Table 12.
Intra-nucleotide distances (Å) in the 1YFV system. Experimental values are taken from Santa Lucia et al.[89] MD values are the time averages of the 1-μs simulation. Error bars for the MD data are the RMS fluctuations over the entire time series.
| Nucleotide | H8/H6-H1’ | H8/H6-H2’ | H8/H6-H3’ | |||
|---|---|---|---|---|---|---|
| Expt. | MD | Expt. | MD | Expt. | MD | |
| G1 | 3.9 ± 0.8 | 3.7 ± 0.1 | 4.0 ± 0.8 | 4.3 ± 0.2 | 3.5 ± 0.6 | 3.1 ± 0.3 |
| G2 | 4.4 ± 0.8 | 3.8 ± 0.1 | 3.6 ± 0.8 | 4.0 ± 0.2 | > 2.4 | 2.8 ± 0.2 |
| C3 | 3.5 ± 0.8 | 3.5 ± 0.1 | 3.3 ± 0.6 | 3.8 ± 0.1 | 3.1 ± 0.6 | 2.6 ± 0.2 |
| G4 | 3.7 ± 0.8 | 3.8 ± 0.1 | 3.5 ± 0.7 | 4.0 ± 0.2 | 2.8 ± 0.6 | 2.7 ± 0.2 |
| A5 | 3.7 ± 0.8 | 3.7 ± 0.1 | 4.0 ± 0.8 | 4.2 ± 0.2 | 3.0 ± 0.6 | 3.1 ± 0.3 |
| G6 | > 3.5 | 4.0 ± 0.2 | 2.9 ± 0.6 | 2.8 ± 0.2 | ||
| C7 | 3.6 ± 0.8 | 3.5 ± 0.1 | 2.7 ± 0.5 | 2.5 ± 0.2 | ||
| C8 | 3.7 ± 0.8 | 3.6 ± 0.1 | 3.2 ± 0.6 | 2.7 ± 0.6 | 2.5 ± 0.5 | 3.8 ± 0.7 |