Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Project

Friday, April 26, 2024 Home Members Project Protocols Progress Discussion References

Project Design Project Overview Main article: Biomod/2011/Caltech/DeoxyriboNucleicAwesome/ProjectOverview/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 [7]. 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. Domain Level Design Main article: Domain Level Project 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]. 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 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. References [1] Lulu Qian and Erik Winfree. A simple DNA gate motif for synthesizing large-scale circuits. In International Meeting on DNA Computing, 2008. [2] David Soloveichik, Georg Seelig and Erik Winfree. DNA as a Universal Substrate for Chemical Kinetics. DNA 14, LNCS 5347: 57-69, 2009 [3] David Soloveichik, Matthew Cook, Erik Winfree and Jehoshua Bruck. Computation with Finite Stochastic Chemical Reaction Networks. Natural Computing Feburary, 2008. [4] Ye Tian, Yu He, Yi Chen, Peng Yin, and Chengde mao. A DNAzyme That Walks Processively and Autonomously along a One-Dimensional Track. Angewandte Chemie International EditionVol. 44, 4355-4358, 2005 [5] Kyle Lund, Anthony J. Manzo, Nadine Dabby, Nicole Michelotti, Alexander Johnson-Buck, Jeanette Nangreave, Steven Taylor, Renjun Pei, Milan N. Stojanovic, Nils G. Walter, Erik Winfree, and Hao Yan. Molecular Robots Guided by Prescriptive Landscapes. Nature, 206-210, 2010 [6] Hongzhou Gu, Jie Chao, Shou-Jun Xiao, Nadrian C. Seeman. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205. 2010 [7] Paul W. K. Rothemund. Folding DNA to Create Nanoscale Shapes and Patterns. Nature, 297-302, 2006