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Computing in Science and Engineering
Challenges and Applications for Self-Assembled DNA Nanostructures
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Biomolecular autonomous solution of the Hamiltonian path problem via hairpin formation
International Journal of Bioinformatics Research and Applications
Autonomous programmable nanorobotic devices using DNAzymes
DNA13'07 Proceedings of the 13th international conference on DNA computing
DNA computing: a research snapshot
Algorithms and theory of computation handbook
A framework for modeling DNA based molecular systems
DNA'06 Proceedings of the 12th international conference on DNA Computing
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We provide designs for the first autonomous DNA nanome-chanical devices that execute cycles of motion without external environmental changes. These DNA devices translate across a circular strand of ssDNA and rotate simultaneously. The designs use various energy sources to fuel the movements, include (i) ATP consumption by DNA ligase in conjunction with restriction enzyme operations, (ii) DNA hybridization energy in trapped states, and (iii) kinetic (heat) energy. We show that each of these energy sources can be used to fuel random bidirectional movements that acquire after n steps an expected translational deviation of O(驴n). For the devices using the first two fuel sources, the rate of stepping is accelerated over the rate of random drift due to kinetic (heat) energy. Our first DNA device, which we call walking DNA, achieves random bidirectional motion around a circular ssDNA strand by use of DNA ligase and two restriction enzymes. Our other DNA device, which we call rolling DNA, achieves random bidirectional motion without use of DNA ligase or any restriction enzyme, and instead using either hybridization energy (also possibly just using kinetic (heat) energy at a unfeasible low rate of resulting movement).