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$66.37 $22 – DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology – Kenneth Douglas
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
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
$66.37 $22 – DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology – Kenneth Douglas