Effects of macromolecular crowding and DNA looping on gene regulation kinetics

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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.”
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. (2014, background): “The crowded space on DNA imposes constraints on the abundance of TFs because overcrowding by nonspecifically associated DNA-bindingproteins coulddrastically reduce theoverall binding kinetics (Hammar et al., 2012; Li et al., 2009).”
Network resilience (2020, unknown): “ers [369, 370].”
Intermittent search strategies (2011, background): “A first limitation of this simple description appears in the case of many proteins binding to DNA, as it is the case in vivo, which are likely to create traffic jams (Li et al., 2009; Sokolov et al., 2005).”
Stochastic models of intracellular transport (2013, background): “…BHW model and its extensions provide a plausible mechanism for facilitated diffusion that has some support from experimental studies, which demonstrate that proteins do indeed slide along DNA (Gorman and Greene, 2008; Gowers et al., 2005; Li et al., 2009; Tafvizi et al., 2008; Winter et al., 1981).”