TABLE 2.
Summary of fits to time-resolved fluorescence data for the IRES junction measured in the presence of 1 mM Mg2+
| A. Fits for individual vectors, using single distance distributions | |||
| Vector | Distance (range) | Half-width (range) | χ2 |
| Duplex | 69.8 (69.5–69.9) | 19.0 (16.3–20.1) | 7.5 |
| CS | 63.2 (63.0–63.3) | 26.0 (24.8–26.3) | 6.2 |
| BA | 74.9 (74.6–75.0) | 40.2 (37.1–40.6) | 7.7 |
| AC | 52.0 (51.9–52.6) | 38.4 (36.9–38.5) | 8.6 |
| BS | 51.4 (50.2–52.5) | 54.9 (52.8–57.1) | 12.9 |
| SA | 53.5 (53.4–54.7) | 47.5 (45.0–47.7) | 9.2 |
| BC | 46.1 (45.4–46.7) | 39.0 (38.0–40.0) | 11.7 |
| B. Fits using two distance distributions for nonstacked vectors (each fitted individually) | |||||
| Distance (range) | Half-width (range) | Distance (range) | Half-width (range) | ||
| Vector | Antiparallel | Parallel | χ2 | ||
| Distances are given in Å and distribution widths are reported as full width at half maximum. The range indicates the mean distance ± 1 standard deviation evaluated by Bootstrap analysis. | |||||
| (A) Phase and modulation data for the six vectors were fitted individually to a model based on a single Gaussian distribution of D-A distances in each case. The duplex was a 24-bp RNA corresponding to coaxially stacked A and B helices. | |||||
| (B) The data for the four nonstacked vectors were fitted to a model corresponding to a scissor-like rotation of the helical axes to give populations of parallel and antiparallel species. For each vector, two Gaussian distributions of D-A distances were used. For the fits shown a ratio of 1:1 was used. | |||||
| AC | 65.7 (65.0–66.8) | 28.6 (18.5–32.0) | 46.6 (46.0–47.3) | 14.5 (9.0–16.0) | 6.1 |
| BS | 76.5 (75.1–76.8) | 40.7 (20.6–45.6) | 48.4 (47.6–48.9) | 12.2 (6.8–12.7) | 6.2 |
| SA | 51.0 (50.3–51.5) | 15.0 (12.5–15.80) | 71.7 (70.7–73.7) | 68.4 (55.4–75.6) | 4.6 |
| BC | 46.2 (44.5–47.1) | 15.8 (9.1–16.1) | 57.2 (55.7–61.6) | 41.5 (25.7–45.6) | 8.3 |