Thermodynamic Stabilities of Multibranch Loops in Bacteriophage Packaging RNA

Abstract

Multibranch loops are key determinants of structural and functional roles in RNAs. In prohead RNA (pRNA), an essential component of the Φ29-like bacteriophage packaging motor, the three-way junction (3WJ) is a multibranch loop that imparts flexibility on the RNA, correctly placing helices in the spatial orientation necessary for in vivo self-assembly and packaging. In vitro, pRNA self-assembles, and some species are capable of forming dimers, trimers, and thermostable higher-order multimers. Although different pRNAs have very different interlocking loop sequences and thereby different base pairing stabilities, the overall energetics for pRNA self-assembly are conserved. We present thermodynamic data that support the hypothesis that 3WJ stabilities counterbalance loop-loop interaction stabilities in pRNA.