PT - JOURNAL ARTICLE AU - Fabrice Leclerc AU - Giuseppe Zaccai AU - Jacques Vergne AU - Martina Řìhovà AU - Anne Martel AU - Marie-Christine Maurel TI - Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study AID - 10.1101/045054 DP - 2016 Jan 01 TA - bioRxiv PG - 045054 4099 - http://biorxiv.org/content/early/2016/03/23/045054.short 4100 - http://biorxiv.org/content/early/2016/03/23/045054.full AB - 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.