Table 1.
The DNA/RNA Molecules and the Respective MD Simulation Details in the Work
| DNA or RNA | Desired Bulk [Mg2+]/[Na+] (mM) | Cell Size (Å 3) | Simulation Time (ns) | Bulk [Mg2+]/[Na+] in Referencea (mM) | Our Bulk [Mg2+]/[Na+]b (mM) |
|---|---|---|---|---|---|
| 24-bp dsDNA | 1/20 | 150 × 150 × 90 | 200 | – | 1.1 ± 0.1/20.2 ± 0.3 |
| 5/20 | 150 × 150 × 90 | 200 | 7/18 | 5.4 ± 0.1/20.0 ± 0.2 | |
| 5/40 | 150 × 150 × 90 | 200 | 8/36 | 5.3 ± 0.1/40.4 ± 0.3 | |
| 5/70 | 150 × 150 × 90 | 200 | 8/72 | 5.2 ± 0.1/70.3 ± 0.2 | |
| 5/240 | 150 × 150 × 90 | 200 | 6/237 | 5.2 ± 0.2/241.6 ± 0.4 | |
| 5/420 | 150 × 150 × 90 | 200 | 7/418 | 5.3 ± 0.1/421.1 ± 0.3 | |
| 10/20 | 150 × 150 × 90 | 200 | – | 10.1 ± 0.1/20.8 ± 0.3 | |
| 20/20 | 150 × 150 × 90 | 200 | – | 20.9 ± 0.2/19.7 ± 0.2 | |
| 50/20 | 150 × 150 × 90 | 200 | – | 50.8 ± 0.7/20.7 ± 0.5 | |
| 8-bp dsRNA | 1/20 | 150 × 150 × 48 | 200 | – | 1.0 ± 0.1/21.5 ± 0.1 |
| 10/20 | 150 × 150 × 48 | 200 | – | 10.9 ± 0.2/20.4 ± 0.2 | |
| 12-bp dsRNA | 1/20 | 150 × 150 × 58 | 200 | – | 1.0 ± 0.1/21.6 ± 0.8 |
| 10/20 | 150 × 150 × 58 | 200 | – | 10.5 ± 0.3/19.7 ± 0.2 | |
| 24-bp dsRNA | 1/20 | 150 × 150 × 90 | 200 | – | 1.1 ± 0.1/20.2 ± 0.3 |
| 5/20 | 150 × 150 × 90 | 200 | – | 5.1 ± 0.2/21.6 ± 0.3 | |
| 10/20 | 150 × 150 × 90 | 200 | – | 10.1 ± 0.1/21.6 ± 0.1 | |
| 50/20 | 150 × 150 × 90 | 200 | – | 50.8 ± 0.3/21.7 ± 0.1 | |
| 28-nt BWYV Pseudoknot | 1/20 | 120 × 110 × 110 | 200 | – | 1.0 ± 0.1/20.8 ± 0.2 |
| 10/20 | 120 × 110 × 110 | 200 | – | 10.9 ± 0.2/20.5 ± 0.1 | |
| 58-nt rRNA Fragment | 1/20 | 130 × 130 × 120 | 200 | – | 1.1 ± 0.2/20.5 ± 0.1 |
| 10/20 | 130 × 130 × 120 | 200 | – | 10.2 ± 0.2/19.5 ± 0.1 | |
| 76-nt Yeast tRNAPhe | 1/20 | 130 × 145 × 160 | 200 | – | 1.1 ± 0.1/19.4 ± 0.3 |
| 10/20 | 130 × 145 × 160 | 200 | – | 10.3 ± 0.1/19.1 ± 0.1 | |
| 94-nt SAM-I Riboswitch | 1/20 | 120 × 145 × 140 | 200 | – | 1.0 ± 0.1/21.0 ± 0.2 |
| 10/20 | 120 × 145 × 140 | 200 | – | 10.1 ± 0.1/20.5 ± 0.1 |
In the table, the sequences of dsDNA and dsRNAs are listed in Table S1, and BWYV pseudoknot, rRNA fragment, Yeast tRNAPhe, and SAM-I riboswitch represent a 28-nt beet western yellow virus (BWYV) pseudoknot fragment (PDB: 437D) (88), a 58-nt ribosomal RNA fragment (PDB: 1HC8) (89), 76-nt Yeast tRNAPhe (PDB: 1TRA) (90), and 94-nt S-adenosylmethionine riboswitch mRNA (PDB: 2GIS) (91), respectively.
a
The bulk [Mg2+]/[Na+] values are obtained from Yoo and Aksimetiev (82).
b
The bulk [Mg2+]/[Na+] values are obtained from our MD simulations.