RNA structure controls composition and network dynamics of condensates

Biomolecular condensates can form by phase separation and likely serve myriad functions in cells. Many studies have characterized protein condensates, and sometimes these include model RNAs that are often nonspecific and/or homopolymeric, unlike native RNAs found in biomolecular condensates. How complex RNA sequences and structures control condensation with proteins remains poorly understood. We studied the influence of mRNA structure in phase separation using the Whi3 protein and a native mRNA binding partner, CLN3. We first created an evolutionary algorithm that designs shuffled CLN3 RNA sequences which maximize or minimize predicted free energies of folding while preserving mass, known Whi3 protein binding sites, encoded amino acid sequence, and nucleotide composition. RNAs with minimized free energies of folding contain many stable duplexes, while RNAs with maximized energies have unstable structures and long single-stranded regions. Using mass photometry, we show that RNAs with stable structures are mostly monomeric, while RNAs with unstable structures can multimerize. When mixed with protein, these differential RNA-RNA interactions affect dense phase compositions. Specifically, unstable RNAs form condensates with high RNA and low protein concentrations, while the converse is true for RNAs with stable structures. Using microbead rheology, we observe that unstable RNAs form condensates with long viscoelastic relaxation times that increase with condensate age, indicating elastic properties at many timescales. By contrast, stably-structured RNAs form less elastic condensates with shorter relaxation times that increase to a lesser degree with time. We hypothesize that such aging is controlled by the exchange of intra- for inter-molecular base pairing amongst RNAs whose folding free energies determine the timescale of these exchanges. Thus, RNA structure can have multi-scale consequences for biomolecular condensates, with impacts on condensate composition and material properties. This work underscores how specific RNA sequences can encode physical properties of condensates.