Table 2.
Backbone torsion angles [°] of the 10 dinucleoside monophosphate B-DNA double strands[a]
| ds | ss[b] | PO3′–C3′– C4’ (ε) | O5′–PO3′– C3’ (ζ) | C5′–O5′– PO3’ (α) | C4′–C5′– O5′P (β) | C3′–C4′– C5′–O5’ (γ) | C2–N1/C4–N9– C1′–O4’ (χ)[c] |
|---|---|---|---|---|---|---|---|
| d(ApT)2 | d(ApT) | 154.5 | −81.8 | −60.9 | −173.3 | 50.9 | −97.8 (6) |
| d(ApT) | 153.6 | −81.3 | −60.9 | −172.6 | 50.6 | −97.7 (6) | |
| d(ApA)2 | d(ApA) | 158.0 | −82.4 | −63.1 | −171.8 | 48.4 | −93.8 (5) |
| d(TpT) | 164.5 | −86.8 | −62.9 | −174.2 | 50.7 | −105.3 (2) | |
| d(TpA)2 | d(TpA) | 164.1 | −90.1 | −69.6 | −152.7 | 45.4 | −106.2 (3) |
| d(TpA) | 164.9 | −90.2 | −70.4 | −152.5 | 42.2 | −106.0 (4) | |
| d(GpT)2 | d(GpT) | 148.4 | −79.4 | −59.7 | −169.2 | 51.8 | −95.4 (6) |
| d(ApC) | 148.9 | −79.8 | −59.1 | −170.4 | 51.8 | −97.0 (6) | |
| d(ApG)2 | d(ApG) | 150.9 | −79.2 | −62.2 | −167.7 | 48.4 | −99.7 (7) |
| d(CpT) | 164.6 | −87.4 | −64.8 | −164.6 | 49.3 | −107.0 (4) | |
| d(GpA)2 | d(GpA) | 158.2 | −84.7 | −78.5 | −131.5 | 43.5 | −102.9 (11) |
| d(TpC) | 169.9 | −92.2 | −67.6 | −162.0 | 48.3 | −112.4 (1) | |
| d(CpA)2 | d(CpA) | 164.0 | −85.9 | −78.5 | −132.8 | 41.0 | −101.0 (8) |
| d(TpG) | 164.8 | −90.1 | −70.6 | −149.7 | 44.2 | −106.5 (3) | |
| d(GpC)2 | d(GpC) | 158.6 | −86.4 | −65.6 | −159.9 | 48.3 | −106.8 (4) |
| d(GpC) | 158.9 | 86.0 | −67.2 | −156.8 | 47.8 | −107.6 (3) | |
| d(CpG)2 | d(CpG) | 164.4 | −86.7 | −76.7 | −136.3 | 41.2 | −103.0 (5) |
| d(CpG) | 164.1 | −86.2 | −77.1 | −135.8 | 41.1 | −103.0 (5) | |
| d(GpG)2 | d(GpG) | 152.0 | −82.6 | −63.7 | −159.4 | 47.5 | −99.0 (4) |
| d(CpC) | 170.3 | −90.8 | −69.3 | −160.0 | 46.8 | −111.5 (4) | |
| Av (SD)[d] | 159.9 (7) | −76.9 (38) | −67.4 (6) | −157.7 (14) | 47.0 (4) | −103.0 (7) | |
| Exptl (SD)[e] | 184 (11) | −95 (10) | −62 (15) | 176 (9) | 48 (11) | −102 (14) | |
[a] Computed at BLYP-D/TZ2P and COSMO for simulating aqueous solution. See Figure 2 for definitions and Figure 3–5 for structures. [b] Single strands that constitute the double strand. [c] Average of the two χ angles present in each dinucleoside monophosphate (see Figure 2). [d] Average with standard deviation (SD) over the 10 dinucleoside monophosphate double strands. [e] Experimental values with standard deviation (SD) from X-ray crystal structures of oligodeoxynucleotides in B-DNA conformation (ref. [21]).