In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.

IBS CEA Grenoble F 38044 France

IBS Univ Grenoble Alpes Grenoble F 38044 France

Institut de Biologie Structurale CNRS Grenoble F 38044 France

Institut de Systématique Evolution Biodiversité ISyEB UMR 7205 CNRS MNHN UPMC EPHE UPMC Sorbonne Universités 57 rue Cuvier CP 50 Paris F 75005 France

Institut Laue Langevin Grenoble F 38042 France

Institute for Integrative Biology of the Cell Dept of Genome Biology CEA CNRS Université Paris Sud Gif sur Yvette F 91198 France

Institute of Physics Charles University Faculty of Mathematics and Physics Prague 2 CZ 121 16 Czech Republic

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