Table 2.
MP2(full)/6-311G** Calculated B-Form DNA Hydrogen Bonding, Intra-Strand Base-Stacking, and Inter-Strand Base-Stacking Energies (kcal/mol).a
| Hydrogen-Bonding Energies (kcal/mol)
| |||||
|---|---|---|---|---|---|
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
| A–T | −13.53 | −13.92 | C–G | −27.31 | −27.40 |
| (−14.54) | (−15.05) | (−20.35) | (−20.40) | ||
|
| |||||
|
Intra-Strand Base-Stacking Energies (kcal/mol)
| |||||
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
|
|
|
||||
| 5’A | −1.60 | −4.81 | 5’G | −6.66 | −5.33 |
| 3’A | (−7.31) | (−11.52) | 3’A | (−10.75) | (−12.19) |
| 5’A | −3.03 | −0.41 | 5’G | −8.04 | −8.34 |
| 3’C | (−8.46) | (−8.73) | 3’C | (−9.01) | (−10.17) |
| 5’A | −5.48 | −6.63 | 5’G | −1.05 | −2.39 |
| 3’G | (−9.85) | (−11.35) | 3’G | (−10.27) | (−11.86) |
| 5’A | −3.81 | −3.38 | 5’G | −2.64 | −3.87 |
| 3’T | (−9.00) | (−10.51) | 3’T | (−9.17) | (−10.40) |
|
|
|
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| 5’C | −1.82 | −3.35 | 5’T | −2.62 | −4.66 |
| 3’A | (−5.80) | (−7.40) | 3’A | (−5.55) | (−7.47) |
| 5’C | +0.30 | −0.68 | 5’T | −2.43 | −3.39 |
| 3’C | (−5.86) | (−6.98) | 3’C | (−6.37) | (−7.39) |
| 5’C | −4.24 | −5.29 | 5’T | −3.16 | −3.47 |
| 3’G | (−5.75) | (−6.94) | 3’G | (−6.03) | (−9.38) |
| 5’C | −3.61 | −5.00 | 5’T | −6.26 | −2.94 |
| 3’T | (−6.91) | (−8.45) | 3’T | (−11.10) | (−12.41) |
|
| |||||
|
Inter-Strand Base-Stacking Energies (kcal/mol)
| |||||
| Bases | Ebind,H | Ebind,Me | Bases | Ebind,H | Ebind,Me |
|
|
|
||||
| 5’A_3’ | +3.72 | −0.42 | 5’_A3’ | −1.49 | −1.51 |
| 3’_A5’ | (−2.31) | (−2.37) | 3’A_5’ | (−4.28) | (−4.39) |
| 5’A_3’ | +3.99 | +0.27 | 5’_A3’ | +0.79 | +0.72 |
| 3’_C5’ | (+2.27) | (−1.07) | 3’C_5’ | (−1.83) | (−1.94) |
| 5’A_3’ | −2.99 | −3.22 | 5’_A3’ | −3.40 | −3.39 |
| 3’_G5’ | (−2.70) | (−2.81) | 3’G_5’ | (−5.15) | (−5.08) |
| 5’A_3’ | −2.29 | −2.13 | 5’_A3’ | −0.12 | −2.87 |
| 3’_T5’ | (−2.80) | (−2.45) | 3’T_5’ | (−1.17) | (−3.33) |
|
|
|
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| 5’C_3’ | +1.31 | +1.15 | 5’_C3’ | +3.05 | +2.80 |
| 3’_C5’ | (−0.37) | (−0.43) | 3’C_5’ | (−0.16) | (−0.20) |
| 5’C_3’ | −4.07 | −4.24 | 5’_C3’ | −2.80 | −3.06 |
| 3’_G5’ | (−1.00) | (−1.13) | 3’G_5’ | (−2.45) | (−2.65) |
| 5’C_3’ | −2.19 | −2.12 | 5’_C3’ | −1.89 | −1.94 |
| 3’_T5’ | (−2.16) | (−1.93) | 3’T_5’ | (−2.26) | (−2.11) |
|
|
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| 5’G_3’ | −3.01 | +1.36 | 5’_G3’ | −3.01 | −3.65 |
| 3’_G5’ | (−5.79) | (−3.18) | 3’G_5’ | (−5.79) | (−6.13) |
| 5’G_3’ | −3.01 | −1.66 | 5’_G3’ | −1.61 | −1.80 |
| 3’_T5’ | (−2.56) | (−2.27) | 3’T_5’ | (−3.99) | (−3.81) |
|
|
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| 5’T_3’ | −1.34 | −1.42 | 5’_T3’ | −1.14 | −1.30 |
| 3’_T5’ | (−2.03) | (−2.01) | 3’T_5’ | (−2.12) | (−2.11) |
a
Non-solvated Ebind,H and Ebind,Me values on top and not in parentheses. Solvated Ebind,H and Ebind,Me values on bottom and in parentheses. Solvation accounted for via the PCM method.