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BIOMOD Handbook

Pre-release edition

Shawn Douglas

Learn how to organize a team, engineer biomolecules at the nanoscale, and share your results. All sales proceeds go to BIOMOD Foundation, a 501(c)3 nonprofit organized to promote science and science education.

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About

About

About the Book

The BIOMOD Handbook is an introduction to biomolecular engineering. Topics include molecular self-assembly, structural DNA nanotechnology, DNA computing, and molecular robotics. We've tailored the Handbook for undergraduate students participating in BIOMOD, but concepts and skills may be applicable beyond the scope of the competition, such as in undergraduate-level laboratory courses. The Handbook originated as a translation of a Japanese-language guide by the Molecular Robotics Study Group. All sales proceeds go directly to support the BIOMOD Foundation, a 501(c)(3) non-profit based in California.

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Author

About the Author

Shawn Douglas

Assistant Professor at in the Department of Cellular & Molecular Pharmacology at the University of California, San Francisco.

Lab website: bionano.ucsf.edu

Contents

Table of Contents

About

  1. Support

Chapter 1 Let’s go to BIOMOD

  1. 1. Welcome to the World of DNA Molecule Design
  2. 2. What is BIOMOD?
  3. 3. Judging System of BIOMOD
  4. 4. Days at the Jamboree
  5. 5. Learn from Previous Winners
  6. 6. BIOMOD Calendar
  7. 7. Tips on Group Work
  8. 8. Tips on Website Creation
  9. 9. Tips on Making YouTube Video
  10. 10. Tips on Presentation in English
  11. 11. What You’ll Get From BIOMOD

Chapter 2 Before Starting Your Project

  1. 12. Subject Matter of Project
  2. 13. Types of Brainstorming
  3. 14. Design Process
  4. 15. How to Collect Information
  5. 16. More About Papers

Chapter 3 What Does Design of DNA Molecules Make Possible?

  1. 17. Structural DNA Nanotechnology: Overview
  2. 18. Two-Dimensional DNA Origami
  3. 19. Three-Dimensional DNA Origami
  4. 20. DNA Tiles
  5. 21. DNA-Modified Particles (SNA)
  6. 22. DNA Hydrogels
  7. 23. DNA Nanomachines and Nanorobots: Overview
  8. 24. DNA Tweezers
  9. 25. DNA Walker
  10. 26. DNA Nanomachines
  11. 27. Autonomous DNA Reaction Systems
  12. 28. DNA Computing: Overview
  13. 29. DNA Logic Gates
  14. 30. DNAzyme Logic Gates
  15. 31. Entropy-Driven Gate
  16. 32. Seesaw Gate
  17. 33. DNA Toolbox
  18. 34. DNA-Based Finite State Machine
  19. 35. Traveling Salesman Problem

Chapter 4 Basic Textbook Knowledge

  1. 36. Importance of Multidisciplinary Knowledge: Overview
  2. 37. Thermodynamics
  3. 38. Free Energy and Chemical Equilibrium
  4. 39. Reaction Kinetics
  5. 40. Molecular Structure of DNA
  6. 41. Thermodynamics of DNA Hybridization
  7. 42. Strand Displacement
  8. 43. Secondary Structures of DNA
  9. 44. DNA Synthesis

Chapter 5 Techniques/Materials to Boost DNA

  1. 45. Enzymes
  2. 46. Polymerase Reactions
  3. 47. Restriction Enzymes
  4. 48. Artificial Bases
  5. 49. Non-Watson-Crick Structure
  6. 50. Protein Motors
  7. 51. FRET and Molecular Beacons
  8. 52. Artificial Cell and Liposome (and Some Related Topics)

Chapter 6 Software Techniques

  1. 53. Basic Software Programs: Overview
  2. 54. Document/Table/Graph Preparation
  3. 55. Preparation of Presentation Slides
  4. 56. Figure Preparation
  5. 57. 3D Animation
  6. 58. Image Processing
  7. 59. Video Editing
  8. 60. Numerical Analysis Library
  9. 61. Software for Molecular Design of DNA
  10. 62. DNA Secondary Structure Prediction
  11. 63. Sequence Design
  12. 64. Design of DNA Origami
  13. 65. Simulation of DNA Origami
  14. 66. Molecular Modeling of DNA
  15. 67. Simulation of DNA Logic Gate

Contributors

About the Contributors

Satoshi Murata

Shogo Hamada

Kei Fujiwara

Hisashi Tadakuma

Shinichiro M. Nomura

Akinori Kuzuya

Ken Komiya

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