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

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Monday, October 23, 2017








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

Verification of Mechanisms through Gel Experiments

Main article: Gel Experiments

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.

Verification of Mechanisms through Fluorescent Spectroscopy

Main article: SPEX Experiments

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

Verification of Mechanisms through Atomic Force Microscopy

Main article: AFM Experiment
Main article: AFM Imaging

Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.