Difference in conformational diversity between nucleic acids with a six-membered ‘sugar’ unit and natural ‘furanose’ nucleic acids. Lescrinier Eveline, Froeyen Matheus, Herdewijn Piet. Nucleic Acids Res. 2003;31:2975–2989. doi: 10.1093/nar/gkg407.
The authors would like to apologise as in Figure 8 the picture of l-lyxopyranosyl nucleic acid is given instead of the picture of p-RNA. Please find herewith the corrected version of Figure 8 and Table 3, which contains the parameters for p-RNA. These changes do not affect the discussion and conclusions.
Figure 8.
Comparison between β-homo-DNA and p-RNA duplexes, reconstructed from parameters described in literature [14,23] and after an MD simulation. Scheme of the sugar-ring conformation in duplexes is represented at the bottom.
Table 3. Global helical parameters of duplexes with six membered sugars calculated using Curves 5.1a.
| Type | Average helical twist (°) | Average helical rise per residue (Å) | Number of nucleotides per helix | Base-pair inclination (°) | X-displacement (Å) |
|---|---|---|---|---|---|
| Right handed helix | |||||
| HNA:RNAb | 34.4 | 3.0 | 11.0 | 11.3 | –3.5 |
| ds HNA type 1 (trig)c | 33.2 | 2.2 | 11.0 | 24.2 | –6.2 |
| ds HNA type 2 (hex)c | 24.2 | 3.3 | 15.0 | 3.4 | –6.5 |
| α-homo-DNA:RNAd | 24.0 | 3.6 | 15.0 | –0.2 | 5.7 |
| ds β-homo-DNAe | 10.0 | 4.3 → 4.7 | 36.0 | 30.0 (45.0) | |
| f | 1.9 | 4.5 | 189.5 | 37.3 | 19.4 |
| g | 18.3 | 4.0 | 19.7 | 56.2 | –3.5 |
| Left handed helix | |||||
| ds p-RNAh | 18.9 → 20 | 5.8 → 6.1 | 18.0 → 19.0 | 45.0 → 55.0 | |
| i | –0.3 | 4.2 | 1161.0 | –48.6 | 1.3 |
| j | –27.4 | 4.2 | 13.1 | –87.9 | 0.1 |
aCurves 5.1 (10).
bPDB entry 1EJZ (18).
cNucleic Acid Database (ndb) entries HD0001.pdbs and HD0002.pdbs (coordinates with symmetry related strands) corresponding to pdb entries 481D (trig) and 1D7Z (hex), respectively (20).
dModel from Wippo et al. (16).
eValues from Otting et al. (14).
fLinear model reconstructed from Otting et al. (14).
gCurled model of ds β-homo-DNA after 100 ps of molecular dynamics simulation.
hValues reported in Schlonvogt et al. (23).
iQuasi linear model reconstructed from Schlonvogt et al. (23).
jCurled model of double-stranded p-RNA after 100 ps of molecular dynamics simulation.