Effects of macromolecular crowding and DNA looping on gene regulation kinetics

Proteins seek out binding sites on DNA through diffusion and also by sliding along the strand. Although ‘roadblocks’—other bound proteins on the DNA strand—slow things down, it seems that looping of the DNA aids the search process. DNA-binding proteins control how genomes function. The theory of facilitated diffusion1 explains how DNA-binding proteins can find targets apparently faster than the diffusion limit by using reduced dimensionality2,3—combining three-dimensional (3D) diffusion through cytoplasm with 1D sliding along DNA (refs 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15). However, it does not include a description of macromolecular crowding on DNA as observed in living cells. Here, we show that such a physical constraint to sliding greatly reduces the search speed, in agreement with single-molecule measurements. Interestingly, the generalized theory also reveals significant insights into the design principles of biology. First, it places a hard constraint on the total number of DNA-binding proteins per cell. Remarkably, the number measured for Escherichia coli fits within the optimal range. Secondly, it defines a new role for DNA looping, a ubiquitous topological motif in genomes. DNA looping can speed up the search process by bypassing proteins that block the sliding track close to the target.

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