Table 3 The systems used in Molecular dynamics (MD) simulations.
From: LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures
Model name1 | Box edge (Å) | [Na+] | simulation time |
|---|---|---|
Single strand | ||
ON1 | 70 | 0.12 M|120 ns |
ON2-5′DNA | ||
0.20 M|120 ns | ||
Duplex | ||
c-MYCDS19 | 83 | 0.10 M|120 ns |
c-MYCDS19Hetero | 0.25 M|140 ns | |
Triplex | ||
c-MYCDS19 ⦁ ON2-5′DNA | 85 | 0.12 M|120 ns, 140 ns |
c-MYCDS19Hetero ⦁ ON2-5′DNA | 0.27 M|220 ns | |
c-MYCDS19 ⦁ ON2-3′LNA ⦁ reduced | 85 | 0.27 M|200 ns, 140 ns |
c-MYCDS19 ⦁ ON2-5′LNA ⦁ reduced | ||
FXNDS19 ⦁ ON4-3′LNA ⦁ reduced | 85 | 0.27 M|200 ns |
FXNDS19 ⦁ ON4-5′LNA ⦁ reduced | ||
c-MYCDS19 ⦁ ON3-3′LNA ⦁ reduced-c/t | 77 | 0.15 M|140 ns |
c-MYCDS19 ⦁ ON3-5′LNA ⦁ reduced-c/t | ||
