2'-F-Ac-C-CE Phosphoramidite

default
10-3415

5'-Dimethoxytrityl-N-acetyl-deoxyCytidine,2'-fluoro-3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Formula:
C41H49FN5O8P
M.W.:
789.84
F.W.:
307.18
CAS Number:
159414-99-0
Catalog: Make Selections to Reveal

Description

2'-Deoxy-2'-fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity of fluorine. Because of this sugar conformation, RNA duplexes (A-form) are generally more thermodynamically stable than DNA duplexes (B-form). As expected, the addition of 2'-F-RNA residues to oligodeoxynucleotides progressively increases the thermal stability of their duplexes with RNA. The stabilization is additive at approximately 2° per residue. This compares favorably with 2'-OMe-RNA at around 1.5° and RNA at 1.1° per residue. In the meantime, base pair specificity remains intact. 

2'-F-RNA phosphodiester linkages are not nuclease resistant, although the corresponding phosphorothioate linkages are highly resistant. Researchers usually design antisense oligonucleotides to form duplexes with RNA, which are then substrates for RNase H. Uniformly modified 2'-F-RNA/RNA duplexes are not substrates for RNase H. However, it is straightforward to prepare chimeric 2'-F-RNA/DNA phosphorothioate oligonucleotides which exhibit enhanced binding to the RNA target, are substrates for RNase H, and are highly nuclease resistant.

Details

Usage

  • Coupling: 3 minute coupling time recommended.
  • Deprotection: Ammonium Hydroxide for 17 hours at 55°C or 30% Ammonia Hydroxide/40% Methylamine 1:1 (AMA) for 2 hours at Room Temperature. (Note - heating in AMA will lead to some degradation of the 2'-Fluoro nucleotides.)
Specifications
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry
Stability 24 hours


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
10-3415-02 0.25 g .25grams 3.17 92.33 55.4 34.63 25.18 18.47 4.62
10-3415-05 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
10-3415-02 0.25 g .25grams 4.72 0.07 88 55 40 5.5
10-3415-05 0.5 g .5grams 9.45 0.07 182.6 114.13 83 11.41

References

REFERENCE(S)| 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.