How does a protein search for the specific site on DNA: the role of disorder

Abstract

Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to non-specific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such one-dimensional route towards the target "antenna". We studied the role of the dispersion of nonspecific binding energies within the antenna due to quasi random sequence of natural DNA. Random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for the macroscopic and mesoscopic antennas.

arXiv comment4 pages, 4 figures

References in corpus (5)

• Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction
• How do proteins search for their specific sites on coiled or globular DNA
• The long reach of DNA sequence heterogeneity in diffusive processes
• Facilitated diffusion of DNA-binding proteins
• Base sequence dependent sliding of proteins on DNA

Cited by in corpus (6)

• Intermittent search strategies
• Anomalous Localization in Low-Dimensional Systems with Correlated Disorder
• Spatial effects on the speed and reliability of protein-DNA search
• Thermodynamic restrictions on evolutionary optimization of transcription factor proteins
• Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
• Sequence Heterogeneity Accelerates Protein Search for Targets on DNA