Chemical modification studies and the secondary structure of HeLa cell 5.8S rRNA

Abstract

Various secondary structure models have been proposed for 5.8 S rRNA. In this paper HeLa cell 5.8 S rRNA is shown to possess several sites that are reactive to carbodiimide at 25 degrees, and other regions that are unreactive. Previous work has established the distribution of reactive and unreactive cytidine residues along the primary structure (11). The secondary structure model of Nazar et al. (7) is fully compatible with the chemical reactivity data whereas other models are partly incompatible. We conclude that the model of Nazar et al. provides the best approximation so far available to the conformation of isolated 5.8 S rRNA. Findings on the effect temperature on the chemical reactivity of different parts of the structure are summarized. The findings described in this paper should provide a basis for examining the specific interaction of 5.8 S rRNA with 28 s rRNA.

Nucleotide sequence and structure of cytoplasmic 5S RNA and 5.8S RNA of Chlamydomonas reinhardii

“…Similarly we have constructed a secondary structure model for C. reinhardii 5.8S RNA based on the proposal of Nazar et al 24and on the relative susceptibilities of the nucleotide bonds towards T1 and bI RNases in 0.1 M Tris-HCl pH 7,5 (see figure 5). The structure model presented for C. reinhardii 5.8S RNA is very similar to that of Hela cell 5.8S RNA (25), and is in good agreement with the nuclease susceptibility of the RNA except for two single stranded loops. These two loops are located at positions 74-78 and 121-128 and are poorly cut by the nucleases in contrast to what is predicted from the structure model, unless they are involved in a tertiary structure and then protected from nuclease digestion.…”

Nucleotide sequences of Acanthamoeba castellanii 5S and 5.8S ribosomal ribonucleic acids: phylogenetic and comparative structural analyses

“…The extensive mis-matching and looping-out of nucleotides required to form helix a in A. castellanii and other 5.8S rRNAs may indicate that this helix is formed only in free molecules in solution [41,42] and has little significance in the ribosome.…”

Somatic Mutation Detection in Human Biomonitoring

“…Cleavage products of different lengths are resolved by denaturing gel electrophoresis ( fig. Carbodiimide is a bulky reagent that reacts with the imino sites of T and G bases (Kelly & Maden 1980). Using a probe of the opposite sense, mismatched A and G bases are converted to T and C mismatches thereby permitting their detection (Tindall & Whitaker 1991;Dianzani et al 1993).…”

“…The carbodiimide technique remains a viable alternative to the chemical cleavage method. Carbodiimide is a bulky reagent that reacts with the imino sites of T and G bases (Kelly & Maden 1980). The reagent reacts more rapidly with unpaired bases, which exist in heteroduplexes between mutant and wild-type DNA, than with paired bases, e.g., homoduplexes.…”