DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology – Kenneth Douglas

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DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology – Kenneth Douglas

$28.00

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. 

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Book 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 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

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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

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