Secondary structure in heterogeneous nuclear RNA: involvement of regions from repeated DNA sites

Heterogeneous nuclear RNA was found to contain regions of secondary structure based on a relative resistance to nuclease treatment compared with mRNA or poliovirus RNA and a shift in density toward double-stranded RNA early in the course of nuclease digestion. The regions involved in this secondary structure are enriched for RNA segments transcribed from repeated sites in the DNA. Thus, to maximize hybridization to repetitive sites heterogeneous nuclear RNA molecules must be both denatured and fragmented. Some of the self-complementary regions in heterogeneous nuclear RNA are released by alkali denaturation and fragmentation below 1500 nucleotides but maximum release is not achieved until fragmentation below 500 nucleotides. These results indicate that these self-complementary regions (“loops” plus “stems”) are mainly below 500 nucleotides in length.