DNA Self-Assembly for Constructing 3D Boxes

Ming-Yang Kao and Vijay Ramachandran

Abstract

We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model is a more precise superset of their Tile Assembly Model that facilitates building scalable 3D molecules. Under our model, we present algorithms to build a hollow cube, which is intuitively one of the simplest 3D structures to construct. We also introduce five basic measures of complexity to analyze these algorithms. Our model and algorithmic techniques are applicable to more complex 2D and 3D nanostructures.

Current Citation

M.-Y. Kao and V. Ramachandran. "DNA Self-Assembly for Constructing 3D Boxes" (extended abstract). In Proc. ISAAC 2001, LNCS vol. 2223, pp. 429-440, December 2001. Full version available at arXiv.org CoRR cs.CC/0112009.

@inproceedings{kr01-dna3d,
	title = {{DNA} Self-Assembly for Constructing {3D} Boxes},
	author = {Ming-Yang Kao and Vijay Ramachandran},
	booktitle = {Proc.\ {ISAAC} 2001},
	pages = {429--440},
	year = {2001},
	month = {December},
	series = {LNCS},
	volume = {2223},
	publisher = {Springer},
	note = {Full version available at arXiv.org CoRR cs.CC/0112009.},
	url = {http://arxiv.org/abs/cs.CC/0112009} } 

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Filetype	Version
(216K)	Full version of the paper (posted to arXiv.org)
(159K)	Extended abstract: published conference version of the paper
(417K)	Revised version of slides used for ISAAC'01 talk