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Coarse-Grained Modelling of DNA and DNA Self-Assembly

  • Book
  • © 2012

Overview

Authors:
  1. Thomas E. Ouldridge

    1. University of Oxford, Oxford, United Kingdom

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  • Nominated as an outstanding contribution by the University of Oxford
  • Presents a novel model with remarkable explanatory power
  • Holds important potential for dynamic DNA nanotechnology
  • Includes supplementary material: sn.pub/extras
  • Includes supplementary material: sn.pub/extras

Part of the book series: Springer Theses (Springer Theses)

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Table of contents (9 chapters)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Introduction

    • Thomas E. Ouldridge
    Pages 1-20

  3. A Novel DNA Model

    • Thomas E. Ouldridge
    Pages 21-37

  4. Methods

    • Thomas E. Ouldridge
    Pages 39-49

  5. Finite Size Effects

    • Thomas E. Ouldridge
    Pages 51-58

  6. Stuctural and Mechanical Properties of Model DNA

    • Thomas E. Ouldridge
    Pages 59-69

  7. Thermodynamic Properties of Model DNA

    • Thomas E. Ouldridge
    Pages 71-92

  8. Modelling DNA Tweezers

    • Thomas E. Ouldridge
    Pages 93-100

  9. Modelling a DNA Walker

    • Thomas E. Ouldridge
    Pages 101-117

  10. Conclusions

    • Thomas E. Ouldridge
    Pages 119-122

  11. Back Matter

    Pages 123-176
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Keywords

About this book

This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker — the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.

Authors and Affiliations

  • University of Oxford, Oxford, United Kingdom

    Thomas E. Ouldridge

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