Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project

Thursday, April 18, 2024 Home Members Project Protocols Progress Discussion References

Project Design Project Overview What are we aiming to achieve? 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 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]. Main article: Domain Level Project Design Sequence Level 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. Main article: Sequence Design Experimental Design Verification of Mechanisms through 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. Main article: Gel Experiments Verification of Mechanisms through Fluorescent Spectroscopy Various DNA strands were tagged with fluorophores and quenchers in order to investigate different mechanisms more directly, both in solution and on origami. Main article: SPEX Experiments Verification of Mechanisms through Atomic Force Microscopy Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM. Main article: AFM Imaging References [1] Paul W. K. Rothemund. Folding DNA to Create Nanoscale Shapes and Patterns. Nature, 297-302, 2006