Figure 3.

Effective concentration c₁₂ of domain 2 at RNA site 2, when at least one RNA site is already bound. (A) In the simplest approximation, the concentration is uniform inside the sphere of radius l₁₂ around the bound domain. l₁₂ is the RNA chain length between binding sites. (B) More realistically, when the RNA chain is treated as a ‘worm like chain’ the concentration c₁₂ has a Gaussian density (for large l₁₂). Its size depends on l₁₂ and the 3D distance d₁₂ between binding domains on the protein. (C) Comparison of the effective concentration in the simple case described in (A), with the more realistic worm-like chain in (B). The concentration decays much more slowly if modelled by a Gaussian. The distance between binding sites on the protein is d₁₂ = 3 nm.