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Revision as of 22:21, 2 November 2011 by Zibo Chen (talk | contribs) (Domain Level Design)
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Monday, December 11, 2017








Project Design

Project Overview

Our goal for the summer is to develop a system that autonomously sorts DNA tagged structures. Our base system involves randomly placed DNA tagged cargo on a rectangular DNA origami [1]. One edge of the origami is tagged with goal strands, and the rest of the origami is filled with track strands. The origami is then populated with random walkers that traverse the origami, picking up cargo and dropping them off at the goal. The motion of the walker and cargos will be examined by atomic force microscopy imaging. Bulk behavior of the system, kinetics of walking, and mechanisms of cargo picking up, and cargo dropping off will be analyzed by SPEX experiment.

Main article: Project Overview


Domain Level Design

Overall domain level design is illustrated in the figure below. 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].

Main article: Domain Level Project Design
Overall domain level design.

Origami Layout

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

Main Article: List of Origami Layouts

Sequence Level Design

Main article: Sequence Design

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.

Experimental Design

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
Main article: SPEX Results

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.


[1] Paul W. K. Rothemund. Folding DNA to Create Nanoscale Shapes and Patterns. Nature, 297-302, 2006