DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology

DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology melds two tales of DNA. One is a look at the first 35 years of DNA nanotechnology to better appreciate what lies ahead in this emerging field. The other story looks back 4 billion years to the possible origins of DNA which are shrouded in mystery. The book is divided into three parts comprised of 15 chapters and two Brief Interludes. Part I includes subjects underpinning the book such as a primer on DNA, the broader discipline of nanoscience, and experimental tools used by the principals in the narrative. Part II examines the field of structural DNA nanotechnology, founded by biochemist/crystallographer Nadrian Seeman, that uses DNA as a construction material for nanoscale structures and devices, rather than as a genetic material. Part III looks at the work of physicists Noel Clark and Tommaso Bellini who found that short DNA (nanoDNA) forms liquid crystals that act as a structural gatekeeper, orchestrating a series of self-assembly processes using nanoDNA. This led to an explanation of the polymeric structure of DNA and of how life may have emerged from the prebiotic clutter.

Table of Contents:
A Note to the Reader Preface Author Biography Acknowledgments INTRODUCTION: Grandma Needs a Walker PART I — The Story Line and Its Underpinnings CHAPTER ONE — Down the Road and the Gemisch Dramatis Personae, Part I: Nadrian Seeman Molecular Crystals—Inspiration from Escher Perspiration and Reinvention Dramatis Personae, Part II: Noel Clark, Tommaso Bellini Liquid Crystals and Self-Assembly Seeman, Bellini and Clark, and Base Complementarity Conventional Wisdom and an Alternative View Endnotes CHAPTER TWO — DNA: The Molecule That Makes Life Work—and More Erwin Chargaff Rosalind Franklin James Watson, Francis Crick, and Maurice Wilkins DNA Sequencing Polyacrylamide Gel Electrophoresis (PAGE) DNA Synthesis Exercises for Chapter Two Endnotes CHAPTER THREE — Travels to the Nanoworld The Scanning Tunneling Microscope (STM) Moving Atoms With an STM Standing Waves Quantum Corrals Nanomethodology Spherical Nucleic Acids (SNAs) Biodiagnostic Detection Using SNAs Exercises for Chapter Three Endnotes CHAPTER FOUR—Liquid Crystals: Nature’s Delicate Phase of Matter Phase Transitions Classes of Liquid Crystals Cell Membranes and the Langmuir Trough Micelles Liquid Crystal Displays Exercises for Chapter Four Endnotes CHAPTER FIVE — Tools of the Trade Polarized Light Microscopy Liquid Crystal Texture Seen Through a Depolarized Light Microscope Transmission Electron Microscopy (TEM) Atomic Force Microscopy (AFM) X-Ray Diffraction and Bragg’s Law The Phase Problem Synchrotron X-Ray Diffraction Exercises for Chapter Five Endnotes PART II — The Emerging Technology: Nanomaterials Constructed From DNA CHAPTER SIX — The Three Pillars of Structural DNA Nanotechnology Branched DNA and DNA Junctions Sticky Ends Immobile Four-Arm DNA Junction Two-Dimensional Ligation of DNA Junctions Deconstruction of Concatenated Nucleic Acid Junctions Macrocycles Three-Dimensional Constructions and Catenanes The DNA Cube Exercises for Chapter Six Endnotes CHAPTER SEVEN — Motif Generation, Sequence Design, Nanomechanical Devices Flexible Junctions Redux The Double-Crossover (DX) Molecule Design and Self-Assembly of Two-Dimensional DNA Crystals Two-Dimensional Nanoparticle Arrays Sequence Design Nanomechanical Devices Exercises for Chapter Seven Endnotes CHAPTER EIGHT—DNA Origami, DNA Bricks Scaffolded DNA Origami DNA Origami Patterns Strand Invasion also called Strand Displacement DNA Origami With Complex Curvatures in Three Dimensions DNA Tiles in Two Dimensions DNA Bricks in Three Dimensions DNA Brick Shapes in Three Dimensions DNA Brick Crystals Seeman, Rothemund, and Yin Exercises for Chapter Eight Endnotes CHAPTER NINE — DNA Assembly Line and the Triumph of Tensegrity Triangles DNA Nanoscale Assembly Line (Overview) DNA Walkers DNA Machines and Paranemic Crossover Molecules DNA Cassette With Robot Arm and DNA Origami Track DNA Assembly Line The Triumph of Tensegrity Triangles Exercises for Chapter Nine Endnotes BRIEF INTERLUDE I — Back to Methuselah Molecular-Scale Weaving Moors and Crossover Molecules Tensegrity Sculpting Mayan Pottery, Chirality, and the Handedness of Life Endnotes CHAPTER TEN — DNA Nanotechnology Meets the Real World Cell Membrane Channels Synthetic Membrane Channels via DNA Nanotechnology Current Gating Channels as Single-Molecule Sensors Molecular Nanorobots Built by DNA Origami: Cell-Targeted Drug Delivery Tests of Nanorobot Function Test of Binding Discrimination: Healthy Cells vs. Leukemia Cells (NK Cells) Exercises for Chapter Ten Endnotes PART III — The Possible Origins of Life’s Information Carrier CHAPTER ELEVEN — Chance Findings Onsager’s Criterion for an Isotropic-Nematic Liquid Crystal Phase Transition NanoDNA Seems to Violate Onsager’s Venerable Criterion The Details Shifting Gears Phase Separation into Liquid Crystal Droplets The Depletion Interaction Flory’s Model Exercises for Chapter Eleven Endnotes CHAPTER TWELVE — Unexpected Consequences Hierarchical Self-Assembly NanoRNA Blunt Ends and Sticky Ends Base Stacking Forces The Scope of the Self-Assembly Mechanisms of Nucleic Acids Random-Sequence NanoDNA The Strange World of Random-Sequence NanoDNA Liquid Crystal Ordering of Random-Sequence NanoDNA Non-Equilibrium Statistical Mechanics: Kinetic Arrest and Nonergodic Behavior Exercises for Chapter Twelve Endnotes CHAPTER THIRTEEN — Ligation: Blest be the Tie That Binds NanoDNA Stacking: Weak Physical Attractive Forces vs. Chemical Ligation Abiotic Ligation Experiments with EDC The Scheme: Polyethylene glycol (PEG)-Induced Phase Separation Gel Electrophoresis of D1p Oligomers With Polyacrylamide and Agarose Gels Another Stellar Contribution by Chemist Paul J. Flory Analysis of Gel Profiles: The Experimental Data is Well Described by the Flory Model The Lowdown on Ligation Efficiency The Liquid Crystal Phase as Gatekeeper Cascaded Phase Separation Exercises for Chapter Thirteen Endnotes BRIEF INTERLUDE II — The Handedness of Life Chirality Life is Homochiral Macroscopic Chiral Helical Precession of Molecular Orientation Bellini and Clark Examine NanoDNA Chirality A Lighter Take on Chirality Exercises for Brief Interlude II Endnotes CHAPTER FOURTEEN — All the World’s a Stage and Life’s a Play—Did it Arise From Clay? Emergence and Complexity Miller-Urey Experiment RNA World Hypothesis Other Plausible Venues Replicator-First vs. Metabolism-First Feats of Clay The Lipid World Liquid Crystals in the Work of Deamer and the Work of Bellini/Clark Manfred Eigen and Stuart Kauffman Exercises for Chapter Fourteen Endnotes CHAPTER FIFTEEN — The Passover Question: Why is This Origins Proposal Different From All Other Proposals? Emergence and Broken Symmetry About-Face Occam’s Razor The RNA World Revisited Sticky Business, Part I: What Constitutes Plausible Prebiotic Conditions? Sticky Business, Part II: The Origins Question—Whose Home Turf Is It? Discovering the Physical Processes that Enabled the Chemistry of Life Metabolism-First Revisited Computer Simulations and Mathematical Modeling An Ancient "Liquid Crystal World" Endnotes Epilogue APPENDIX — Texture of Liquid Crystal Optical Images Smectic Phase Liquid Crystal Texture Bent-Core Molecules Extinction Brushes Chiral Nematic Texture of NanoDNA Liquid Crystals Columnar Texture of NanoDNA Liquid Crystals Endnotes Glossary Index

About the Author :
Kenneth Douglas is a member of the Research Faculty in the Department of Physics at the University of Colorado-Boulder. He received his B.A. (mathematics) and M.S. (physics) at the University of Chicago and his Ph.D. (physics) at the University of Colorado-Boulder. His area of specialization is biomimetic nanofabrication. He devised a strategy that employs the surface layers of bacterial extremophiles — e.g., Sulfolobus acidocaldarius — as masks to fabricate nanoscale periodic patterns on inorganic substrates. He is co-inventor of the first-ever U.S. patents for parallel fabrication of nanoscale multi-device structures. His work has appeared in Science, Nature, Biophysical Journal, Applied Physics Letters, Physical Review B, Surface Science, FEMS Microbiology Reviews, Journal of Applied Physics, Popular Science and elsewhere. Douglas has authored multiple book chapters and seven U.S. patents.

Review :
‘DNA Nanoscience takes us on a journey into the future, where sub-microscopic gadgets built from DNA may be used to detect specific molecules one-at-a-time or to deliver therapeutic drugs specifically to cancer cells. Looking in the other direction, the journey takes us back 4 billion years to a time when the self-organization of DNA into liquid crystals may have facilitated the reproduction of what would become our genetic material, arguably the key step in the origin of life. DNA Nanoscience is scholarly and full of technical figures. But the science is accompanied by clear explanations that make it accessible to college student and science-savvy citizens. It is a pleasure to find a book that is so true to the science while being so enjoyable to read.’ – Thomas R. CechDistinguished Professor, University of Colorado-Boulder; Director, BioFrontiers Institute; Nobel Laureate (Chemistry 1989). ‘Douglas’ DNA Nanoscience is something of a miracle.’ – Stuart Kauffman Emeritus Professor Biochemistry and Biophysics, University of Pennsylvania; Affiliate Professor, The Institute for Systems Biology, Seattle; Author of At Home in the Universe. ‘This book changed my life. Every seven years, as my sabbatical approaches, I search about for a new direction to focus my research and Ken Douglas’ book, DNA Nanoscience, appeared just in time.’ – Seth Fraden Professor of Physics; Director, The Bioinspired Soft Materials Center, Brandeis University. ‘Instructive like a textbook and exciting like a novel! For everybody interested in modern natural sciences, this book is a must to read.’ – Andreas Herrmann Professor of Polymer Chemistry and Bioengineering; Chair of the Board, The Zernike Institute for Advanced Materials; University of Groningen, The Netherlands. ‘To sum up, this is both a lively and profound book, the reading of which I strongly recommend.’ – Jacques Prost Director Emeritus of CNRS (Le Centre national de la recherche scientifique) at Institut Curie, Paris; Distinguished Professor, National University of Singapore. ‘This book tells a fascinating new story about DNA. The subject matter also stretches as needed into biology to teach basic ideas about cell membranes and metabolism. It provides a wonderful taste of DNA nanoscience at the research frontier.’ – Arjun G. Yodh James M. Skinner Professor of Science, Endowed Chair; Director, PENN Laboratory for Research on the Structure of Matter, University of Pennsylvania. ‘The only way that the general public will continue to trust the proclamation of the scientific establishment is through books like this one – where the foibles and fears and eccentricities of the scientists are shown to be the same as those of the artist, musician and businessman. Scientists are just artists who want to work with mother nature, without the freedom to make up new worlds as we go along. The real world is magical enough for them.’ – Joseph A. Zasadzinski 3M Harry Heltzer Chair in Multidisciplinary Science and Technology; Chemical Engineering and Materials Science, University of Minnesota. 'The book’s eclectic and elaborate vision, looking back to the ancient past and forward to the equally unknowable future sets Douglas’ DNA Nanoscience apart from other attempts to present DNA nanoscience.... Written in beautiful prose and richly illustrated with over 200 full-color figures ... it also serves as a bird’s-eye survey for a more general readership, viz., for those in the public who are curious and enjoy thinking. These citizens are aware of DNA nanoscience snippets making it into the daily news but would like to acquire a deeper, more meaningful and thorough understanding of what the fuss is all about. Douglas’ book DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology covers an astoundingly broad ground.... By writing this book on the emerging field of DNA nanoscience Kenneth Douglas has thus done a double service—to science as well as to its public image. I believe that the reception of the book will do justice to the meticulous research and artistry of this tome.' – Rudolf Podgornik (Jožef Stefan Institute) Journal of Biological Physics (August 2016), DOI: 10.1007/s10867-016-9425-4. ‘DNA Nanoscience takes us on a journey into the future, where sub-microscopic gadgets built from DNA may be used to detect specific molecules one-at-a-time or to deliver therapeutic drugs specifically to cancer cells. Looking in the other direction, the journey takes us back 4 billion years to a time when the self-organization of DNA into liquid crystals may have facilitated the reproduction of what would become our genetic material, arguably the key step in the origin of life. DNA Nanoscience is scholarly and full of technical figures. But the science is accompanied by clear explanations that make it accessible to college student and science-savvy citizens. It is a pleasure to find a book that is so true to the science while being so enjoyable to read.’ – Thomas R. Cech Distinguished Professor, University of Colorado-Boulder; Director, BioFrontiers Institute; Nobel Laureate (Chemistry 1989). ‘Douglas’ DNA Nanoscience is something of a miracle.’ – Stuart Kauffman Emeritus Professor Biochemistry and Biophysics, University of Pennsylvania; Affiliate Professor, The Institute for Systems Biology, Seattle; Author of At Home in the Universe. ‘This book changed my life. Every seven years, as my sabbatical approaches, I search about for a new direction to focus my research and Ken Douglas’ book, DNA Nanoscience, appeared just in time.’ – Seth Fraden Professor of Physics; Director, The Bioinspired Soft Materials Center, Brandeis University. ‘Instructive like a textbook and exciting like a novel! For everybody interested in modern natural sciences, this book is a must to read.’ – Andreas Herrmann Professor of Polymer Chemistry and Bioengineering; Chair of the Board, The Zernike Institute for Advanced Materials; University of Groningen, The Netherlands. ‘To sum up, this is both a lively and profound book, the reading of which I strongly recommend.’ – Jacques Prost Director Emeritus of CNRS (Le Centre national de la recherche scientifique) at Institut Curie, Paris; Distinguished Professor, National University of Singapore. ‘This book tells a fascinating new story about DNA. The subject matter also stretches as needed into biology to teach basic ideas about cell membranes and metabolism. It provides a wonderful taste of DNA nanoscience at the research frontier.’ – Arjun G. Yodh James M. Skinner Professor of Science, Endowed Chair; Director, PENN Laboratory for Research on the Structure of Matter, University of Pennsylvania. ‘The only way that the general public will continue to trust the proclamation of the scientific establishment is through books like this one – where the foibles and fears and eccentricities of the scientists are shown to be the same as those of the artist, musician and businessman. Scientists are just artists who want to work with mother nature, without the freedom to make up new worlds as we go along. The real world is magical enough for them.’ Joseph A. Zasadzinski 3M Harry Heltzer Chair in Multidisciplinary Science and Technology; Chemical Engineering and Materials Science, University of Minnesota. 'The book’s eclectic and elaborate vision, looking back to the ancient past and forward to the equally unknowable future sets Douglas’ DNA Nanoscience apart from other attempts to present DNA nanoscience.... Written in beautiful prose and richly illustrated with over 200 full-color figures ... it also serves as a bird’s-eye survey for a more general readership, viz., for those in the public who are curious and enjoy thinking. These citizens are aware of DNA nanoscience snippets making it into the daily news but would like to acquire a deeper, more meaningful and thorough understanding of what the fuss is all about. Douglas’ book DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology covers an astoundingly broad ground.... By writing this book on the emerging field of DNA nanoscience Kenneth Douglas has thus done a double service—to science as well as to its public image. I believe that the reception of the book will do justice to the meticulous research and artistry of this tome.' – Rudolf Podgornik (Jožef Stefan Institute) Journal of Biological Physics (August 2016), DOI: 10.1007/s10867-016-9425-4.