Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments: Difference between revisions
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====Experiment 3-3==== | ====Experiment 3-3==== | ||
'''Gel Identity:''' 2-8<br> | '''Gel Identity:''' 2-8<br> | ||
'''Equation:''' (W - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) | '''Equation:''' (W - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | ||
'''Purpose:''' To show that the Walker can move between tracks, specifically from Track 1 to Track 2. The system should equalize with walkers on both tracks.<br> | '''Purpose:''' To show that the Walker can move between tracks, specifically from Track 1 to Track 2. The system should equalize with walkers on both tracks.<br> | ||
'''Controls:''' W, TR<sub>1</sub>, TR<sub>2</sub>, PTR<sub>2</sub>, (W - TR<sub>1</sub>), (TR<sub>2</sub> - PTR<sub>2</sub>), (W - TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Controls:''' W, TR<sub>1</sub>, TR<sub>2</sub>, PTR<sub>2</sub>, (W - TR<sub>1</sub>), (TR<sub>2</sub> - PTR<sub>2</sub>), (W - TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
'''Positive Result:''' We should see a dark bands corresponding to all of the reagents and products.<br> | '''Positive Result:''' We should see a dark bands corresponding to all of the reagents and products.<br> | ||
'''Negative Result:''' We should not see any other dark bands. These would indicate that This indicates that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | '''Negative Result:''' We should not see any other dark bands. These would indicate that This indicates that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | ||
<br> | |||
====Experiment 3-4==== | |||
'''Gel Identity:''' 2-9<br> | |||
'''Equation:''' TR<sub>1</sub> + (W - TR<sub>2</sub> - PTR<sub>2</sub>) ↔ (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>)<br> | |||
'''Purpose:''' To show that the Walker can move between tracks, specifically from Track 2 to Track 1. The system should equalize with walkers on both tracks.<br> | |||
'''Controls:''' W, TR<sub>1</sub>, TR<sub>2</sub>, PTR<sub>2</sub>, (W - TR<sub>1</sub>), (TR<sub>2</sub> - PTR<sub>2</sub>), (W - TR<sub>2</sub> - PTR<sub>2</sub>)<br> | |||
'''Positive Result:''' We should see a dark bands corresponding to all of the reagents and products.<br> | |||
'''Negative Result:''' We should not see any other dark bands. These would indicate that either the Walker did not move as intended or that the movement interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | |||
<br> | |||
====Experiment 3-5==== | |||
'''Gel Identity:''' 2-12<br> | |||
'''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) → (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | |||
'''Purpose:''' To show that the Walker Inhibitor does in fact inhibit walking.<br> | |||
'''Controls:''' W, TR<sub>1</sub>, TR<sub>2</sub>, PTR<sub>2</sub>, (W - TR<sub>1</sub>), (TR<sub>2</sub> - PTR<sub>2</sub>), (W - TR<sub>2</sub> - PTR<sub>2</sub>)<br> | |||
'''Positive Result:''' We should see a dark bands corresponding to only the reagents, since we are looking for no change in the system.<br> | |||
'''Negative Result:''' We should not see any other dark bands. These would indicate that either the Walker Inhibitor did not work as intended or that the Walker Inhibitor interfered with another binding. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | |||
<br> | |||
====Experiment 3-5==== | |||
'''Gel Identity:''' 2-13<br> | |||
'''Equation:''' (W - WI - TR<sub>1</sub>) + (TR<sub>2</sub> - PTR<sub>2</sub>) + WT → (WI - WT) + (TR<sub>2</sub> - PTR<sub>2</sub>) + (W - TR<sub>1</sub>) + (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | |||
'''Purpose:''' To show that the Walker Trigger initiates walking.<br> | |||
'''Controls:''' W, TR<sub>1</sub>, TR<sub>2</sub>, PTR<sub>2</sub>, (W - TR<sub>1</sub>), (TR<sub>2</sub> - PTR<sub>2</sub>), (W - TR<sub>2</sub> - PTR<sub>2</sub>)<br> | |||
'''Positive Result:''' We should see a dark bands corresponding to only the products, since these correspond to the result of random walking<br> | |||
'''Negative Result:''' We should not see any other dark bands. These would indicate that either the Walker Trigger affected the system in some unintended way. The controls should give us enough information to determine which (if any) of the bindings is preferred by the system.<br> | |||
<br> | <br> | ||
Revision as of 15:33, 1 July 2011
Friday, March 29, 2024
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Gel ExperimentsExampleExperiment 0-1The 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 List of ExperimentsX + Y indicates strand X and strand Y exist independently in the same solution. Block 1: Walker Binding to trackExperiment 1-1Gel Identity: 1-6 Experiment 1-2Gel Identity: 1-7 Experiment 1-3Gel Identity: 1-12 Block 2: Walker Triggering MechanismExperiment 2-1Gel Identity: 1-8 Experiment 2-2Gel Identity: 1-9 Experiment 2-3Gel Identity: 1-10 Experiment 2-4Gel Identity: 1-11 Block 3: Random Walking MechanismExperiment 3-1Gel Identity: 2-5 Experiment 3-2Gel Identity: 2-6 Experiment 3-3Gel Identity: 2-8 Experiment 3-4Gel Identity: 2-9 Experiment 3-5Gel Identity: 2-12 Experiment 3-5Gel Identity: 2-13 Block 4: Cargo Pickup MechanismBlock 5: Goal Triggering MechanismBlock 6: Cargo Drop Off MechanismBlock 7: Time-based TestsBlock 8: Walker Goal FunctionalityGel Layout |