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

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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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