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Nanotechnology : science and computation (Natural Computing Series)
Chen J., Jonoska N., Rozenberg G., Springer-Verlag New York, Inc., Secaucus, NJ, 2006. 393 pp. Type: Book (9783540302957)
Date Reviewed: Aug 2 2007

This new title in Springer’s “Natural Computing Series” will undoubtedly attract a wide range of practitioners interested in nanoscale technology, DNA computing, and more generally alternative computing techniques. A renewed interest in nanoscale technologies has pervaded the last decade. Indeed, possibilities that were only heralded by theorists have reached notable milestones, thanks to a sustained aim at industrial applications. DNA computing, in particular, has known fluctuating interest after various attempts at harnessing the gigantic amount of information encoded in polynucleotide strands have been formulated, tried, and, for some, exhausted. This book expounds the latest applications in DNA nanotechnology and computing and reveals brilliantly the promises of this field.

As is usual with Springer, the printing quality is excellent and the book is very compact. A large amount of data is condensed in 20 chapters structured like research articles, many being adapted for this edition. What is notable about this book is the structure: it offers a unified presentation of varied topics. All chapters contain a well-written introduction and reveal an effort to meticulously explain the often-arcane subjects presented. Thus, instead of encountering the usual patchwork of research articles sewn into a monograph, one finds here a well-unified body of fundamental concepts in DNA nanotechnology, developed through research-level problems and solutions.

Self-assembly of DNA strands is thoroughly covered, both from the algorithmic and molecular viewpoints. Self-resilient assembly algorithms are explained in detail and the underlying hybridization and ligations are expounded at the molecular level with very good illustrations. The creative potential of DNA self-assembly reaches its peak in a gem of a chapter where, building on Seeman’s ideas [1], techniques for building a scaffold-supported polyhedral DNA structure are presented. Therein, building a complex geometric structure is explained step by step from the strand junction level, to multistrand lattices, to a complete dodecahedron, while presenting a general tiling technique based on triangular double-crossover DNA junctions. One can find there an open intellectual playground where organic chemists and origami fans can meet. Nitty-gritty details of DNA nanostructure manipulation, tiled assembly, and synthesis are not neglected, as many chapters detail the in-vitro experiments supporting the techniques presented. Graph-theoretic algorithms for error-resilient self-assembly of DNA tilings are also analyzed.

The issue of undesirable hybridizations, although covered as needed in most chapters, is disentangled in a few chapters dedicated to robust coding of generated DNA combinations. Several theoretical and in-vitro selective manufacturing techniques are presented. Experimental results validate the algorithms when applicable. The techniques used are different (Zucker-Stiegler-based minimum free energy, overlap-free codeword generation, ad hoc in-vitro selection of independent strings) and give a good sampling of existing techniques.

Some nanomechanical aspects of DNA strings, maybe better known in pop nanotechnology, are detailed in a few dedicated chapters. Morphological synthesis and mechanical locomotion are thus presented, but this topic is a weak point of the book. This section falls short of assessing the state of the art or the breadth of current nanomechanical studies. The strength of the book lies in the other sections.

DNA-based electronics and large-scale integration topics are well covered in the book, with a set of comprehensive chapters with diligently written introductions. The state of the art in DNA-based circuit integration is nicely presented and should interest a broad audience of readers, especially computer scientists aiming to bridge the challenging gap between traditional very large-scale integration and nano-gates integration. Multicomponent assembly is presented with comparison to complementary metal oxide semiconductor structures, along with a focused analysis on gate-level building blocks. All problems facing this potentially fruitful area of nanotechnology are detailed. Chapters on metallization of oligo-nucleotide structure are particularly interesting. Computational aspects of multicomponent assemblies are covered in another section of the book. Rather exhaustively, multiple techniques to build general computing machines, for example, automata, gate-based structures, and even a Turing machine, are modeled. In particular, the hairpin technique build-up on Adleman’s algorithm [2] is a good introduction to his string-centric computation, hopefully encouraging readers to explore other titles in this series that are more focused on that fundamental topic [3,4]. Algorithms specific to gene assembly are also covered.

The biomolecular aspects of nanotechnology obviously pervade the whole book. However, dedicated chapters focus on intrinsic computation in eukaryotic cells. Self-assembly through surface-layer bacteria and an analysis of transcription in ciliates (a particular family of eukaryotes [3]) are also included.

Finished by an appendix containing a bibliography of Ned Seeman, a pioneer of DNA computing, this book is very exciting to read. Although targeted at researchers studying or engineering nanoscale DNA-based structures, computer scientists and graduate students in related fields (for example, biomolecular synthesis, computation, nanotechnology, and microelectromechanical systems) will also benefit from the book, as all of the chapters contain a fine introduction to bridge the gap for nonspecialized readers.

Reviewer:  Cherif Keramane Review #: CR134598 (0807-0657)
1) Seeman, N.C. Construction of three-dimensional stick figures from branched DNA. DNA and Cell Biology 7, 10(1991), 475–486.
2) Adleman, L.M. Molecular computation of solutions to combinatorial problems. Science 266, (1994), 1021–1024.
3) Ehrenfeucht, A.; Harju, T.; Petre, I.; Prescott, D.M.; Rozenberg, G. Computation in living cells. Springer, Leiden, 2004.
4) Amos, M. Theoretical and experimental DNA computation. Springer, Leiden, 2005.
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