Dwyer-ICCAD05

Dwyer-ICCAD05 - Computer-Aided Design for DNA...

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Computer-Aided Design for DNA Self-Assembly: Process and Applications Chris Dwyer Department of Electrical and Computer Engineering Department of Computer Science Duke University Durham, USA. dwyer@ece.duke.edu Abstract CAD plays a fundamental role in both top-down and bottom-up system fabrication. This paper presents a bottom-up circuit patterning process based on DNA self- assembly in terms of the design tool requirements and the new opportunities self-assembly creates for circuit designers. The paper also connects recent demonstrations of addressable self- assembly to applications in computer architecture and system design. I. INTRODUCTION Since the introduction of the idea that nucleic acids could be used to synthesize nanoscale grids and lattice structures the development of DNA self-assembly into a practical method for creating nanoscale circuit patterns has garnered increasing support [1-3]. However, the exotic nature of DNA self-assembly as compared to conventional photolithography introduces new challenges for system designers and CAD tool makers. Rudimentary tools exist for DNA sequence and structure design and are routinely used in the development of high yield and robust DNA self-assembly processes [4-10]. However, there is no shortage of future work and the next generation of tools must incorporate higher level awareness of the system task, such as a computing function or target fabrication yield, for DNA self-assembly to gain wider support in the circuits and systems design community. This task is challenging because it requires a wide audience from sub-fields with experience in system and circuit design to solve new problems in CAD for self- assembly. In that context this paper will serve as a focused tutorial on DNA self-assembly and feature a few of the potential applications of the method. Section II discusses the DNA self-assembly process and the fabrication of nanoscale patterns. Section III discusses the new capabilities self-assembly introduces to the circuit design challenge and section IV describes some of the benefits and challenges DNA self-assembly presents to system design. Final remarks and conclusions are in section V. II. DNA SELF-ASSEMBLY Nucleotide basics — The study of DNA has a rich and extensive past owing to its many decades as an important part of the central theme in molecular genetics. This tutorial will not be a summary of that work but instead will narrowly focus on DNA as a substrate for the fabrication of nanostructures. DNA is an acronym that stands for a class of chemicals known as deoxyribonucleic acids which have a basic block called a nucleotide. Nucleotides are composed of a phosphodiester covalently bound to a nucleoside or a derivative of a deoxyribose sugar and either a purine or pyrimidine nucleobase. The nucleobases commonly used in DNA self-assembly are the purines: adenine (A) and guanine (G), and the pyrimidines: thymine (T) and cytosine (C). The nucleotides can be bound to each other to form a linear chain
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Dwyer-ICCAD05 - Computer-Aided Design for DNA...

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