DNA nanotechnology has proliferated in recent years as investigators have increasingly harnessed the selectivity of DNA base pairing to form multitudes of diverse structures, with a wide range of applications. The stiffness of the double-strand DNA (dsDNA) with a persistence length of around 50nm (≅150bp) provides rigid structural properties to form the most stable duplexes. Single-strand DNA (ssDNA) with much less rigidity acts as hinges between duplex sections allowing extra flexibility to the structure. This specificity of DNA properties gives considerable functional control in designing anisotropic nanoparticles or nano-sized scaffolds as building blocks. These functionalised DNA building blocks enable the formation of varied DNA functionalised systems, such as DNA liquid crystals, DNA hydrogels or DNA functionalised micelles, amongst other DNA-based materials. The properties of these large-scale DNA-based systems are hard to represent by experiments owing to technical limits and cost restrictions. Computer modelling can offer significant insight into the DNA structures with thermodynamics and mechanical properties and has the potential to simulate a detailed model of DNA nanostructures. In this thesis, I applied a homemade multi-level strategy to demonstrate new horizons of coarse-grained simulation systems. From the detailed oxDNA molecular dynamics simulation of mimicking the most detailed behaviours of an individual DNA nanoparticle, to a second-level coarse-grained system with thousands of repeated units of accelerating large-scaled simulation. I outlined further investigation for the existence of exotic DNA liquid crystal phases and proved a self-loop behaviour on the role of flexibility in our linker-mediated DNA hydrogels. I also presented phase diagrams and simulated radial distribution functions by adding extra temperature-controlled mechanisms in our DNA functionalised pluronic systems. With the service of this multi-level coarse-grained strategy, I can devote a more realistic simulation system to illustrate more reliable physical properties.