RNA homopolymers form higher-curvature virus-like particles than do normal-composition RNAs

Abstract Unlike double-stranded (ds)DNA, single-stranded (ss)RNA can be spontaneously packaged into spherical capsids by viral capsid protein because it is a more compact and flexible polymer. Many systematic investigations of this self-assembly process have been carried out using capsid protein from cowpea chlorotic mottle virus (CCMV), with a wide range of sequences and lengths of ssRNA. Among these studies are measurements of the relative packaging efficiencies of these RNAs into spherical capsids. In the present work we address a fundamental issue that has received very little attention, namely the question of the preferred curvature of the capsid formed around different RNA molecules. We show in particular that homopolymers of RNA – polyU and polyA – form exclusively T = 2-sized (22 nm-diameter) virus-like particles (VLPs) when mixed with CCMV capsid protein, independent of their length, ranging from 500 to more than 4000 nt. This is in contrast to “normal-composition” RNAs, i.e., molecules with comparable numbers of each of the four nucleotides and hence capable of developing a large amount of secondary structure due to intramolecular complementarity/base-pairing; a curvature corresponding to T = 3-size (28 nm in diameter) is preferred for the VLPs formed with such RNAs. Our work is consistent with the preferred curvature of VLPs being a consequence of interaction of capsid protein with RNA – in particular, the presence or absence of short RNA duplexes – and that the equilibrium size of the capsid results from a trade-off between this optimum size and the cost of confinement.