DNA Origami-Protein Interactions and the Role of Steric Hindrance

Abstract

DNA origami -- a novel class of synthetic DNA nanostructures -- are designed to fold into predetermined shapes that can undergo dynamic changes. Here, we characterize the structure and dynamics of a DNA origami with a triangular-shape, using Langevin-type molecular dynamics simulations, and the coarse-grained OxDNA model. In particular, we focus on two different network geometries of DNA strands and analyse the different fluctuations properties. We link the local and global conformational changes, and the local DNA network properties, to the binding propensity of the DNA cleaving protein HinP1I. Finally, we use the Michaelis-Menten theory to connect the binding propensity predictions with time-dependent gel electrophoresis experiments.