Table 1. Estimates of Relative Affinity of RNAs for JAZ Zinc Fingers.
| no. base pairs22 |
binding to JAZ |
|||||||
|---|---|---|---|---|---|---|---|---|
| RNA | no. nucleotides | W–C | wobble | no. bulge | no. loop | no. overhang | EMSA (ZF34)a | NMR (ZF3)a |
| VAI | ||||||||
| full-length | 160 | 46 | 8 | 16 | 31 | 5 (CUUUU) | ++ | nd |
| apical | 50 | 20 | 1 | 3 | 5 (AAUU) | 0 | ++ | ++ |
| T52 | 52 | 17 | 3 | 8 | 4 (AAUU) | 0 | ++ | nd |
| T57A | 57 | 17 | 3 | 8 | 4 (AAUU) | 5 (CUUUU) | ++ | ++ |
| T57B | 57 | 17 | 3 | 8 | 4 (GGGA) | 5 (CUUUU) | ++ | ++ |
| T57C | 57 | 18 | 3 | 6 | 4 (AAUU) | 5 (CUUUU) | ++ | nd |
| T57D | 57 | 18 | 3 | 6 | 4 (AAUU) | 5 (CUUUU) | ++ | nd |
| T57E | 57 | 20 | 2 | 6 | 4 (AAUU) | 5 (CAAAA) | ++ | nd |
| T84 | 84 | 21 | 4 | 12 | 17 (GGGA) | 5 (CUUUU) | ++ | nd |
| T44 | 44 | 13 | 3 | 4 | 3 | 5 (CUUUU) | + | nd |
| T37 | 37 | 10 | 3 | 4 | 4 | 5 (CUUUU) | + | ++ |
| duplex I | 53 | 17 | 3 | 8 | 0 | 5 (CUUUU) | + | nd |
| duplex II | 49 | 17 | 3 | 4 | 0 | 5 (CUUUU) | + | nd |
| duplex III | 61 | 21 | 3 | 8 | 0 | 5 (CUUUU) | + | ++ |
| duplex IIIA | 66 | 21 | 3 | 8 | 0 | 10 (2× CUUUU) | + | nd |
| T57 DNA | 57 | 17 | 3 | 8 | 4 (AATT) | 5 (CAAAA) | – | – |
| VAImin | 38 | 16 | 2 | 2 | 0 | 0 | nd | ++ |
| VAIminMut | 38 | 19 | 0 | 0 | 0 | 0 | nd | ++ |
| ssRNA | 10 | 0 | 0 | 0 | 0 | 0 | – | nd |
| pre-miR34a | 33 | 7 | 16 | 13 | 1 | ++ | nd | |
a
++ corresponds to affinity (C50) ∼ 0.05–0.2 μM, +, to C50 ∼ 0.2–2 μM, and −, to C50 > 2 μM.