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Gel Experiments
Example
Experiment 0-1
The number to the left of the dash in the title represents which block of tests it belongs to, and the number to the right of the dash represents it's identity within the block
Gel Identity: The number to the left of the dash in this entry represents which gel the experiment will be observed on, and the right of the dash represents which lane it will occupy.
Equation: This shows the reagents and expected outcomes.
Purpose: This explains why this particular experiment is necessary or what it shows.
Controls: These are the controls necessary to read the results.
Positive Result: This is what we should observe to verify that this particular reaction worked as intended.
Negative Result: This is what we expect not to see. If this occurs, we will need to explore further for the cause of failure.
List of Experiments
X + Y indicates strand X and strand Y exist independently in the same solution.
(X - Y) indicates that strand X and strand Y bind to form a complex.
Block 1: Walker Binding to track
Experiment 1-1
Gel Identity: 1-6
Equation: W + TR1 → (W - TR1)
Purpose: To show that the Walker binds to one of the track strands
Controls: W, TR1
Positive Result: We should see a dark band not corresponding to either of the controls. We might see faint bands corresponding with the controls. This indicates that the two strands did in fact bind.
Negative Result: We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.
Experiment 1-2
Gel Identity: 1-7
Equation: W + TR2 → (W - TR2)
Purpose: To show that the Walker binds to the other track strand
Controls: W, TR2
Positive Result: We should see a dark band not corresponding to either of the controls. We might see faint bands corresponding with the controls. This indicates that the two strands did in fact bind.
Negative Result: We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.
Experiment 1-3
Gel Identity: 1-12
Equation: TR1 + TR2 → TR1 + TR2
Purpose: To show that the Tracks do not bind to each other.
Controls: TR1, TR2
Positive Result: Because TR1 and TR2 are the same length, we should only see one dark band at the same position as those in the control lane.
Negative Result: We should not see one dark band positioned differently than the bands in the control lanes. This indicates that the strands bound in a way that we did not intend.
Block 2: Walker Triggering Mechanism
Experiment 2-1
Gel Identity: 1-8
Equation: W + WI → (W - WI)
Purpose: To show that the Walker Inhibitor Binds to the Walker
Controls: W, WI
Positive Result: We should see a dark band not corresponding to either of the controls. We might see faint bands corresponding with the controls. This indicates that the two strands did in fact bind.
Negative Result: We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.
Experiment 2-2
Gel Identity: 1-9
Equation: WI + WT → (WI - WT)
Purpose: To show that the Walker Inhibitor Binds to the Walker Trigger
Controls: WI, WT
Positive Result: We should see a dark band not corresponding to either of the controls. We might see faint bands corresponding with the controls. This indicates that the two strands did in fact bind.
Negative Result: We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.
Experiment 2-3
Gel Identity: 1-10
Equation: W + WI + TR1 → (W - WI - TR1)
Purpose: To show that the Track binding to the Walker does not interfere with the binding between the Walker and Walker Inhibitor
Controls: W, WI, TR, (W - WI), (W - TR1)
Positive Result: We should see a dark band not corresponding to any of the controls. We might see faint bands corresponding with the controls. This indicates that the two strands did in fact bind.
Negative Result: We should not see dark bands corresponding to any of the control lanes. This indicates that the strands did not bind as intended. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.
Experiment 2-4
Gel Identity: 1-11
Equation: (W - WI - TR1) + WT → (W - TR1) + (WI - WT)
Purpose: To show that the Walker Trigger strips the Walker inhibitor off of the Walker
Controls: W, WI, WT, TR1, (W - WI), (W - TR1), (W - WI - TR1)
Positive Result: We should see dark bands corresponding to the control lanes of the products of this reaction( (WI - WT) and (W - TR1) ). We may see light bands corresponding to the reagents.
Negative Result: We should not see dark bands corresponding to any other control lanes. This indicates that the strands either did not react or preferred some other undesired configuration. The control lanes should give us enough information to determine which configuration was preferred.
Block 3: Random Walking Mechanism
Experiment 3-1
Gel Identity: 2-5
Equation: TR2 + PTR2 → (TR2 - PTR2)
Purpose: To show that Track 2 binds with its probe. This will allow us to distinguish between Track 2 and Track 1 in future experiments.
Controls: TR2, PTR2
Positive Result: We should see a dark band different from either of the controls. We may see light bands corresponding to the reagents.
Negative Result: We should not see dark bands corresponding to either of the controls. This indicates that the strands did not bind.
Block 4: Cargo Pickup Mechanism
Block 5: Goal Triggering Mechanism
Block 6: Cargo Drop Off Mechanism
Block 7: Time-based Tests
Block 8: Walker Goal Functionality
Gel Layout
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