Table 5.
Summary of testing structural stability and structural conversion in MD simulations.
| System | Length (ns) | Average BB RMSD (Å) | Notes on GB results | |||
|---|---|---|---|---|---|---|
| starting structure | GB-neck2 | explicit water | GB-neck2 | explicit water | ||
| DNA (CCAACGTTGG)2 | A-form | 1000 | 100 | 4.3 (A); 4.3 (B) | 4.2 (A); 3.1 (B) | A → B, stable |
| B-form | 1000 | 100 | 4.2(A); 4.3(B) | 4.0(A); 3.1(B) | Stable | |
| DNA (CGCGAATTCGCG)2 | A-form | 1000 | 100 | 5.2 (A); 4.2 (B) | 5.3 (A); 3.0 (B) | A → B, stable |
| B-form | 1000 | 100 | 5.2 (A); 4.2 (B) | 5.4 (A); 2.9 (B) | Stable | |
| RNA (CCAACGUUGG)2 | A-form | 1000 | 100 | 2.1 (A); 6.1 (B) | 2.8 (A); 5.6 (B) | Stable |
| B-form | 1000 | 100 | 2.2 (A); 6.4 (B) | 2.8 (A); 5.5 (B) | B → A, stable | |
| RNA (CGCGAAUUCGCG)2 | A-form | 1000 | 100 | 2.3 (A); 6.7 (B) | 3.6 (A); 6.3 (B) | Stable |
| B-form | 1000 | 100 | 2.7 (A); 6.7 (B) | 3.7(A); 5.8(B) | B → A, stable | |
| DNA seq2 (CTAGGTGGATGACTCATT)2 | A-form | ~1000 | 100 | 6.2 (A) 6.9 (B) |
6.1 (A) 5.1 (B) |
|
| B-form | 1000 | 100 | 5.7 (A) 6.5 (B) |
6.0 (A) 5.0 (B) |
Stable | |
| DNA quadruplex (GGGG)4 | 1000 | 200 | 1.6 (NMR) | 4.4 (NMR) | Stable | |
| DNA quadruplex (GGGGTTTTGGGG)2 (PDB ID: 1L1H) | 1000 | 300 | 1.7 (X-ray) | 4.4 (X-ray) | Stable | |
| DNA-protein complex (PDB ID: 1GCC) | 50 | 50 | 2.7 (NMR) | 2.4 (NMR) | Stable | |
For duplex simulations, the canonical structure used as reference (A or B) is given in parentheses after the RMSD value. “A → B” or “B → A” indicates the conversion of A to B-form in DNA simulation (starting from A-form) or B to A for in RNA simulation (starting from B-form), respectively.