Proposed Secondary Structure of Eukaryote Specific Expansion Segment 15 in 28S rRNA from Mice, Rats, and Rabbits

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• 作者：Sofia L. Larsson and Odd Nygå ; rd
• 刊名：Biochemistry
• 出版年：2001
• 出版时间：March 13, 2001
• 年：2001
• 卷：40
• 期：10
• 页码：3222 - 3231
• 全文大小：157K
• 年卷期：v.40,no.10(March 13, 2001)
• ISSN：1520-4995

文摘

The expansion segments in eukaryotic ribosomal RNAs are additional RNA sequences notfound in the RNA core common to both prokaryotes and eukaryotes. These regions show large species-dependent variations in sequence and size. This makes it difficult to create secondary structure modelsfor the expansion segments exclusively based on phylogenetic sequence comparison. Here we have useda combination of experimental data and computational methods to generate secondary structure modelsfor expansion segment 15 in 28S rRNA in mice, rats, and rabbits. The experimental data were collectedusing the structure sensitive reagents DMS, CMCT, kethoxal, micrococcal nuclease, RNase T₁, RNaseCL3, RNase V₁, and lead(II) acetate. ES15 was folded with the computer program RNAStructure 3.5using modification data and phylogenetic similarities between different ES15 sequences. This programuses energy minimization to find the most stable secondary structure of an RNA sequence. The presentedsecondary structure models include several common structural motifs, but they also have characteristicsunique to each organism. Overall, the secondary structure models showed indications of an energeticallystable but dynamic structure, easily accessible from the solution by the modification reagents, suggestingthat the expansion segment is located on the ribosomal surface.