How do site-specific DNA-binding proteins find their targets?

By S. Halford, J. Marko. Nucleic Acids Research, 2004

865 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/77f192a4c20b26135dd2937f0371c7a8c289561a

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Citations in the corpus

How a protein searches for its site on DNA: the mechanism of facilitated diffusion (2009, background): “Recent theoretical studies of protein–DNA search include work by Halford and Marko [7], Coppey et al [8], Hu et al [9–11], Lomholt et al [12, 13] and other groups [14–16].”
Modelling and analysis of gene regulatory networks (2008, background): “Although it overlooks some biological processes that affect regulation, such as diffusio”
Intermittent search strategies (2011, methodology): “A first example is given by Halford and Marko (2004), where scaling arguments are used to roughly estimate the time for the protein to find the DNA coil, and then the time to find the target inside the coil, which eventually yields an optimal sliding length.”
Rapid spontaneous accessibility of nucleosomal DNA (2005, background): “The rate constant for binding of proteins to specific DNA target sites is often extremely fast, comparable to or faster than the diffusion-controlled limit of ∼10 9 M −1 s −1 (refs”
Stochastic switching in biology: from genotype to phenotype (2017, background): “(i) Transcription: synthesis of a messenger RNA molecule (mRNA) with a nucleotide sequence complementary to the DNA strand from which it is copied—this serves as the template for protein synthesis.”
Stochastic models of intracellular transport (2013, background): “E, such a search process is thought to involve a combination of mechanisms, including one–dimensional sliding along the DNA and uncorrelated 3D diffusion (Berg et al., 1981; Halford and Marko, 2004).”
Effects of macromolecular crowding and DNA looping on gene regulation kinetics (2009, background): “Equation (9) is the effective target size for binding through nonspecific sites.”