Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments

Friday, April 19, 2024 Home Members Project Protocols Progress Discussion References

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. Block 2: Walker Triggering Mechanism Block 3: Random Walking Mechanism 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