Computer modeling and display of RNA secondary and tertiary structures

Probing RNA structure with chemical reagents and enzymes

This unit provides thorough coverage of the most useful chemical and enzyme probes that can be used to examine RNA secondary and tertiary structure. Footprinting methods are presented using dimethyl sulfate, diethyl pyrocarbonate, ethylnitrosourea, kethoxal, CMCT, and nucleases. For chemical probes, both strand scission and primer extension detection protocols are included.

RnaViz, a program for the visualisation of RNA secondary structure

RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to a newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program.

Probing the hammerhead ribozyme structure with ribonucleases

Susceptibility to RNase digestion has been used to probe the conformation of the hammerhead ribozyme structure prepared from chemically synthesised RNAs. Less than about 1.5% of the total sample was digested to obtain a profile of RNase digestion sites. The observed digestion profiles confirmed the predicted base-paired secondary structure for the hammerhead. Digestion profiles of both cis and trans hammerhead structures were nearly identical which indicated that the structural interactions leading to self-cleavage were similar for both systems. Furthermore, the presence or absence of Mg2+ did not affect the RNase digestion profiles, thus indicating that Mg2+ did not modify the hammerhead structure significantly to induce self-cleavage. The base-paired stems I and II in the hammerhead structure were stable whereas stem III, which was susceptible to digestion, appeared to be an unstable region. The single strand domains separating the stems were susceptible to digestion with the exception of sites adjacent to guanosines; GL2.1 in the stem II loop and G12 in the conserved GAAAC sequence, which separates stems II and III. The absence of digestion at GL2.1 in the stem II hairpin loop of the hammerhead complex was maintained in uncomplexed ribozyme and in short oligonucleotides containing only the stem II hairpin region. In contrast, the G12 site became susceptible when the ribozyme was not complexed with its substrate. Overall the results are consistent with the role of Mg2+ in the hammerhead self-cleavage reaction being catalytic and not structural.

Rainbow trout mitochondrial DNA: sequence and structural characteristics of the non-coding control region and flanking tRNA genes

We have determined the sequence of the 1003-bp control region (also referred to as the 'displacement-loop region') and flanking tRNA genes in the mitochondrial DNA (mtDNA) of the rainbow trout, Oncorhynchus mykiss. This region has the same overall structure (i.e., trnT-trnP-control region-trnF) as in mammalian and amphibian (Xenopus laevis) mitochondrial (mt)DNAs. The trout control region contains apparent homologues of the conserved sequence blocks (CSB) and termination-associated sequences identified in all other vertebrate mtDNA control regions; however, it is distinguished by having an imperfect direct repeat (68/73 bp; 77% positional identity) in the right domain (proximal to the phenylalanine tRNA gene), downstream from CSB-3 in the direction of heavy-strand transcription. Within the control region, rainbow trout mtDNA shares considerable sequence similarity with the mtDNAs of Atlantic cod, Gadus morhua (Johansen et al., Nucleic Acids Res. 18 (1990) 411-419] and white sturgeon, Acipenser transmontanus (Buroker et al., Genetics 124 (1990) 157-163). The highest level of identity in pairwise comparisons is 60-70% over about 80 bp in the right domain (encompassing CSB-2 and CSB-3). About 270 bp comprising the central domain of the control region (encompassing a polypyrimidine tract) are more moderately conserved (55-60% identity in pairwise comparisons), while the left domain is highly divergent. Comparison of five trout mitochondrial tRNA sequences with their human and X. laevis homologues emphasizes the strong A+T substitution bias shown by the human sequences.

Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria

Recent work has shown that amino acid sequence comparisons can be used to infer sites of C-to-U RNA editing in plant mitochondrial mRNAs (1). In order to test such predictions further and to search for conserved mRNA structural motifs that might provide insight into the mechanism of recognition of editing sites, the complete sequences of the cytochrome c oxidase subunit II (COXII) mRNAs of wheat, maize and pea were determined by reverse transcriptase sequencing. The results affirm the high reliability of editing predictions based on amino acid sequence alignments, and prompt us to make the further inference that COXI (cytochrome oxidase subunit I) mRNA is extensively edited in dicotyledonous plants but not in monocotyledons. In plant COXII mRNAs, additional non-predicted editing occurs such that the resulting derived amino acid sequences are more similar to those of non-plants than is indicated by the respective plant COXII DNA sequences. A number of homologous sites show differences in editing among species, and certain positions show partial editing within a species. Despite some deviation from expected nucleotide frequencies in the vicinity of editing sites, no extensive conserved primary or secondary structural motifs are apparent. The relevance of these data to the mechanism of RNA editing in plant mitochondria is discussed.