RNA secondary structure analysis of the packaging signal for Moloney murine leukemia virus

We have examined the cis-acting RNA packaging signal (psi) from Moloney murine leukemia virus using a combination of chemical and primary sequence analysis techniques. For our chemical analyses, we used dimethyl sulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene sulfonate as probes for RNA secondary structure. The structural information obtained from these studies was used to constrain computer algorithms for prediction of RNA secondary structure. In addition, we generated and analyzed a phylogenetic comparison of homologous sequences from related retroviruses. From these data, we have developed two models for the RNA secondary structure of the packaging signal psi. Both of these models suggest the presence of secondary structure elements in a region of the psi RNA known to be required for function.