The main applications of this modification are ribozyme development - to increase Tm, aptamer selection, and nuclease resistance. A substitution of 2’-fluoro for 2’-hydroxyl group in a RNA monomer does not substantially change the conformation of sugar ring puckering and other structural parameters thus making 2’-deoxy-2’-fluoro RNA oligonucleotide analogs (FRNA) a virtual mimic of natural RNAs. FRNA and RNA have many similar physical properties which allow FRNAs to form stable duplexes with RNA targets. The stability of FRNA-RNA duplexes is even higher than that for normal RNA-RNA duplexes (about 1-2oC per each substitution ). With DNA targets there is a moderate increase of Tm for DNA-FRNA duplexes (up to 1oC per substitution) compared to normal DNA-DNA duplexes. Oligonucleotides containing 2’ fluoros have been reported to increase DNA-DNA Tm by 1.3°C per insertion.
The absence of the 2’-hydroxyl group makes the internucleotide linkages in oligonucleotides with 2’-deoxy-2’-fluoro much more stable to a chemical hydrolysis at ahigh pH compared to internucleotide linkages in unmodified RNA oligonucleotides. The increased chemical stability of 2’-deoxy-2’-fluoro RNA oligonucleotide analogs is accompanied by high resistance of 2’-deoxy-2’-fluoro linkages to ribonucleases and, consequently, leads to a longer survival time of FRNAs in biological environment (cell cultures, plasma, animals, etc.).
The biological activity of siRNAs constructed from 2’-deoxy-2’-fluoro units in cell culture systems and in vivo is similar or higher compared to activity of unmodified RNAs. Notably, siRNAs containing 2’-deoxy-2’-fluoro units have lower level of activation of immune response compared to unmodified siRNAs. However, duplexes of FRNA and RNA do not support RNAse H activity and therefore the use of FRNA oligonucleotides is questionable for antisense applications.
In addition, 2’-deoxy-2’-fluoro RNA analogs have been used in the construction and studies of ribozymes and oligonucleotide aptamers with enhanced affinity.