Computing Handbook Set - Computer Science (Volume I) Chapter: DNA Computing Sudhanshu Garg, Reem Mokhtar, Tianqi Song, Hieu Bui, Nikhil Gopalkrishnan, John Reif
[email protected] Department of Computer Science, Duke University (Reif is also Adjunct, Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi Arabia) Organization of Chapter Molecular computing is computation done at the molecular scale. DNA computing is a class of molecular computing that does computation by the use of reactions involving DNA molecules. DNA computing has been by far the most successful (in scale and complexity of the computations and molecular assemblies done) of all known approaches to molecular computing, perhaps due in part to the very well established biotechnology and biochemistry on which its experimental demonstration relies, as well as the frequent teaming of scientists in the field with multiple essential disciplines including chemistry, biochemistry, physics, material science, and computer science. This chapter surveys the field of DNA computing. It begins in Section 1 with a discussion of the underlying principles, including motivation for molecular and DNA computations (Section 1.1), brief overviews of DNA structures (Section 1.2), chemical reaction systems (Section 1.3), DNA reactions (Section 1.4), and classes of protocols and computations (Section 1.5). Then, the chapter discusses potential applications of DNA computing research (Section 2). The main section on research issues (Section 3.1) overviews how DNA computation is done, with a discussion of DNA hybridization circuits, including both solution-based as well as localized hybridization circuits. It also discusses design and simulation software for the same. We discuss DNA detectors in Section 3.2, DNA replicators in Section 3.3, DNA nanorobotic devices in Section 3.4, and DNA dynamical systems in Section 3.5.