Table 2. Predicted Duplexes Formed between the Tomato CalS12-like mRNA Target and vd-sRNAs Derived from the VMRs of PSTVd Variants.
PSTVd Variant | CalS12-like mRNA/vd-sRNA | ∆Ga | % Pairing |
---|---|---|---|
PSTVd-I | 3670 GG A G A A 3690 | −22.06 | 71.4 |
5′-U UUC U UC GCUCAGGA -3′ | |||
3′-A AAG A AG CGAGUCCU -5′ | |||
59 AA A A A C 39 | |||
PSTVd-I | 3668 GG A G A 3689 | −22.95 | 77.3 |
5′-CUU UUC U UC GCUCAGGA-3′ | |||
3′-GAA AAG A AG CGAGUCCU-5′ | |||
61 AA A A A 40 | |||
PSTVd-M | 3670 GG A G A A A 3690 | −16.21 | 66.7 |
5′-U UUC U UC GCTC GGA -3′ | |||
3′-A AAG A AG CGAG UCU -5′ | |||
59 AA A A A C C 39 | |||
PSTVd-M | 3668 GG AG A A 3689 | −17.1 | 68.2 |
5′-CUU UUC U UC GCUC GGA-3′ | |||
3′-GAA AAG A AG CGAG UCU-5′ | |||
61 AA A A A C 40 |
The PairFold online tool was used to predict the minimum secondary structure free energy of pairs of RNA sequences.
Underlined nucleotides represent G:U wobble base pairs.