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2' Fluoro RNA Modification

2' Fluoro RNA oligonucleotides contain a fluorine molecule at the 2' ribose position (instead of a 2'-hydroxyl group in an RNA monomer). The main benefit is increased binding affinity (Tm) and nuclease resistance. Fluoro RNA and standard RNA bases share similar properties which allow 2'-F RNA to form stable duplexes with RNA targets. Furthermore, the stability of 2' Fluro RNA-RNA duplexes is higher than normal RNA-RNA duplexes by about 1-2 degrees-C per each substitution. 
 
Replacement of 2'-hydroxyl group with 2'-fluoro has also shown to be more stable for chemical hydrolysis at high pH as compared with internucleotide linkages in unmodified RNA oligonucleotides. 
 
2' fluoro modified bases can be purified using standard DNA purification methods. However, yields may vary depending on the oligonucleotide design. 
 

Product Information

 

Product Name:
2' Fluoro RNA Modification

Alternate Name:
2' F RNA

Category:

Backbone Modified RNA

Modification Code:
[fA],[fC],[fU], [fG]

Structure:
Bio-Synthesis Inc. Oligo Structure

Purification:
HPLC

Delivery Format:
Lyophilized

Shipping Conditions:
Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.


References/Citations:

  1. Goringer, H.U.; Adler, Annette; Forster, Nicole; Homann, Matthias. Post-SELEX Chemical Optimization of a Trypanosome-Specific RNA Aptamer. Combinatorial Chemistry & High Throughput Screening (2008), 11: 16-23. 5.
  2. Allerson, C.R.; et al. Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. Journal of Medicinal Chemistry (2005), 48: 901-904. - 2'-Fluoro deoxyadenosine (2'-F-A)
  3. Kumudha A, Selvakumar S, Dilshad P, Vaidyanathan G, Thakur MS, Sarada R. Methylcobalamin – A form of vitamin B12 identified and characterised in Chlorella vulgaris. Food Chemistry, 170, 1 March 2015, 316-320
  4. Hernandez FJ, Stockdale KR, Huang L, Horswill AR, Behlke MA, McNamara JO. Degradation of Nuclease-Stabilized RNA Oligonucleotides in Mycoplasma-Contaminated Cell Culture Media. Nucleic Acid Ther. 2012 Jan 9. doi: 10.1089/nat.2011.0316.
  5. Shu D, Shu Y, Haque F, Abdelmawla S, Guo P. Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. (2011) Nature Nanotechnology, doi: 10.1038/nnano.2011.105. [Epub ahead of print]
  6. Manoharan M, et. al. Unique gene-silencing and structural properties of 2'-fluoro-modified siRNAs. Angew Chem Int Ed Engl. 2011 Mar 1;50(10):2284-8.
  7. Pallan PS, Greene EM, Jicman PA, Pandey RK, Manoharan M, Rozners E, Egli M. Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA. Nucleic Acids Res. 2011 Apr;39(8):3482-95.
  8. Blidner RA, Hammer RP, Lopez MJ, Robinson SO, Monroe WT. Fully 2'-deoxy-2'-fluoro substituted nucleic acids induce RNA interference in mammalian cell culture. Chem Biol Drug Des. 2007 Aug;70(2):113-22.
  9. Morrissey DV, et. al. Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nat Biotechnol. 2005 Aug;23(8):1002-7.
  10. Layzer JM, McCaffrey AP, Tanner AK, Huang Z, Kay MA, Sullenger BA. In vivo activity of nuclease-resistant siRNAs. RNA. 2004 May;10(5):766-71.
  11. Khati M, Schüman M, Ibrahim J, Sattentau Q, Gordon S, James W. Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2'F-RNA aptamers. J Virol. 2003 Dec;77(23):12692-8.
  12. Chiu YL, Rana TM. siRNA function in RNAi: a chemical modification analysis. RNA. 2003 Sep;9(9):1034-48.
  13. Yazbeck DR, Min KL, Damha MJ. Molecular requirements for degradation of a modified sense RNA strand by Escherichia coli ribonuclease H1. Nucleic Acids Res. 2002 Jul 15;30(14):3015-25.
  14. Sabahi A, Guidry J, Inamati GB, Manoharan M, Wittung-Stafshede P. Hybridization of 2'-ribose modified mixed-sequence oligonucleotides: thermodynamic and kinetic studies. Nucleic Acids Res. 2001 May 15;29(10):2163-70.
  15. Rhie A, Kirby L, Sayer N, Wellesley R, Disterer P, Sylvester I, Gill A, Hope J, James W, Tahiri-Alaoui A. Characterization of 2'-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. J Bi
  16. Kawasaki AM, et. al. Uniformly modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets. J Med Chem. 1993 Apr 2;36(7):831-41.
  17. Kubik MF, Bell C, Fitzwater T, Watson SR, Tasset DM. Isolation and characterization of 2'-fluoro-, 2'-amino-, and 2'-fluoro-/amino-modified RNA ligands to human IFN-gamma that inhibit receptor binding. J Immunol. 1997 Jul 1;159(1):259-67.
  18. Ruckman J, Green LS, Beeson J, Waugh S, Gillette WL, Henninger DD, Claesson-Welsh L, Janjić N. 2'-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). J Biol Chem. 1998 Aug 7;273(32):20556-67.
  19. Fell PL, Hudson AJ, Reynolds MA, Usman N, Akhtar S. Cellular uptake properties of a 2'-amino/2'-O-methyl-modified chimeric hammerhead ribozyme targeted to the epidermal growth factor receptor mRNA. Antisense Nucleic Acid Drug Dev. 1997 Aug;7(4):319-26.
  20. Pieken WA, Olsen DB, Benseler F, Aurup H, Eckstein F. Kinetic characterization of ribonuclease-resistant 2'-modified hammerhead ribozymes. Science. 1991 Jul 19;253(5017):314-7.
  21. Beigelman L, et. al. Chemical modification of hammerhead ribozymes. Catalytic activity and nuclease resistance. J Biol Chem. 1995 Oct 27;270(43):25702-8.

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