Introduction -- A Novel DNA Model -- Methods -- Finite Size Effects -- Stuctural and Mechanical Properties of Model DNA -- Thermodynamic Properties of Model DNA -- Modelling DNA Tweezers -- Modelling a DNA Walker -- Conclusions
Summary
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
