Self-cleaving viroid and newt RNAs may only be active as dimers

Abstract

Avocado sunblotch viroid (ASBV) is a 247-nucleotide, single-stranded, circular RNA¹. It is considered to replicate via a rolling-circle mechanism^2–4 in which circular, monomeric plus and minus RNAs act as templates for the synthesis of longer-than-unit-length precursor RNAs. Processing of these RNAs in vivo may occur by a self-cleavage reaction, as indicated by ability of dimeric, linear plus and minus ASBV RNAs to specifically self-cleave in vitro with the excision of a monomeric RNA with 5′-hydroxyl and 2′,3′-cyclic phosphodiester termini⁴. A similar self-cleavage reaction has also been reported to occur in an RNA transcript containing a dimeric copy of a tandemly repeated, 330-base-pair sequence of the newt genome⁵. Based on comparisons with self-cleaving plant viral satellite RNAs^6,7, hammerhead-shaped active structures, each containing one self-cleavage site, were proposed for the plus and minus ASBV RNAs⁴ and the newt RNA⁵, but the stability of these hammerheads has been questioned^4,8. Here, more stable active structures that contain two self-cleavage sites are proposed and data supporting these models are presented.