Table 2.
Structural Parameters of (AP)2 Duplexesa.
| (AP)2−3 duplex | (AP)2+3 duplex | |
|---|---|---|
| Helix shortening (%) | 2.0 to 3.6 | 2.4 to 3.5 |
| Bend angle (°) | 15 to 34 | 26º to 33º |
| Bend direction | major groove | major groove |
| T7 or G7 X-disp(Å); Y-disp (Å); inclin (°) | −1.4; 0.2; 10.8 | −3.1; −0.2; 0.2º |
| A22 or C22 X-disp(Å); Y-disp (Å); inclin (°) | −1.5; 0.1; 7.2 | −2.5; −0.1; 0.0º |
| G8 or T8 X-disp(Å); Y-disp (Å); inclin (°) | −1.8; 0.3; 2.9 | −2.7; 0.1; −0.3º |
| C21or A21 X-disp(Å); Y-disp (Å); inclin (°) | −1.0; −0.1; −3.6 | −2.5; −0.2; 1.0º |
| Sugar Puckers | ||
| T7 or G7 | C2’-endo | C2’-endo |
| A22 or C22 | C2’-endo | C2’-endo |
| G8 or T8 | C2’-endo | C2’-endo |
| C21or A21 | C2’-endo | C2’-endo |
| F9 or F6 | C1’-exob | C2’-endoc |
| F23 or F20 | C2’-endo | C2’-endo |
Structural parameters computed using CURVES (53).
a
Average values measured from the converging refined structures.
b
Two structures appeared in the C2’-endo range.
c
One structure in the C1’-exo range.
In both duplexes, the AP residues are fully intra-helical exhibiting no rotation towards any of the duplex grooves.