Searching fast for a target on a DNA without falling to traps

Abstract

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other non-specific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox by allowing the target sites to be located by proteins within short time scales even in the presence of traps. Our theoretical analysis shows that the mechanism is robust in the presence of generic disorder in the DNA sequence and does not require a specially designed target site.

5 pages, 5 figures

References in corpus (6)

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Cited by in corpus (28)

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• Classes of fast and specific search mechanisms for proteins on DNA
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• Intracellular facilitated diffusion: searchers, crowders and blockers
• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• Diffusion with Resetting Inside a Circle
• Defects in Crystalline Packings of Twisted Filament Bundles: I. Continuum Theory of Disclinations
• Comparison of two models of tethered motion
• Diffusion toward non-overlapping partially reactive spherical traps: fresh insights onto classic problems
• Optimization and universality of Brownian search in quenched heterogeneous media
• Transcription factor search for a DNA promoter in a three-states model
• Viscoelastic subdiffusion in a random Gaussian environment
• Persistent Sinai type diffusion in Gaussian random potentials with decaying spatial correlations
• Optimality of spatially inhomogeneous search strategies
• Finite-range viscoelastic subdiffusion in disordered systems with inclusion of inertial effects
• Facilitated diffusion on confined DNA
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Stochastic single-gene auto-regulation
• Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences
• Searching for clusters of targets under stochastic resetting
• Electrostatic map of T7 DNA. Comparative analysis of functional and electrostatic properties of T7 RNA polymerase specific promoters
• Facilitated diffusion framework for transcription factor search with conformational changes
• Drunken robber, tipsy cop: First passage times, mobile traps, and Hopf bifurcations
• Thermodynamics of quantum-jump trajectories of open quantum systems subject to stochastic resetting
• Poissonian resetting of subdiffusion in a linear potential