TABLE 1.
Frequencies and estimated thermodynamic stability of variant stem-loops
| Straina | Stem-loop sequencec | Frequency (%) | ΔG° (kcal/mol at 37°C)c |
|---|---|---|---|
| NL4-3 | UCUGGCCUUCCCACAAGGGAAGGCCAGG | 98 (36.2) | −23.5 |
| Natural variants (wild type) | |||
| C15U/A26G/A33G | -U----------G------G-------- | 1 (0.4) | −24.3 |
| G41A | ---------------------------A | 1 (0.4) | −24.0 |
| A29G | ---------------G------------ | 1 (0.4) | −23.4 |
| U22G/C23U/A26C/G32A/A33C | --------GU--C-----AC-------- | 1 (0.4) | −23.1 |
| U21C/A26G | -------C----G--------------- | 1 (0.4) | −23.1 |
| A26C | ------------C--------------- | 1 (0.4) | −23.0 |
| A33Gd | -------------------G-------- | 66 (24.3) | −23.0 |
| C27G/A33G | -------------G-----G-------- | 1 (0.4) | −23.0 |
| A29G/A33G | ---------------G---G-------- | 2 (0.7) | −22.9 |
| C27G/A29G/A33G | -------------G-G---G-------- | 2 (0.7) | −22.9 |
| A39G | -------------------------G-- | 21 (4.1) | −22.8 |
| InsA29AGG/A33Gb | ----------------I--G-------- | 1 (0.4) | −22.6 |
| A33G/A39G | -------------------G-----G-- | 2 (0.7) | −22.3 |
| C25U | -----------U---------------- | 2 (0.7) | −21.3 |
| C15U | -U-------------------------- | 3 (1.1) | −21.1 |
| C25U/A26G/A33G | -----------UG------G-------- | 2 (0.7) | −21.1 |
| C25U/A26C | -----------UC--------------- | 7 (2.6) | −21.0 |
| C25U/A33G | -----------U-------G-------- | 3 (1.1) | −20.8 |
| C19U | -----U---------------------- | 4 (1.5) | −20.8 |
| C19U/C27G | -----U-------G-------------- | 1 (0.4) | −20.8 |
| C15A | -A-------------------------- | 2 (0.7) | −20.6 |
| C15U/A33G | -U----------------G-------- | 3 (1.1) | −20.6 |
| C25A/A26G/G30A | -----------AG---A----------- | 1 (0.4) | −20.4 |
| C24U/C27G/A28G/A29G | ----------U--GGG------------ | 1 (0.4) | −20.4 |
| C25A | -----------A---------------- | 4 (1.5) | −20.3 |
| C25A/A26G | -----------AG--------------- | 2 (0.7) | −20.3 |
| C25A/A29G | -----------A---G------------ | 1 (0.4) | −20.3 |
| C24U/C27A/A33G | ----------U--A-----G-------- | 1 (0.4) | −20.0 |
| A26C/G30A | ------------C---A----------- | 1 (0.4) | −19.9 |
| G30A | ----------------A----------- | 2 (0.7) | −19.9 |
| C15A/A39G | -A-----------------------G-- | 1 (0.4) | −19.9 |
| C25A/G30A/A33G | -----------A----A--G-------- | 1 (0.4) | −19.9 |
| A26G/G30C | ------------G---C----------- | 1 (0.4) | −19.8 |
| G30C | ----------------C----------- | 2 (0.7) | −19.8 |
| C25A/A26G/A33G | -----------AG------G-------- | 2 (0.7) | −19.8 |
| C25A/A33G | -----------A-------G-------- | 4 (1.5) | −19.8 |
| C15U/A33G/A39G | -U-----------------G-----G-- | 1 (0.4) | −19.8 |
| A34Cd | --------------------C------- | 3 (1.1) | −19.4 |
| U21C | -------C-------------------- | 1 (0.4) | −19.4 |
| U22A/A33G | --------A----------G-------- | 1 (0.4) | −19.1 |
| U22C | --------C------------------- | 1 (0.4) | −19.1 |
| U22C/C25U/A26G | --------C--UG--------------- | 1 (0.4) | −19.0 |
| C15U/C25A/G30A | -U---------A----A----------- | 1 (0.4) | −18.0 |
| C15A/C24U | -A--------U----------------- | 2 (0.7) | −17.6 |
| C15U/C25A/G30A/A33G | -U---------A----A--G-------- | 1 (0.4) | −17.5 |
| C15U/C25A/A26G/A33G | -U---------AG------G-------- | 7 (2.6) | −17.4 |
| C15U/C25A/A33G | -U---------A-------G-------- | 4 (1.5) | −17.4 |
| G17U | ---U------------------------ | 1 (0.4) | −17.0 |
| G32Ad | ------------------A--------- | 2 (0.7) | −16.7 |
| C25U/G32A | -----------U------A--------- | 1 (0.4) | −16.6 |
| C25U/G32A/A33C | -----------U------AC-------- | 1 (0.4) | −16.6 |
| G18C | ----C----------------------- | 2 (0.7) | −16.4 |
| Consensus | U-U---C--------A----AGGCC-G- | ||
| Laboratory mutants | |||
| mut2ad | -------AA------------------- | NAe | −17.6 |
| mut4ad | -------AAAA----------------- | NAe | −10.2 |
| mut6ad | -------AAAAAA--------------- | NAe | −4.3 |
a
In bold are the strains whose stem-loops were analyzed for frameshift activity.
b
Ins, insertion (AGG).
c
ΔG°, calculated thermodynamic stability.
d
Virions produced.
e
NA, not applicable.