locarna tool  (Informatik Inc)

Journal: Molecular Microbiology

Article Title: Expression of the H elicobacter pylori virulence factor vacuolating cytotoxin A ( vac A ) is influenced by a potential stem‐loop structure in the 5′ untranslated region of the transcript

doi: 10.1111/mmi.13160

Figure Lengend Snippet: Nucleotide sequences and prevalence of 20 different stem‐loop variants in 67 clinical H . pylori isolates. A. The +4 to +30 nucleotide stem‐loop DNA sequences from 67 clinical H . pylori isolates were aligned. The upstream‐, loop‐ and downstream stem are marked by red, green and blue lines respectively. Positions of common polymorphisms are indicated by numbered arrows. The prevalence of each variant is indicated by the number of strains in the right hand column. The ability of the mRNA to form a stem‐loop structure at the +4 to +30 position is indicated by Y (yes) and N (no). The asterisk denotes minor variation in the stem of the +4 to +30 structure. The strain lacking a stem‐loop at position +4 to +30 was predicted to form a small alternative stem‐loop at position +7 to +19. The predicted minimum free energy (Δ G °) values for each structure, determined using the online Fold RNAstructure webserver (Reuter and Mathews, ) for each variant are also indicated ( NA = not applicable). For comparison, the equivalent stem‐loop sequences in four commonly used reference strains of H . pylori are also included. These are represented among the clinical varieties as well. B. Alignment of each stem‐loop variant (position +1 to +34) subjected to consensus secondary structure analysis by the Freiburg Tools online webserver LocARNA (Smith et al ., ). Nucleotide conservation is indicated by colour, see guide in (C). C. Consensus secondary structure of stem‐loop variants, generated by the Freiburg Tools online webserver LocARNA (Smith et al ., ). Circled nucleotides indicate positions were base substitutions have occurred but base pairing has been maintained (consistent mutations). Grey lettering represents sites where base changes have disrupted base pairing and the colour coding reflects the number of base pairing types at that position and the number of incompatible base changes as given in the colour legend.

Article Snippet: Consensus structures of mRNA were analysed using the online Freiburg Tools LocaRNA webserver ( http://rna.informatik.uni‐freiburg.de ) (Smith et al ., ).

Techniques: Variant Assay, Comparison, Generated

Journal: Molecular Microbiology

Article Title: Expression of the H elicobacter pylori virulence factor vacuolating cytotoxin A ( vac A ) is influenced by a potential stem‐loop structure in the 5′ untranslated region of the transcript

doi: 10.1111/mmi.13160

Figure Lengend Snippet: H . pylori 60190 wild type and stem‐loop mutants. A. DNA sequence alignment of H . pylori 60190 wild type and mutant strains. The inverted stem‐loop forming structure is marked by coloured boxes: red for the upstream side of the stem, green for the loop and blue for the downstream side. The −10 region (Pribnow box) and the transcriptional start point ( TSP ) are also indicated. B. Schematic representation of vac A m RNA 5′ UTR stem‐loop structure in (i) 60190 (wild type), (ii) 60190:: SL dis, (iii) 60190:: SL mir and (iv) 60190:: SLGtoA . Mutational changes are shown in grey. Binding strength between pairing nucleotides is indicated by = (strong), – (relatively strong) and · (relatively weak). The predicted minimum free energy values for each mutant structure, determined using the online Fold RNA structure webserver (Reuter and Mathews, ), are indicated below the schematic representations.

Article Snippet: Consensus structures of mRNA were analysed using the online Freiburg Tools LocaRNA webserver ( http://rna.informatik.uni‐freiburg.de ) (Smith et al ., ).

Techniques: Sequencing, Mutagenesis, Binding Assay