Table 3.
Hydrogen-bond structure (in Å) and stability (in kcal mol−1) of the 10 dinucleoside monophosphate B-DNA double strands[a]
| ds | ss 1/ss 2[b] | Distance | ΔEstrain[c] | ΔEint[c] | ΔEdouble[c] | ΔEdouble,rel[c] | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| N6–O4 (AT) | N1–N3 (AT) | O6–N4 (GC) | N1–N3 (GC) | N2–O2 (GC) | ||||||
| d(ApA)2 | d(ApA) | 2.88 | 2.81 | – | – | – | 2.9 | −22.1 | −19.2 | 7.9 |
| d(TpT) | 2.99 | 2.77 | – | – | – | – | – | – | – | |
| d(ApT)2 | d(ApT) | 2.93 | 2.78 | – | – | – | 3.6 | −22.1 | −18.7 | 8.5 |
| d(ApT) | 2.93 | 2.78 | – | – | – | – | – | – | – | |
| d(TpA)2 | d(TpA) | 2.92 | 2.79 | – | – | – | 10.3 | −24.0 | −13.8 | 13.4 |
| d(TpA) | 2.92 | 2.79 | – | – | – | – | – | – | – | |
| d(ApG)2 | d(ApG) d(CpT) | 2.88 | 2.80 | 2.87 | 2.88 | 2.80 | 2.6 | −25.7 | −23.1 | 4.0 |
| d(GpA)2 | d(GpA) d(TpC) | 2.98 | 2.78 | 2.81 | 2.88 | 2.88 | 3.0 | −25.7 | −22.7 | 4.4 |
| d(GpT)2 | d(ApC) d(GpT) | 2.88 | 2.82 | 2.85 | 2.87 | 2.82 | 5.4 | −27.2 | −21.9 | 5.3 |
| d(CpA)2 | d(CpA) d(TpG) | 2.92 | 2.78 | 2.84 | 2.86 | 2.84 | 9.4 | −27.9 | −18.5 | 8.6 |
| d(GpC)2 | d(GpC) | – | – | 2.84 | 2.90 | 2.81 | 4.3 | −31.4 | −27.1 | 0.0 |
| d(GpC) | – | – | 2.84 | 2.89 | 2.82 | – | – | – | – | |
| d(GpG)2 | d(CpC) | – | – | 2.81 | 2.89 | 2.84 | 4.9 | −29.9 | −25.1 | 2.0 |
| d(GpG) | – | – | 2.84 | 2.88 | 2.84 | – | – | – | – | |
| d(CpG)2 | d(CpG) | – | – | 2.85 | 2.85 | 2.85 | 11.3 | −34.8 | −23.5 | 3.6 |
| d(CpG) | – | – | 2.85 | 2.85 | 2.85 | – | – | – | – | |
| (AT)2 | AT | 2.89 | 2.80 | – | – | – | – | – | −19.1 | – |
| AT | 2.89 | 2.81 | – | – | – | – | – | – | – | |
| (GC)2 | GC | – | – | 2.84 | 2.88 | 2.84 | – | – | −25.1 | – |
| GC | – | – | 2.84 | 2.88 | 2.84 | – | – | – | – | |
| AT[d] | 2.91 | 2.82 | – | – | – | – | – | −9.8 | – | |
| GCd | – | – | 2.85 | 2.90 | 2.84 | – | – | −13.6 | - | |
[a] Computed at BLYP-D/TZ2P and COSMO for simulating aqueous solution. Parameters of the two base pair dimers (AT)2 and (GC)2 have been calculated for comparison. See Figure 2 for definitions and Figure 3–6 for structures. [b] Single strands that constitute the double strand. [c] See Equations 1 and 3. [d] From ref. [4g].