5'-Dimethoxytrityl-N4-acetyl-2'-deoxy-2'-fluoroarabinocytidine, 3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Arabinonucleosides are epimers of ribonucleosides with the chiral switch being at the 2' position of the sugar residue. 2'-F-ANA adopts a more DNA-like B-type helix conformation, not through the typical C2'-endo conformation but, rather, through an unusual O4'-endo (east) pucker. However, the presence of the electronegative fluorine leads to a still significant increase (DTm1.2°C/mod) in melting temperature per modification.1 2'-F-ANA-containing oligonucleotides exhibit very high binding specificity to their targets. Indeed, a single mismatch in a 2'-F-ANA – RNA duplex leads to a DTm of -7.2°C and in a 2'-F-ANA - DNA duplex a DTm of -3.9°C.2
The presence of fluorine at the 2' position in 2'-F-ANA leads to increased stability to hydrolysis under basic conditions relative to RNA and even 2'-F-RNA.1,3 The stability of 2'-F-ANA to nucleases also makes this a useful modification for enhancing the stability of oligonucleotides in biological environments.2 2'-F-ANA hybridizes strongly to target RNA and, unlike most 2' modifications, induces cleavage of the target by RNase H. Phosphorothioate (PS) 2'-F-ANA is routinely used in these applications due to its increased nuclease resistance. Alternating 2'-F-ANA and DNA units provide among the highest potency RNase H-activating oligomers. Both the "altimer" and "gapmer" strand architectures consistently outperform PS-DNA and DNA/RNA gapmers.4
siRNA oligos were found to tolerate the presence of 2'-F-ANA linkages very well. High potency gene silencing was demonstrated5 with siRNA chimeras containing 2'-F-RNA and/or LNA and 2'-F-ANA. The high efficacy of these chimeras was attributed to the combination of the rigid RNA-like properties of 2'-F-RNA and LNA with the DNA-like properties of 2'-F-ANA.
| Specifications | |
|---|---|
| Diluent | Anhydrous Acetonitrile |
| Storage | Refrigerated storage, maximum of 2-8�C, dry |
| Stability | 1-2 days |
The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.
| Catalog # | Pack Size | Grams/Pack | 0.1M Dil. (mL) | Approximate Number of Additions | |||||
|---|---|---|---|---|---|---|---|---|---|
| LV40 | LV200 | 40nm | 0.2μm | 1μm | 10μm | ||||
| 10-3815-02 | 0.25 g | .25grams | 3.17 | 92.33 | 55.4 | 34.63 | 25.18 | 18.47 | 4.62 |
| 10-3815-05 | 0.5 g | .5grams | 6.33 | 197.67 | 118.6 | 74.13 | 53.91 | 39.53 | 9.88 |
| Catalog # | Pack Size | Grams/Pack | Dilution (mL) | Approximate Number of Additions | ||||
|---|---|---|---|---|---|---|---|---|
| Molarity | 50nm | 0.2μm | 1μm | 15μm | ||||
| 10-3815-02 | 0.25 g | .25grams | 4.72 | 0.07 | 88 | 55 | 40 | 5.5 |
| 10-3815-05 | 0.5 g | .5grams | 9.45 | 0.07 | 182.6 | 114.13 | 83 | 11.41 |
References
1. E. Viazovkina, M.M. Mangos, M.I. Elzagheid, and M.J. Damha, Curr Protoc Nucleic Acid Chem, 2002, Chapter 4, Unit 4 15.
2. J.K. Watts, and M.J. Damha, Can. J. Chem., 2008, 86, 641-656.
3. J.K. Watts, A. Katolik, J. Viladoms, and M.J. Damha, Org Biomol Chem, 2009, 7, 1904-10.
4. A. Kalota, et al., Nucleic Acids Res., 2006, 34, 451.
5. G.F. Deleavey, et al., Nucleic Acids Res., 2010, 38, 4547-4557, J.K. Watts, et al., Nucleic Acids Res., 2007, 35, 1441-1451, T. Dowler, et al., Nucleic Acids Res., 2006, 34, 1669-1675.
