Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments: Difference between revisions
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{{Template:DeoxyriboNucleicAwesomeHeader}} | {{Template:DeoxyriboNucleicAwesomeHeader}} | ||
=Gel Experiments= | =Design for the Gel Experiments= | ||
__NOTOC__ | __NOTOC__ | ||
:''See also: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design#List of Strands|List of Strands]]'' | |||
==Example== | ==Example== | ||
====Experiment 0-1==== | ====Experiment 0-1==== | ||
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(X - Y) indicates that strand X and strand Y bind to form a complex. | (X - Y) indicates that strand X and strand Y bind to form a complex. | ||
===Block 1: Walker Binding to track=== | ===Block 1: Walker Binding to track=== | ||
====Experiment 1-1==== | ====Experiment Design 1-1==== | ||
'''Gel Identity:''' 1-6<br> | '''Gel Identity:''' 1-6<br> | ||
'''Equation:''' W + TR<sub>1</sub> → (W - TR<sub>1</sub>)<br> | '''Equation:''' W + TR<sub>1</sub> → (W - TR<sub>1</sub>)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 1-2==== | ====Experiment Design 1-2==== | ||
'''Gel Identity:''' 1-7<br> | '''Gel Identity:''' 1-7<br> | ||
'''Equation:''' W + TR<sub>2</sub> → (W - TR<sub>2</sub>)<br> | '''Equation:''' W + TR<sub>2</sub> → (W - TR<sub>2</sub>)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 1-3==== | ====Experiment Design 1-3==== | ||
'''Gel Identity:''' 1-12<br> | '''Gel Identity:''' 1-12<br> | ||
'''Equation:''' TR<sub>1</sub> + TR<sub>2</sub> → TR<sub>1</sub> + TR<sub>2</sub><br> | '''Equation:''' TR<sub>1</sub> + TR<sub>2</sub> → TR<sub>1</sub> + TR<sub>2</sub><br> | ||
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===Block 2: Walker Triggering Mechanism=== | ===Block 2: Walker Triggering Mechanism=== | ||
====Experiment 2-1==== | ====Experiment Design 2-1==== | ||
'''Gel Identity:''' 1-8<br> | '''Gel Identity:''' 1-8<br> | ||
'''Equation:''' W + WI → (W - WI)<br> | '''Equation:''' W + WI → (W - WI)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 2-2==== | ====Experiment Design 2-2==== | ||
'''Gel Identity:''' 1-9<br> | '''Gel Identity:''' 1-9<br> | ||
'''Equation:''' WI + WT → (WI - WT)<br> | '''Equation:''' WI + WT → (WI - WT)<br> | ||
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'''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the control lanes. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 2-3==== | ====Experiment Design 2-3==== | ||
'''Gel Identity:''' 1-10<br> | '''Gel Identity:''' 1-10<br> | ||
'''Equation:''' W + WI + TR<sub>1</sub> → (W - WI - TR<sub>1</sub>)<br> | '''Equation:''' W + WI + TR<sub>1</sub> → (W - WI - TR<sub>1</sub>)<br> | ||
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'''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.<br> | '''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.<br> | ||
<br> | <br> | ||
====Experiment 2-4==== | ====Experiment Design 2-4==== | ||
'''Gel Identity:''' 1-11<br> | '''Gel Identity:''' 1-11<br> | ||
'''Equation:''' (W - WI - TR<sub>1</sub>) + WT → (W - TR<sub>1</sub>) + (WI - WT)<br> | '''Equation:''' (W - WI - TR<sub>1</sub>) + WT → (W - TR<sub>1</sub>) + (WI - WT)<br> | ||
'''Purpose:''' To show that the Walker Trigger strips the Walker inhibitor off of the Walker<br> | '''Purpose:''' To show that the Walker Trigger strips the Walker inhibitor off of the Walker<br> | ||
'''Controls:''' W, WI, WT, TR<sub>1</sub>, (W - WI), (W - TR<sub>1</sub>), (W - WI - TR<sub>1</sub>)<br> | '''Controls:''' W, WI, WT, TR<sub>1</sub>, (W - WI), (W - TR<sub>1</sub>), (W - WI - TR<sub>1</sub>)<br> | ||
'''Positive Result:''' We should see dark bands corresponding to the control lanes of the products of this reaction( (WI - WT) and (W - TR<sub>1</sub>) ). We may see light bands corresponding to the reagents.<br> | '''Positive Result:''' We should see dark bands corresponding to two of the control lanes of the products of this reaction( (WI - WT) and (W - TR<sub>1</sub>) ). We may see light bands corresponding to the reagents.<br> | ||
'''Negative Result:''' We should not see dark bands corresponding to any other 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 other bindings is preferred by the system.<br> | '''Negative Result:''' We should not see dark bands corresponding to any other 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 other bindings is preferred by the system.<br> | ||
<br> | <br> | ||
===Block 3: Random Walking Mechanism=== | ===Block 3: Random Walking Mechanism=== | ||
====Experiment 3-1==== | ====Experiment Design 3-1==== | ||
'''Gel Identity:''' 2-5<br> | '''Gel Identity:''' 2-5<br> | ||
'''Equation:''' TR<sub>2</sub> + PTR<sub>2</sub> → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Equation:''' TR<sub>2</sub> + PTR<sub>2</sub> → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
Line 85: | Line 86: | ||
'''Negative Result:''' We should not see dark bands corresponding to either of the controls. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see dark bands corresponding to either of the controls. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 3-2==== | ====Experiment Design 3-2==== | ||
'''Gel Identity:''' 2-6<br> | '''Gel Identity:''' 2-6<br> | ||
'''Equation:''' W + (TR<sub>2</sub> - PTR<sub>2</sub>) → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | '''Equation:''' W + (TR<sub>2</sub> - PTR<sub>2</sub>) → (TR<sub>2</sub> - PTR<sub>2</sub>)<br> | ||
Line 93: | Line 94: | ||
'''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.<br> | '''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.<br> | ||
<br> | <br> | ||
====Experiment 3-3==== | ====Experiment Design 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>) ↔ (W - TR<sub>2</sub> - PTR<sub>2</sub>) + TR<sub>1</sub><br> | '''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> | ||
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'''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> | <br> | ||
====Experiment 3-4==== | ====Experiment Design 3-4==== | ||
'''Gel Identity:''' 2-9<br> | '''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> | '''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> | ||
Line 109: | Line 110: | ||
'''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> | '''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> | <br> | ||
====Experiment 3-5==== | ====Experiment Design 3-5==== | ||
'''Gel Identity:''' 2-12<br> | '''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> | '''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> | ||
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<br> | <br> | ||
====Experiment 3-6==== | ====Experiment Design 3-6==== | ||
'''Gel Identity:''' 2-13<br> | '''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> | '''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> | ||
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===Block 4: Cargo Pickup Mechanism=== | ===Block 4: Cargo Pickup Mechanism=== | ||
====Experiment 4-1==== | ====Experiment Design 4-1==== | ||
'''Gel Identity:''' 4-4<br> | '''Gel Identity:''' 4-4<br> | ||
'''Equation:''' | '''Equation:''' C<sub>1</sub> + CA → (C<sub>1</sub> - CA)<br> | ||
'''Purpose:''' To show that the Cargo binds to the Cargo Attaching point.<br> | '''Purpose:''' To show that the Cargo binds to the Cargo Attaching point.<br> | ||
'''Controls:''' | '''Controls:''' C<sub>1</sub>, CA<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to either of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to either of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see two dark bands corresponding to the controls. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the controls. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 4-2==== | |||
====Experiment Design 4-2==== | |||
'''Gel Identity:''' 4-5<br> | '''Gel Identity:''' 4-5<br> | ||
'''Equation:''' W + | '''Equation:''' W + C<sub>1</sub> → (W - C<sub>1</sub>)<br> | ||
'''Purpose:''' To show that the Cargo binds to the Walker.<br> | '''Purpose:''' To show that the Cargo binds to the Walker.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub><br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to either of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to either of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see two dark bands corresponding to the controls. This indicates that the strands did not bind.<br> | '''Negative Result:''' We should not see two dark bands corresponding to the controls. This indicates that the strands did not bind.<br> | ||
<br> | <br> | ||
====Experiment 4-3==== | |||
====Experiment Design 4-3==== | |||
'''Gel Identity:''' 4-6<br> | '''Gel Identity:''' 4-6<br> | ||
'''Equation:''' W + ( | '''Equation:''' W + (C<sub>1</sub> - CA) → (W - C<sub>1</sub>) + CA<br> | ||
'''Purpose:''' To show that the Walker strips the Cargo off of the Cargo Attaching point.<br> | '''Purpose:''' To show that the Walker strips the Cargo off of the Cargo Attaching point.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub>, CA, (W - C<sub>1</sub>), (C<sub>1</sub> - CA)<br> | ||
'''Positive Result:''' We should see two dark bands that correspond to products of the reaction. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see two dark bands that correspond to products of the reaction. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Cargo did not transfer to the Walker as intended.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the Cargo did not transfer to the Walker as intended.<br> | ||
<br> | <br> | ||
====Experiment 4-4==== | |||
====Experiment Design 4-4==== | |||
'''Gel Identity:''' 4-8<br> | '''Gel Identity:''' 4-8<br> | ||
'''Equation:''' W + | '''Equation:''' W + C<sub>1</sub> + TR<sub>1</sub> → (W - C<sub>1</sub> - TR<sub>1</sub>)<br> | ||
'''Purpose:''' To show that Track 1 does not interfere with the binding between the Walker and Cargo.<br> | '''Purpose:''' To show that Track 1 does not interfere with the binding between the Walker and Cargo.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub>, TR<sub>1</sub>, (W - C<sub>1</sub>), (W - TR<sub>1</sub>)<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any dark bands corresponding to the controls. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | '''Negative Result:''' We should not see any dark bands corresponding to the controls. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | ||
<br> | <br> | ||
====Experiment 4-5==== | |||
====Experiment Design 4-5==== | |||
'''Gel Identity:''' 4-9<br> | '''Gel Identity:''' 4-9<br> | ||
'''Equation:''' W + | '''Equation:''' W + C<sub>1</sub> + TR<sub>2</sub> → (W - C<sub>1</sub> - TR<sub>2</sub>)<br> | ||
'''Purpose:''' To show that Track 2 does not interfere with the binding between the Walker and Cargo.<br> | '''Purpose:''' To show that Track 2 does not interfere with the binding between the Walker and Cargo.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub>, TR<sub>2</sub>, (W - C<sub>1</sub>), (W - TR<sub>2</sub>)<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any dark bands corresponding to the controls. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | '''Negative Result:''' We should not see any dark bands corresponding to the controls. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | ||
<br> | <br> | ||
====Experiment 4-6==== | |||
====Experiment Design 4-6==== | |||
'''Gel Identity:''' 4-10<br> | '''Gel Identity:''' 4-10<br> | ||
'''Equation:''' (W - TR<sub>1</sub>) + ( | '''Equation:''' (W - TR<sub>1</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>1</sub>) + CA<br> | ||
'''Purpose:''' To show that Track 1 does not interfere with the Walker stripping the Cargo off of the Cargo Attaching point.<br> | '''Purpose:''' To show that Track 1 does not interfere with the Walker stripping the Cargo off of the Cargo Attaching point.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub>, CA, TR<sub>1</sub>, (W - C<sub>1</sub>), (W - TR<sub>1</sub>), (C<sub>1</sub> - CA)<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to one of the controls(for (W - | '''Positive Result:''' We should see one dark band that doesn't correspond to one of the controls(for (W - C<sub>1</sub> - TR<sub>1</sub>) ), and one dark band that corresponds with the remaining strand (CA). We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | ||
<br> | <br> | ||
====Experiment 4-7==== | ====Experiment Design 4-7==== | ||
'''Gel Identity:''' 4-11<br> | '''Gel Identity:''' 4-11<br> | ||
'''Equation:''' (W - TR<sub>2</sub>) + ( | '''Equation:''' (W - TR<sub>2</sub>) + (C<sub>1</sub> - CA) → (W - C<sub>1</sub> - TR<sub>2</sub>) + CA<br> | ||
'''Purpose:''' To show that Track 2 does not interfere with the Walker stripping the Cargo off of the Cargo Attaching point.<br> | '''Purpose:''' To show that Track 2 does not interfere with the Walker stripping the Cargo off of the Cargo Attaching point.<br> | ||
'''Controls:''' W, | '''Controls:''' W, C<sub>1</sub>, CA, TR<sub>2</sub>, (W - C<sub>1</sub>), (W - TR<sub>2</sub>), (C<sub>1</sub> - CA)<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to any | '''Positive Result:''' We should see one dark band that doesn't correspond to one any the controls(for (W - C<sub>1</sub> - TR<sub>2</sub>) ), and one dark band that corresponds with the remaining strand (CA). We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that Track 1 interferes with the binding between the Walker and Cargo.<br> | ||
<br> | <br> | ||
===Block 5: Goal Triggering Mechanism=== | ===Block 5: Goal Triggering Mechanism=== | ||
====Experiment 5-1==== | ====Experiment Design 5-1==== | ||
'''Gel Identity:''' 3-4<br> | '''Gel Identity:''' 3-4<br> | ||
'''Equation:''' | '''Equation:''' CG<sub>1</sub> + CGI → (CG<sub>1</sub> - CGI)<br> | ||
'''Purpose:''' To show that the apropreate inhibitor binds to the goal.<br> | '''Purpose:''' To show that the apropreate inhibitor binds to the goal.<br> | ||
'''Controls:''' | '''Controls:''' CG<sub>1</sub>, CGI<br> | ||
'''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | ||
<br> | <br> | ||
====Experiment 5-2==== | |||
====Experiment Design 5-2==== | |||
'''Gel Identity:''' 3-5<br> | '''Gel Identity:''' 3-5<br> | ||
'''Equation:''' CGI + CGT → (CGI - CGT)<br> | '''Equation:''' CGI + CGT → (CGI - CGT)<br> | ||
Line 203: | Line 210: | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | '''Negative Result:''' We should not see any other dark bands. This indicates that the inhibitor does not bind with the goal.<br> | ||
<br> | <br> | ||
====Experiment 5-3==== | ====Experiment Design 5-3==== | ||
'''Gel Identity:''' 3-6<br> | '''Gel Identity:''' 3-6<br> | ||
'''Equation:''' ( | '''Equation:''' (CG<sub>1</sub> - CGI) + CGT → CG<sub>1</sub> + (CGI - CGT)<br> | ||
'''Purpose:''' To show that the trigger is capable of stripping the inhibitor off of the goal.<br> | '''Purpose:''' To show that the trigger is capable of stripping the inhibitor off of the goal.<br> | ||
'''Controls:''' | '''Controls:''' CG<sub>1</sub>, CGI, CGT, (CG<sub>1</sub> - CGI), (CGI - CGT)<br> | ||
'''Positive Result:''' We should see one dark band that corresponds to one of the controls(for (CGI - CGT) ), and one dark band that corresponds with the remaining strand (CG<sub>1</sub>). We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the trigger does not interract with the inhibitor properly.<br> | |||
<br> | |||
===Block 6: Cargo Drop Off Mechanism=== | |||
====Experiment Design 6-1==== | |||
'''Gel Identity:''' 6-7<br> | |||
'''Equation:''' C1 + CG1 → (C1 - CG1)<br> | |||
'''Purpose:''' To show that the cargo binds to the goal.<br> | |||
'''Controls:''' C1, CG1<br> | |||
'''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | '''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the | '''Negative Result:''' We should not see any other dark bands. This indicates that the cargo does not bind with the goal.<br> | ||
<br> | <br> | ||
===Block 7: Time-based Tests=== | ===Block 7: Time-based Tests=== | ||
====Experiment Design 7-1==== | |||
'''Gel Identity:''' 3-6<br> | |||
'''Equation:''' (W - C1) + (CG1 - CGI) → (C1 - CG1) + W + CGI<br> | |||
'''Purpose:''' There is a potential for 4 way strand displacement to occur with an undesired affect. We wish to find the rate at which this reaction occurs in these timed reactions.<br> | |||
'''Controls:''' W, C1, CG1, CGI, (W - C1), (CG1 - CGI), (C1 - CG1)<br> | |||
'''Positive Result:''' Because we are hoping that this reaction doesn't occur, a result that indicates that everything is working correctly would show two dark bands corresponding to (W - C1) and (GC1 - GCI).<br> | |||
'''Negative Result:''' Any other dark bands would be indicative of the Goal Inhibitor not actually inhibiting the function of the Goal. <br> | |||
<br> | |||
===Block 8: Walker Goal Functionality=== | ===Block 8: Walker Goal Functionality=== | ||
=== | ====Experiment Design 8-1==== | ||
'''Gel Identity:''' 8-6<br> | |||
==Gel | '''Equation:''' W + WG → (W - WG)<br> | ||
=== | '''Purpose:''' To show that the Walker binds to a Walker goal intended to be used in timing the speed of our random walking mechanism.<br> | ||
'''Controls:''' W, WG<br> | |||
=== | '''Positive Result:''' We should see one dark band that doesn't correspond to anu of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | |||
===Gel | <br> | ||
====Experiment Design 8-2==== | |||
=== | '''Gel Identity:''' 8-7<br> | ||
'''Equation:''' WG + PWG → (WG - PWG)<br> | |||
=== | '''Purpose:''' To show that the Walker Goal binds to its probe. This will help us easily distinguish between the walker goal and Track strands.<br> | ||
'''Controls:''' WG, PWG<br> | |||
=== | '''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | ||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker does not bind to the goal.<br> | |||
=== | <br> | ||
====Experiment Design 8-3==== | |||
'''Gel Identity:''' 8-6<br> | |||
'''Equation:''' W + (WG - PWG) → (W - WG - PWG)<br> | |||
'''Purpose:''' To show that the Walker Goal Probe does not interfere with the bond between the Walker and Walker goal<br> | |||
'''Controls:''' W, WG, PWG, (WG - PWG), (W - WG)<br> | |||
'''Positive Result:''' We should see one dark band that doesn't correspond to any of the controls. We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal Probe interferes with the Walker and Walker Goal bond.<br> | |||
<br> | |||
====Experiment Design 8-4==== | |||
'''Gel Identity:''' 8-10<br> | |||
'''Equation:''' (W - TR<sub>1</sub>) + (WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | |||
'''Purpose:''' To show that the Walker Goal can strip the Walker off of Track 1.<br> | |||
'''Controls:''' W, WG, PWG, TR<sub>1</sub>, (W - TR<sub>1</sub>), (WG - PWG), (W - WG - PWG)<br> | |||
'''Positive Result:''' We should see two dark bands that correspond to the controls for TR<sub>1</sub> and (W - WG - PWG). We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 1.<br> | |||
<br> | |||
====Experiment Design 8-5==== | |||
'''Gel Identity:''' 8-11<br> | |||
'''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> | |||
'''Purpose:''' To show that the Walker Goal can strip the Walker off of Track 2.<br> | |||
'''Controls:''' W, WG, PWG, TR<sub>2</sub>, (W - TR<sub>2</sub>), (WG - PWG), (W - WG - PWG)<br> | |||
'''Positive Result:''' We should see two dark bands that correspond to the controls for TR<sub>2</sub> and (W - WG - PWG). We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 2.<br> | |||
<br> | |||
====Experiment Design 8-6==== | |||
'''Gel Identity:''' 8-12<br> | |||
'''Equation:''' TR<sub>1</sub> + (W - WG - PWG) → TR<sub>1</sub> + (W - WG - PWG)<br> | |||
'''Purpose:''' To show that the Walker cannot move to Track 1 from the Walker Goal.<br> | |||
'''Controls:''' W, WG, PWG, TR<sub>1</sub>, (W - TR<sub>1</sub>), (WG - PWG), (W - WG - PWG)<br> | |||
'''Positive Result:''' We should see two dark bands that correspond to the controls for TR<sub>1</sub> and (W - WG - PWG). We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker is capable of leaving the walker goal.<br> | |||
<br> | |||
====Experiment Design 8-7==== | |||
'''Gel Identity:''' 8-13<br> | |||
'''Equation:''' (W - TR<sub>2</sub>) + (WG - PWG) → TR<sub>2</sub> + (W - WG - PWG)<br> | |||
'''Purpose:''' To show that the Walker cannot move to Track 1 from the Walker Goal.<br> | |||
'''Controls:''' W, WG, PWG, TR<sub>1</sub>, (W - TR<sub>1</sub>), (WG - PWG), (W - WG - PWG)<br> | |||
'''Positive Result:''' We should see two dark bands that correspond to the controls for TR<sub>1</sub> and (W - WG - PWG). We may see light bands corresponding with the reagents.<br> | |||
'''Negative Result:''' We should not see any other dark bands. This indicates that the Walker Goal is incapable of stripping the walker off of Track 1.<br> | |||
<br> | |||
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Latest revision as of 23:20, 2 November 2011
Tuesday, April 23, 2024
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Design for the Gel Experiments
ExampleExperiment 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 Design 1-1Gel Identity: 1-6 Experiment Design 1-2Gel Identity: 1-7 Experiment Design 1-3Gel Identity: 1-12 Block 2: Walker Triggering MechanismExperiment Design 2-1Gel Identity: 1-8 Experiment Design 2-2Gel Identity: 1-9 Experiment Design 2-3Gel Identity: 1-10 Experiment Design 2-4Gel Identity: 1-11 Block 3: Random Walking MechanismExperiment Design 3-1Gel Identity: 2-5 Experiment Design 3-2Gel Identity: 2-6 Experiment Design 3-3Gel Identity: 2-8 Experiment Design 3-4Gel Identity: 2-9 Experiment Design 3-5Gel Identity: 2-12 Experiment Design 3-6Gel Identity: 2-13 Block 4: Cargo Pickup MechanismExperiment Design 4-1Gel Identity: 4-4 Experiment Design 4-2Gel Identity: 4-5 Experiment Design 4-3Gel Identity: 4-6 Experiment Design 4-4Gel Identity: 4-8 Experiment Design 4-5Gel Identity: 4-9 Experiment Design 4-6Gel Identity: 4-10 Experiment Design 4-7Gel Identity: 4-11 Block 5: Goal Triggering MechanismExperiment Design 5-1Gel Identity: 3-4 Experiment Design 5-2Gel Identity: 3-5 Experiment Design 5-3Gel Identity: 3-6 Block 6: Cargo Drop Off MechanismExperiment Design 6-1Gel Identity: 6-7 Block 7: Time-based TestsExperiment Design 7-1Gel Identity: 3-6 Block 8: Walker Goal FunctionalityExperiment Design 8-1Gel Identity: 8-6 Experiment Design 8-2Gel Identity: 8-7 Experiment Design 8-3Gel Identity: 8-6 Experiment Design 8-4Gel Identity: 8-10 Experiment Design 8-5Gel Identity: 8-11 Experiment Design 8-6Gel Identity: 8-12 Experiment Design 8-7Gel Identity: 8-13
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