Table 3. RMSD, SASA, and H-Bond Analysis of Unrestrained MD Simulations for Cyclic-Dimer, -Tetramer, and -Hexamer Systemsa.
| entry | components | structure | duplex rmsd (Å) | SASA (Å2 per core) | % loss of H-bonds |
|---|---|---|---|---|---|
| 1 | [5′-C-3′]:[5′-C-3′]′ | hexamer | 6.63 | 122.21 | % 17 |
| 2 | [5′-C-3′]:[5′-C-3′]′ | tetramer | 6.50 | 133.79 | % 22 |
| 3 | [5′-C-3′]:[5′-C-3′]′ | dimer | 6.82 | 200.39 | % 24 |
| 4 | [3′-C-3′]:[3′-C-3′]′ | dimer | 6.64 | 163.56 | % 22 |
| 5 | [5′-C-5′]:[5′-C-5′]′ | dimer | 5.88 | 140.37 | % 31 |
| 6 | [5′-T3CT3-3′]:[5′-T3CT3-3′]′ | dimer | 5.37 | 118.90 | % 5 |
| 7 | [5′-T6-3′]:[5′-T6-3′]′ | dimer | 5.89 | % 9 |
a
One MD simulation was carried out for each of the hexamer and tetramer; four independent MD simulations were carried out for cyclic-dimer systems but only the lowest rmsd results are shown (see Section S6 in the Supporting Information for more details).