Enrichment and sequence analysis of dimers of Φ29 pRNA mutants

Hexamer of packaging RNA (pRNA) is absolutely required in the packaging of bacteriophage Φ29 genomic DNA into their procapsid. More and more evidence confirmed that pRNA dimer may be the building block of pRNA hexamer. To better understand sequence required for the dimer formation of pRNA, the pRNA mutants that could easily form stable dimer in vitro were selected by systematic evolution of ligands by exponential enrichment (SELEX). With help of the RNA structure 3.5 software, we found that the pRNA mutants which could form stable dimer had the "Y"-like secondary structures, while monomer pRNA mutants had the "I"-like secondary structures. Our results suggested that except for the "upper-to-lower" or "head-to-head" intermolecular interaction of wide type pRNAs, the dimer of pRNA could also possibly be formed by "head-to-lower" interaction mechanisms.