Table 5. Predicted Duplexes Formed between vd-sRNA Derived from the VMRs of PSTVd Variants and the CalS11-like mRNA from Tomato cv Moneymaker
PSTVd VariantCalS11-like mRNA/vd-sRNA∆Ga% Pairing
PSTVd-I170 GG A G C 190−19.5876.2
5′-U UUCU UCUGC CAGGAG-3′
3′-A AAGA AGACG GUCCUC-5′
59 AA A A A 39
PSTVd-I168 GG A G C 189−18.9877.3
5′-CUU UUC U UCUGC CAGGA-3′
3′-GAA AAG A AGACG GUCCU-5′
61 AA A A A 40
PSTVd-M170 GG AG C A 189−13.1871.4
5′-U UUC U UCUGC C GGAG-3′
3′-A AAG A AGACG G UCUC-5′
59 AA A A A C 39
PSTVd-M168 GG A G C A 189−12.5872.7
5′-CUU UUC U UCUGC C GGA-3′
3′-GAA AAG A AGACG G UCU-5′
61 AA A A A C 40
  • a The PairFold online tool was used to predict the minimum free energy secondary structure of a pair of RNA sequences.

  • The underlined nucleotides represent G:U wobble base pairs.