Hydration of short DNA, RNA, and 2′-OMe oligonucleotides determined by osmotic stressing. Rozners Eriks, Moulder Janelle. Nucleic Acids Res. 2004;32:248–254. doi: 10.1093/nar/gkh175.
The authors would like to apologize for an error that appears in Table 2. Because of an inadvertent error in the spread sheet calculations, the number of water molecules for d(CG)3 (3a) was underestimated. The correct Table 2 should be:
Thus, in DNA the GC base pairs are hydrated to a similar or slightly higher extent than in RNA. The ΔnW for DNA duplexes is 2–5 and appears to be more sequence dependant than for RNA (ΔnW = 3–4) or 2′-OMe (ΔnW = 2–3) duplexes. Therefore, until more osmotic stressing data on different sequences are accumulated, comparisons of DNA and RNA hydration are perhaps best done with some skepticism.
Table 2. Values of ΔnW (per base pair).
| Sequence | Oligonucleotide | ΔnW Ethylene glycol | ΔnW Glycerol | ΔnW Acetamide | ΔnW Sucrose |
|---|---|---|---|---|---|
| 1a | d(GCGAAUUCGC) | 2.7 ± 0.6 | 2.3 ± 0.8 | 3.8 ± 0.9 | 8.1 ± 3.2 |
| 1b | r(GCGAAUUCGC) | 4.4 ± 0.6 | 3.4 ± 0.9 | 6.1 ± 0.6 | 9.0 ± 3.0 |
| 1c | 2′-OMe(GCGAAUUCGC) | 3.1 ± 0.5 | 2.8 ± 0.7 | 3.5 ± 0.5 | 7.9 ± 2.0 |
| 1d | d(GCGAATTCGC) | 4.1 ± 0.8 | 2.5 ± 0.8 | 5.2 ± 1.0 | 8.6 ± 2.9 |
| 2a | d(UA)6 | 1.8 ± 0.5 | 2.2 ± 0.6 | 4.3 ± 0.5 | ndb |
| 2b | r(UA)6 | 3.0 ± 0.5 | 3.3 ± 0.5 | 5.6 ± 0.5 | ndb |
| 2c | 2′-OMe(UA)6 | 2.1 ± 0.5 | 2.6 ± 0.5 | 4.5 ± 0.4 | ndb |
| 2d | d(TA)6 | 1.8 ± 0.6 | 2.2 ± 0.7 | 3.2 ± 0.5 | ndb |
| 3a | d(CG)3 | 4.8 ± 1.0 | 5.2 ± 1.1 | 8.7 ± 0.9 | ndb |
| 3b | r(CG)3 | 4.3 ± 0.7 | 4.3 ± 0.8 | 5.8 ± 0.9 | ndb |
| 3c | 2′-OMe(CG)3 | 2.6 ± 0.7 | 2.6 ± 1.2 | 3.1 ± 0.6 | ndb |
| 4b | r(CGCAAAUUUGCG) | 1.9a | 1.5a | 3.6a | ndb |
| 4d | d(CGCAAATTTGCG) | 2.3a | 1.8a | 3.7a | ndb |
aThese values may contain significant systematic errors due to discrepancies in −ΔH values (see Table 1).
bNot determined.