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We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein jumps between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite frozen DNA limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in islands within random DNA configurations in solution.
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative charac
Statistics of Poincare recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the decay of rec
DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly v
The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used in the se
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow