Beyond its importance in biology, in the general area of materials science and engineering, the assembly of nanoscale objects on the basis of DNA hybridization is finding an increasing range of applications. In order to interpret results of DNA-based nanoparticle assembly experiments, for example, it is important to develop models capable of describing phenomena occurring at micron length scales while retaining a molecular-level representation capable of capturing hybridization. Similarly, in epigenetics, models capable of describing DNA-protein complexes would be useful.<br/> <br/>This presentation will provide an overview of recent hierarchical models and computational approaches developed by our research group to investigate the effects of confinement, hydrodynamic interactions, salt concentration, and sequence on the structure and properties of DNA, both at equilibrium and beyond equilibrium. Particular emphasis will be placed on recently proposed detailed models and methods designed to describe the manipulation of DNA in microfluidic devices, the melting and rehybridization of DNA at the single nucleotide level, and DNA molecular recognition in DNA-protein complexes. The relevance of the models will be discussed in the context of nanofluidic designs for applications in optimal mapping, and in the context of recent experiments on DNA packaging in chromatin.

Hierarchical view of DNA based recognition, and the role of flexibility and shape

249th National Meeting (2015)

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