Table 3.
Average helical parameters of XNA/RNA, RNA/RNA, and DNA/DNA duplexesa.
| L-aTNA/RNA | SNA/RNA | LNA/RNA | PNA/RNA | dsRNA | dsDNA | |
|---|---|---|---|---|---|---|
| X-displacement [Å]b | −6.4 | −5.7 | −5.4 | −6.2 | −4.2 | −0.5 |
| Inclination [deg]b | 1.6 | 1.2 | 11.6 | 11.5 | 16.6 | 4.4 |
| Helical rise [Å]b | 3.1 | 3.2 | 2.6 | 2.8 | 2.7 | 3.3 |
| Helical twist [deg]b | 22.7 | 24.2 | 30.0 | 25.7 | 33.0 | 34.0 |
| Residues per turn [nt] | 15.8 | 15.3 | 12.0 | 14.1 | 10.9 | 10.6 |
| Helical pitch [Å] | 49.5 | 47.6 | 31.0 | 39.1 | 28.9 | 34.6 |
| Minor groove [Å]c | 9.5 | 9.4 | 9.9 | n.d.d | 10.1 | 5.8 |
aAll parameters were calculated using 3DNA-Web. PDB accession codes were the following: LNA/RNA, 1H0Q; PNA/RNA, 5EMF; dsRNA, 3ND4; and dsDNA, 3BSE.
bLocal base-pair helical parameters.
cMinor groove widths are measured as the closest interstrand P–P distances subtracted by 5.8 Å to account for the van der Waals radii of the phosphate groups.
dDistances cannot be measured due to double conformation.