Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Progress/System Design

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(Design of the experiments)
 
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= Progress 1: System Design =
= Progress 1: System Design =
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==Domain Level Design==
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==Design of the overall system ==
Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].
Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].
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:''Main article about Sequence Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design|Sequence Design]]''
:''Main article about Sequence Level Design: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design|Sequence Design]]''
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:Main Article about Origami Layout Design: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts|List of Origami Layouts]]''
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:''Main Article about Origami Layout Design: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts|List of Origami Layouts]]''
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== Design of the experiments ==
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== Experimental Design==
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We used three different experimental techniques, and here is the design of each experiments.
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==== Verification of Mechanisms through Gel Experiments====
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1. Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.  
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Gel Experiments|Gel Experiments]]''
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Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.  
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2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.
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==== Verification of Mechanisms through Fluorescent Spectroscopy====
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:''Main article about design of the SPEX experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments|SPEX Experiments Design]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/SPEX Experiments|SPEX Experiments]]''
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Various DNA strands were tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.
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3. Individual system is observed directly under AFM.
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==== Verification of Mechanisms through Atomic Force Microscopy====
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:''Main article about desing of the AFM experiment: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design|AFM Experiment Design]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments Design|AFM Experiment]]''
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:''Main article: [[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/AFM Experiments|AFM Imaging]]''
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Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.
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Monday, October 20, 2014

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Progress 1: System Design

Design of the overall system

Overall domain level design is illustrated in figure 1. Following abbreviation will be frequently used: walker [W], walker inhibitor [WI], track 1 [TR1], probe for track 1 [PTR1], track 2 [TR2], probe for track 2 [PTR2], cargo 1 [C1], cargo attacher [CA], probe for cargo attacher [PCA], cargo goal inhibitor [CGI], cargo goal 1 [CG1], probe for cargo goal [PCG], walker goal [WG], and probe for walker goal [PWG].

With our overall design in mind, we must design DNA sequences, down to the base level, which undergo the interactions that we desire, without forming secondary structures and binding in unintended ways. We approach this through a combination of pre-generated noninteracting sequences, and trial-and-error design using NUPACK simulation software.

Also, Random walking playground and cargo sorting playground were designed using a rectangular orgiami.

Main article about Domain Level Design: Domain Level Project Design
Main article about Sequence Level Design: Sequence Design
Main Article about Origami Layout Design: List of Origami Layouts

Design of the experiments

We used three different experimental techniques, and here is the design of each experiments.

1. Before constructing our origami and observing how it behaves, we run a large number of experiments observable through Gel Electrophoresis to verify that many of our mechanisms behave as we expect them to.

2. Various DNA strands are tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami.

Main article about design of the SPEX experiment: SPEX Experiments Design

3. Individual system is observed directly under AFM.

Main article about desing of the AFM experiment: AFM Experiment Design


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