Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project

Saturday, April 20, 2024 Home Members Project Protocols Progress Discussion References

Project Design Overall Project Design Main article: Domain Level Project Design 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 an origami. 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. Sequence 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. Theoretical Work Simulation of Expected Results Main article: Simulation Before undertaking our experiments, it's desirable to have an idea what our results our going to look like, particularly in the case of random walking, which we intend to investigate rather thoroughly. To do this, we use a stochastic simulation, written in MATLAB. Derivation of Random Walk Formula Main article: Random Walk Formula Besides the MATLAB simulation of random walking and cargo sorting, a random walk formula was developed to further investigate and verify the random walking mechanism on DNA origami. 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 Imaging Walkers tagged with biotins were planted onto DNA origami, attempts were made to observe random walking on the origami directly under AFM.