2'-F-U-ANA-CE Phosphoramidite

5'-Dimethoxytrityl-2'-deoxy-2'-fluoroarabinouridine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C39H46FN4O8P
M.W.:
748.79
F.W.:
308.16
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

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.

Details

Usage

  • Coupling: 6 minute coupling time recommended.
  • Deprotection: No changes needed from standard method recommended by synthesizer manufacturer
Specifications
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8C, dry
Stability 1-2 days

Intellectual Property

2'-F-ANA is covered by intellectual property. Key patents covering siRNA and antisense applications are as follows: WO/2009/146556 (siRNA); WO 03064441 and WO 0220773 (antisense).


Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-3830-02 0.25 g .25grams 3.34 98 58.8 36.75 26.73 19.6 4.9
10-3830-05 0.5 g .5grams 6.68 209.33 125.6 78.5 57.09 41.87 10.47

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-3830-02 0.25 g .25grams 4.98 0.07 93.2 58.25 42.36 5.83
10-3830-05 0.5 g .5grams 9.97 0.07 193 120.63 87.73 12.06

References

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.