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| Comparison of A-QLS abundance in real viral genomes vs. simulated genomes reshuffled at (A) single nucleotide and (B) island levels. Green and red indicate enrichment in real and simulated sequences, respectively.
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The DNA secondary structures that deviate from the classic Watson and Crick base pairing are increasingly being reported to form transiently in the cell and regulate specific cellular mechanisms. Human viruses are cell parasites that have evolved mechanisms shared with the host cell to support their own replication and spreading. Contrary to human...
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... quadruplex-like sequences and G-putative quadruplex forming sequences with islands of length four were rarely present across all Baltimore classes (Supplementary Figure 2). When comparing the overall abundance of predicted A-QLSs and G-PQSs (Figure 1), dsRNA viruses showed the most striking difference,as they were most enriched in A-QLS and most depleted in G-PQSs. ...
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... a P-value close to 0 indicates that the median value of A-QLSs found in real genomes is like that of the simulated ones, whereas P-values close to −1 or +1 indicate that the number of A-QLS is significantly enriched in the real or simulated sequences, respectively. The complete results of such comparison are shown as heatmaps in Figure 2, where green and red lines represent enrichment of A-QLSs in the real and reshuffled viral genomes, respectively. Overall, 38% AA, 34.8% AAA, and 20% AAAA QLSs showed a significant difference (p < 0.05) between the real and simulated sequences reshuffled at the single nucleotide level. ...
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... considering island reshuffling, these values slightly decreased to 36.8, 31.2, and 18%. The complete list of P-values is reported in Supplementary Tables 1, 2. Most members of Baltimore classes I, II, and VII (the DNA viruses) showed significantly more A-QLSs in real genomes (green spots in Figure 2) and only some exceptions regarding few members of the dsDNA virus families show an opposite trend (red spots in Figure 2), especially in comparison with simulations reshuffled at the singlenucleotide. ...
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... considering island reshuffling, these values slightly decreased to 36.8, 31.2, and 18%. The complete list of P-values is reported in Supplementary Tables 1, 2. Most members of Baltimore classes I, II, and VII (the DNA viruses) showed significantly more A-QLSs in real genomes (green spots in Figure 2) and only some exceptions regarding few members of the dsDNA virus families show an opposite trend (red spots in Figure 2), especially in comparison with simulations reshuffled at the singlenucleotide. Conversely, the RNA classes present more internal variability among their members and between sense and antisense strands. ...
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... considering island reshuffling, these values slightly decreased to 36.8, 31.2, and 18%. The complete list of P-values is reported in Supplementary Tables 1, 2. Most members of Baltimore classes I, II, and VII (the DNA viruses) showed significantly more A-QLSs in real genomes (green spots in Figure 2) and only some exceptions regarding few members of the dsDNA virus families show an opposite trend (red spots in Figure 2), especially in comparison with simulations reshuffled at the singlenucleotide. Conversely, the RNA classes present more internal variability among their members and between sense and antisense strands. ...
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... thus performed Taq polymerase stop assay on the HIV-1 CTS sequence in different salts to test the best conditions to evaluate oligonucleotide bending, as nucleic acid structures are reported to be highly influenced by the presence of different cations and anions (Meyer and Sühnel, 2003;Bhattacharyya et al., 2016). Based on the reported interaction of A-rich oligonucleotides with different cations and anions (Van Der Wijst et al., 2010), we selected KCl, NaCl, and LiCl salts to test the effect of different monovalent cations, and NaF to test the effect of a different anion. In the absence of additional ions to those required for enzyme activity, full-length elongation product was obtained, with one main stop band at Ter2 and additional milder stops at Ter1, Ter0.5, and Ter0 (Figure 6, lane 5). ...
