Fig. 7: Mechanistic model of tRNA binding to a dynamic T-box mRNA ensemble.

Most initial T-box transcripts comprise three discrete, stable helical elements: stems I (orange), II (blue), and IIA/B pseudoknot (cyan, Ψ) linked by short or zero-length linkers. Due to strong thermodynamic motivations for helical termini to coaxially stack, stem I and the pseudoknot compete for end-to-end stacking with stem II. We posit that this competition is chiefly responsible for the creation of a dynamic mRNA conformational ensemble. Among the open, semi-open, and closed conformers, tRNA mostly engages the two open T-box conformers due to reduced steric hindrance and their larger populations. tRNA engagement triggers rapid stems I–II closure and docking, which traps the tRNA. In the absence of a stably folded pseudoknot, stems I and II stack instead, leading to a static conformation unable to retain the tRNA. Therefore, the polymorphic three-helix module of T-box mRNA is dynamically poised to rapidly recruit and stably retain its tRNA ligand, which in turn chaperones the folding of its multi-domain T-box RNA partner.