Table III.
Total energies (Hartree) and binding energies (kcal/mol) between single-strands for the A-form double-strands having the base sequence 5’-CAG-3’. The binding energy was appropriately corrected by the counterpoise (CP) calculations [12,13] and denoted such as CP-RNA and PNA-CP. The double-strands are listed in decreasing order of binding energy.
| Total energy | Binding energy | ||
|---|---|---|---|
| LNA-RNA | CP-RNA | LNA-CP | LNA-RNA |
| −8308.312 | −4070.718 | −4237.489 | −65.9 |
| RNA-RNA | CP-RNA | RNA-CP | RNA-RNA |
| −8194.038 | −4070.679 | −4123.257 | −64.0 |
| PNA-RNA | CP-RNA | PNA-CP | PNA-RNA |
| −7010.768 | −4070.154 | −2940.520 | −59.0 |
| PNA-PNA | CP-PNA | PNA-CP | PNA-PNA |
| −5867.448 | −2926.841 | −2940.522 | −53.3 |
| PNA-DNA | CP-DNA | PNA-CP | PNA-DNA |
| −6824.110 | −3883.525 | −2940.521 | −40.2 |
| LNA-LNA | CP-LNA | LNA-CP | LNA-LNA |
| −8460.753 | −4223.200 | −4237.492 | −38.3 |
| PNA-LNA | CP-LNA | PNA-CP | PNA-LNA |
| −7163.880 | −2940.520 | −4223.301 | −37.0 |
| RNA-DNA | CP-DNA | RNA-CP | RNA-DNA |
| −8006.624 | −3883.343 | −4123.258 | −14.4 |
| LNA-DNA | CP-DNA | LNA-CP | LNA-DNA |
| −8121.056 | −3883.550 | −4237.491 | −9.4 |
| DNA-DNA | CP-DNA | DNA-CP | DNA-DNA |
| −7781.220 | −3883.540 | −3897.666 | −8.8 |