Ebook: Coarse-Grained Modelling of DNA and DNA Self-Assembly

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.

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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.

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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.
Content:
Front Matter....Pages i-xi
Introduction....Pages 1-20
A Novel DNA Model....Pages 21-37
Methods....Pages 39-49
Finite Size Effects....Pages 51-58
Stuctural and Mechanical Properties of Model DNA....Pages 59-69
Thermodynamic Properties of Model DNA....Pages 71-92
Modelling DNA Tweezers....Pages 93-100
Modelling a DNA Walker....Pages 101-117
Conclusions....Pages 119-122
Back Matter....Pages 123-176

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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.
Content:
Front Matter....Pages i-xi
Introduction....Pages 1-20
A Novel DNA Model....Pages 21-37
Methods....Pages 39-49
Finite Size Effects....Pages 51-58
Stuctural and Mechanical Properties of Model DNA....Pages 59-69
Thermodynamic Properties of Model DNA....Pages 71-92
Modelling DNA Tweezers....Pages 93-100
Modelling a DNA Walker....Pages 101-117
Conclusions....Pages 119-122
Back Matter....Pages 123-176
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