Structural analysis of RNA subunits from avian myeloblastosis virus (AMV)

Subgenomic fragments were released from purified 35S AMV RNA using strongly denaturing conditions of 78% formamide and 3.9 M urea at 53 degrees C. The fragments were characterized by sedimentation and electron microscopic analysis. The presence of five distinct, reproducible size classes of RNA molecules with mean lengths 1.79 +/- 0.07 micron, 1.36 +/- 0.09 micron, 1.03 +/- 0.09 micron, 0.7 +/- 0.08 micron, and 0.42 +/- 0.09 micron were demonstrated. Analysis of poly(A)+ and poly(A)- RNA fragments revealed that splitting of 35S AMV RNA by strongly denaturing agents is not entirely random. Only one main distinct site of preferential splitting of the AMV RNA was located at 1.8 kb from the 3' end of the genome. The other three sites located at 3.2 kb, 4.5 kb, and 5.9 kb from the 3' end were much less distinct and were masked by random degradation of the molecules. The amount of poly(A)- RNA fragments of preferential lengths was increased by additional splitting of RNA molecules at preferential sites. No proteosynthetic activity was detected when subunits obtained by strong denaturation of 35S AMV RNA were analysed in a cell-free protein synthesis system.