read the information of the DNA
given.


Step 4: Identify Criteria and Constraints

There are many guidelines as to how the Gel Electrophoresis DNA Tester will look and
function

Follow the PLTW 12-Step Design Process.
Final design must include the following inventor drawings:
- Fully dimensioned multi-view drawings with an isometric drawing of each part
- A isometric drawing of the chamber, box, lid and comb
- A isometric drawing of the overall design
You must build the project.
Chamber must be watertight. It must sit overnight with water in it to validate there are no
leaks.
Plexiglass thickness cannot be less than 3/16 in thickness.
No hot glue is to be used.
The box must be able to retain the gel.
You must create five wells in the gel. No well can be closer than 1/8 to the side of the
box which contains the gel. The physical dimension of the well is 3/16 x 1/8 x 3/16.
The thickness of the comb is 1/8
Your gel must be 3/8 thick.
The buffer is to be no more than 1/8 above the surface of the gel when it is placed in the
chamber.
Power must be removed from the chamber if the lid is removed.
Final design drawings must be fully dimensioned using Inventor.
Maximum of 60 VDC is to be used as the power source.
Include all mathematical calculations that you use in calculating the optimal size of the
comb, box and chamber. Also include the square footage of the Plexiglas you will need and the
amount of buffer you will need.
You cannot begin constructing your project until I have signed off on your design,
drawings, bill of material and work process.
You must supply all your material except the banana jacks and the associated plugs.
You must supply your own insulated wire (12 gauge single conductor for the electrodes
and 16 or 18 gauge stranded for the power leads) and insulated alligator clips.

Step 5: Explore Possibilities

Explore Possibilities or Potential Solutions

Balance Sheets

Balance Sheet - Xaviers Design

Pros Cons
Cube Shaped
Very Thick Plexiglass
Small Only 1.25 in tall and 3in. length and
width

Very little extra space
Two different sizes of plexiglass
Complicated Lid Design
Costs more due to higher thickness Plexiglass



Balance Sheet - Pawels Design

Pros Cons
Handle Design for Lid
Rectangular with Extra Space
Cheap Plexiglass Design
Easy Design
Large
Specific Dimensions
Thin Walls



Balance Sheet - Carleas Design

Pros Cons
Box has removable pieces for molding gel
Simple geometric shapes of the chamber saves
buffer
Box has to mold the gel outside of the
chamber (more area= less convenient)
Chamber is too long
Non-removable sides of the box slows electric
current through the gel


Select an Approach

Decision Matrix


Carleas Design Pawels Design Xaviers Design
Efficiency 4 2 5
Amount of Changes
Needed
3 3 2
Difficulty to build 4 4 3
Cost 3 2 4
Size 5 3 3
Total 19 14 17

Rationale

Carleas design for the final design was chosen since it was the best designed without
making as many changes. Her design was was very efficient to its size and was designed for a
solid build. The making of the chamber and box will be more difficult compared to the others but
with the use of other drawings to fix what the drawing lacks, we would be able to configure it to
be more accurate. The gel electrophoresis design will be able to meet almost all the constraints
and criteria without many changes.

Design Proposal
Bill of Materials:

PART PART
DESCRIPTION
QUANTITY UNIT COST TOTAL COST
PLEXIGLASS Clear
plexiglass (.22
X 18 X 24)
Optix
1 $20 $20
INSULATED
ELECTRICAL
WIRE
Copper wire
stranded 18
gauge 33 ft. roll
1 Spool $8 $8
INSULATED
ALLIGATOR
CLIPS
2 Pack of
Insulated
Covered Clip
1

$3 $3
BATTERIES 9 Volt DC
Battery
(Duracell) 6
Pack
1 Package $12 $12
INSULATED
ELECTRICAL
WIRE
Solid 12 gauge
wire single
strand
5 ft. $.50 per Ft. $2.50
GLUE Loctite Silicone
Glue 2.5oz bottle
2 $3 $6
BANANA
PLUGS/JACK
.24 D banana
jacks. With
corresponding
plugs
2 Plugs $0 $0
AGAROSE
SOLAR CHEM
1.2% Resolution 50 mL $0 $0
BUFFER 50X TAE 75 mL $0 $0
FINAL PRICE - - - $51.50



Build Process:
Box
Materials Needed:
Plexiglass
Glue
Tools Needed:
Caliper
Speed Square
Band Saw
Belt Sander
Sharpie
Sticky Notes
C Clamps
Procedure:
1. Use a speed square and a Sharpie to draw a rectangle on the plexiglass according to the
length and height of the base of the box (refer to the drawing of the box base for the
dimensions)
2. Use a bandsaw to cut out the part
3. Label this rectangle as Part C1 by writing the part name on a sticky note using a Sharpie,
and placing the sticky note on the piece
4. Repeat steps 1-3 for Parts C2 and C3
5. Use the caliper and a speed square to take the precise measurements of the base, the long
sides, and short sides of the box
6. If necessary, use the belt sander to remove excess plexiglass according to the dimensions
in the drawings
7. Repeat steps 5 and 6 until desired dimensions from the drawings are reached with all
pieces
8. Assemble Parts C1, C2, and C3 to form the box using the glue to adhere the parts
together and the C Clamps to hold the parts together (refer to Drawing C for the
assembly)
9. Allow the glued box to dry overnight to assure that the assembly is secure
Lid

Materials Needed:
Plexiglass
Glue
Tools Needed:
Caliper
Drill Press
Speed Square
Band Saw
Belt Sander
Sharpie
Sticky Notes
C Clamps
Procedure:
1. Use a speed square and a Sharpie to draw a rectangle on the plexiglass according to the
length and height of the base of the lid (refer to the drawing of the lid for dimensions)
2. Use a bandsaw to cut out the part
3. Label this rectangle Part G1 by writing the part name on a sticky note using a Sharpie,
and placing the sticky note on the piece
4. Repeat steps 1-3 for Parts G2 and G3
5. Use the caliper and a speed square to take the precise measurements of the base of the lid,
the long sides, and short sides of the lid
6. If necessary, use the belt sander to remove excess plexiglass according to the dimensions
in the drawings
7. Repeat steps 5 and 6 until desired dimensions from the drawings are reached with all
pieces
8. With a speed square, draw cross marks to locate where the hole for the banana plugs will
be on the lid base, using the dimensions from the drawings
9. Locate a drill bit of 0.25 to use for the holes
10. Using the drill bit and drill press, drill the two holes where the markings were made
11. Assemble Parts G1, G2, and G3 to form the lid using the glue (refer to drawing G for the
assembly)
12. Allow the glued lid to dry overnight to assure that the assembly is secure
Chamber
Materials Needed:
Plexiglass
Glue
Tools Needed:
Caliper
Speed Square
Band Saw
Belt Sander
Sharpie
Sticky Notes
C Clamps
Procedure:
1. Use a speed square and a Sharpie to draw a rectangle on the plexiglass according to the
length and height of the base of the chamber (refer to the drawing of the base of the
chamber)
2. Use a bandsaw to cut out the base
3. Label this rectangle Part B1 by writing the part name on a sticky note using a Sharpie,
and placing the sticky note on the piece
4. Repeat steps 1-3 for Parts B2 and B3
5. Use the caliper and a speed square to take the precise measurements of the base of the
chamber, the long sides, and short sides of the chamber
6. If necessary, use the belt sander to remove excess plexiglass according to the dimensions
in the drawings
7. Repeat steps 5 and 6 until desired dimensions from the drawings are reached with all
pieces
8. Assemble Parts B1, B2, and B3 to form the lid using the glue (refer to drawing B for the
assembly)
9. Allow the glued chamber to dry overnight to assure that the assembly is secure
Comb
Materials Needed:
Plexiglass
Tools Needed:
Sticky Notes
Sharpie
Procedure:
1. Open an Inventor ipt file to create the properly sized comb.
2. Extrude the comb to the proper thickness.
3. Save the comb to your G drive as a stl file.
4. Get your instructor to assist you with moving the stl file from your G drive to the
desktop of the computer connected to the Rapid Prototyping Machine.
5. Open the stl file, orient it for printing, convert it and place it in the proper print
position.
6. Print the comb
Electrical Connections
Materials Needed:
Banana Plugs
Insulated Wire
Alligator Clips
Tools Needed:
Screw Driver
Wire Strippers
Wire Cutters
Procedure:
Note: Repeat this process twice to create two wires with banana plugs and alligator clips to
be used for the Gel Electrophoresis DNA Test
1. Cut 1ft long piece of wire with the wire cutters
2. Use the wire strippers to strip off one inch off of the wire on both ends, using the 18
gauge on the wire strippers
3. Leave the wire off to the side, and locate your banana plugs and the small screwdriver
that is small enough to remove the screw from the banana plug
4. Take one Banana Plug and remove the screw from it, being careful not to drop any of the
pieces
5. Take the stripped wire and put it in the open end of the banana plug
6. With the wire in the banana plug, place the screw back in the banana plug where it
originally was
7. Using the screwdriver from before, place the screw back into the banana plug, making the
screw clamp down onto the wire inside
8. Now locate the alligator clips and remove the insulation covering
9. Place the stripped end into the hole atop of the alligator clips,
10. Use needle nose pliers to pull the wire through
11. Open up the clip and place the insulation covering back over the clip and wire
12. Gently tug at the banana plug and alligator clip to test that the insulation is placed over
the clips properly and that the pieces wont fall off the wire
Final Assembly
Materials Needed:
All subassemblies
Electrical Connections
Batteries
Glue
Agarose
Buffer
Tools Needed:
Wooden Base (to rest drying parts)
Needle Nose Pliers
Speed Square
Ruler
Caliper
Procedure:
1. When the glue on each of the sub-assemblies is dry, put all of the sub-assemblies
together, according to the final assembly drawing
2. While this is happening, have another person connect each of the 6 batteries together by
snapping a positive end of the battery into a negative end of another battery, until all
batteries are connected
3. Connect the batteries to the electrical connections by clipping the alligator clips onto the
batteries
4. Place the banana plugs into the drummed holes of the lid
Test Plan

Test Criteria How Tested Expected Results Actual Results
Chamber Leakage Place water in Water will not leak Water did not leak
chamber and let set from chamber from chamber
Power source less
than or equal to 60V
DC
Use a multimeter The power used will
be between 54V and
60V
57.4 V
Functionality Test Place all parts
together and add the
gel and buffer to the
electrical system
The DNA will
seperate
Test on Friday


Prototype:
The box design had to be changed from the original design with removable sides to the
current one with non-removable sides. This change was made because plexiglass is not cut to
exactly .250 but it is cut to .220 since this was not accounted for in the original design the
sides had to be changed to compensate for this.

Refine:
When ordering the plexiglass the group realized that the sheets are made with a .22
thickness not .25 as thought originally. The dates had to be moved when after the pushing back
of the due date that was after the missing days from the Snow Days. During the building process
glueing had to be done more than once to have complete stability and accuracy. Also a few parts
had to be shaven down to make sure square surfaces and perfect dimensions for maximum
reliability.

Lessons Learned:
With the projects completion the group has learned many things to incorporate the 12
step design process and more. With researching we realized it is needed for members of the
group to rely on each other to learn about their specific parts so that brainstorming everyone can
be trusted. After making a timeline, which for a was done looking for every work process, every
item that gets included into the project, and giving it specific dates to accurately guide the group.
The timeline did in fact help us but we were not able to catch up to our predicted times, this
showed us how time specific hardworking from the beginning we have to be to get the model
finished. Communication was a key part of the process with text messages and chat icon in
Google Drive to help notify one another about the progress. Measurements of the plexiglass was
accounted for late because of late planning but fixed in a matter of a day from .25 to .22. We
also learned how to quickly measure and cut with high accuracy to be as efficient as possible. All
in all the experience was eye-opening and has shaped all three of us into more mature, time
managing students in which would help us to fulfill the dates of future projects and labs.