2'-F-Ac-C-ANA-CE Phosphoramidite

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10-3815

5'-Dimethoxytrityl-N4-acetyl-2'-deoxy-2'-fluoroarabinocytidine, 3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C41H49FN5O8P
M.W.:
789.83
F.W.:
307.17
Catalog Number: Select Pack Size and Format to Reveal

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
10-3815-02 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

Expedite

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

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.