MAGNESIUM-INDUCED CONFORMATIONAL CHANGE OF PACKAGING RNA FOR PROCAPSID RECOGNITION AND BINDING DURING PHAGE PHI-29 DNA ENCAPSIDATION

Bacteriophage phi 29 is typical of double-stranded DNA viruses in that its genome is packaged into a preformed procapsid during maturation. An intriguing feature of phi 29 assembly is that a virus-encoded RNA ( pRNA) is required for the packaging of its genomic DNA. Psoralen cross -linking, primer extension, and T-1 RNase partial digestion revealed t hat pRNA had at least two conformations; one,vas able to bind procapsi ds, and the other was not. In the presence of Mg2+ one stretch of pRNA , consisting of bases 31 to 35, was confirmed to be proximal to base 6 9, as revealed by its efficient cross-linking by psoralen. Two cross-l inking sites in the helical region were identified. Mg2+ induced a con formational change of pRNA that exposes the portal protein binding sit e by promoting the refolding of two strands of the procapsid binding r egion, resulting in the formation of pRNA-procapsid complexes. The pro capsid binding region in this binding-competent conformation could not be cross-linked with psoralen. When the two strands of the procapsid binding region were fastened by cross linking, pRNA could neither bind procapsids nor package phi 29 DNA. A pRNA conformational change was a lso discernible by comparison of migration rates in native EDTA and Mg 2+ polyacrylamide gel electrophoresis and was revealed by T-1 RNase pr obing. The Mg2+ concentration required for the detection of a change i n pRNA cross-linking patterns was 1 mM, which was the same as that req uired for pRNA-procapsid complex formation and DNA packaging and was a lso close to that in normal host cells.