Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/Experimental Results

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(Progress 3: Verification of Overall Mechanisms in Solution)
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==Progress 3: Verification of Overall Mechanisms in Solution==
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==Verification of Overall Mechanisms in Solution==
While the [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project|overall project]] is the sorting of cargos on origami, we expected verification of all of the mechanisms would take longer than one summer.  Therefore, this summer was spent verifying two aspects of the project:
While the [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project|overall project]] is the sorting of cargos on origami, we expected verification of all of the mechanisms would take longer than one summer.  Therefore, this summer was spent verifying two aspects of the project:

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Friday, August 29, 2014

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Verification of Overall Mechanisms in Solution

While the overall project is the sorting of cargos on origami, we expected verification of all of the mechanisms would take longer than one summer. Therefore, this summer was spent verifying two aspects of the project:

  1. Verification of the proposed mechanisms working when the strands are free-floating in solution (i.e. not bound to origami).
  2. Verification of the random walking mechanism on origami.


Gel Verification

Main article: Gel Verification

All of the essential mechanisms in our system were verified in solution using polyacrylamide gel electrophoresis. These mechanisms include: walker-track binding, triggering the walker, walking from one track to another, picking up cargo, walking while carrying cargo, triggering the cargo goal, dropping off cargo, and irreversibly walking from tracks to the walker goal. We are fairly confident that all of these mechanisms work as expected in solution, with a few mysteries that do not seem to interfere with the overall behavior of the system (see Gel Verification).

SPEX Verification

Verification of Random Walking Mechanism on Origami

SPEX Verification

Main article: SPEX Results

We used fluorescent spectroscopy (SPEX) to verify the random walking mechanism on the origami. Goals were tagged with fluorophores whereas walkers were tagged with the corresponding quenchers. Fluorescent signals will decrease when walkers reach their goals. Unlike AFM, which studied individual origami, SPEX experiments studied the collective behavior of all the origami in solution. Hence, the SPEX results were analyzed using both Matlab simulation and mathematical formulae.

AFM Verification

Main article: AFM Experiments

We are in the process of using atomic force microscopy (AFM) to verify the random walking mechanism on origami. We plan to image individual origami rectangles (using the 1D random walking playground layout) with an inhibited, biotin/streptavidin-tagged walker at its start site, and verify that walkers begin at their intended start site at one end of the random-walking track. We will then trigger the walker, wait for some amount of time, and image the origami again to verify that walkers have left their start site and are tending to stop at their goal at the other end of the track. This research is still in progress.


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