Table 3. RNA Molecules Used for Molecular Dynamics Simulations.
| sequence | source | model no. | PDB ID | no. NaCl |
|---|---|---|---|---|
| 5′ GGUGAAGGC 3′ | NMR | 22 | 2DD2(71) | 7 |
| 3′ CCGAAGCCG 5′ | ||||
| 5′ GGCACUUCGGUGCC 3′ | NMR | 11 | 2KOC(29) | 6 |
| 5′ U(UA)6A 3′ | X-ray | 1 | 1RNA(66) | 11 |
| 3′ A(AU)6U 5′ | ||||
| 5′ GCGCAAGC 3′a | NMR | 6 | 1ZIH(77) | 5 |
| 5′ AAAA 3′ | single strand of A-form RNA built using NAB module of Amber24 | 3 | ||
| 5′ CAAU 3′ | ||||
| 5′ CCCC 3′ | ||||
| 5′ GACC 3′ | ||||
| 5′ UUUU 3′ | ||||
| 5′ CCCC 3′ | C2′ endo anti | taken from the work of Condon et al.3,5 | ||
| C2′ endo syn | ||||
| C3′ endo syn | ||||
a
Two base pairs were removed from the 1ZIH sequence for simulations relative to the solution structure.