Selected article for: "base apical loop and codon position"
Author: Tuplin, A.; Evans, D. J.; Buckley, A.; Jones, I. M.; Gould, E. A.; Gritsun, T. S.
Title: Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus
  • Document date: 2011_5_27
    • ID: 0aiaklrn_32
    Snippet: The phylogenetic conservation of thermodynamically stable RNA structures across all TBFV group ORFs was further analyzed using the program STRUCTURE_DIST ( Figure 2 ) (40) . This method quantifies phylogenetically concordant structures predicted using the widely accepted MFold or UNAFold algorithms, which can then be aligned and overlaid with SSSV results (31, 32) . Analysis of the entire ORF showed the most striking evidence for conserved base-p.....
    Document: The phylogenetic conservation of thermodynamically stable RNA structures across all TBFV group ORFs was further analyzed using the program STRUCTURE_DIST ( Figure 2 ) (40) . This method quantifies phylogenetically concordant structures predicted using the widely accepted MFold or UNAFold algorithms, which can then be aligned and overlaid with SSSV results (31, 32) . Analysis of the entire ORF showed the most striking evidence for conserved base-pairing between the initiation codon at position 133 and position 318, after which a large drop in the frequency of base-paired nucleotides was observed. Within this region SL6 was predicted to be the most significant structure, with conserved pairing between 209 and 254 centred on a region with a conserved lack of base pairing between positions 228 to 236, representing the unpaired apical loop of SL6. The base-paired stem of SL6 contained conserved short single-stranded regions between positions 218-220 and nucleotides 244 and 245 consistent with the unpaired bulge, either side of the paired stem. This corresponds exactly to the position and structure of SL6 predicted by MFold (Figure 1 and Supplementary Figure S1A ).

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