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||DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology
Author: Kenneth Douglas
Description: 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 Content: 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: Natures 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 Braggs 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 Lifes Information Carrier CHAPTER ELEVEN — Chance Findings Onsagers Criterion for an Isotropic-Nematic Liquid Crystal Phase Transition NanoDNA Seems to Violate Onsagers Venerable Criterion The Details Shifting Gears Phase Separation into Liquid Crystal Droplets The Depletion Interaction Florys 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 Worlds a Stage and Lifes 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 Occams 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