UNA introduction


UNA (unlocked nucleic acid) is an acyclic analogue of RNA in which the bond between the C2’ and C3’ atoms has been cleaved.
UNA and LNA (locked nucleic acid) are both RNA analogues. However, whereas the additional methylene group linking the O2’ and C4’ atoms of LNA locks its furanose ring into a C3’-endo conformation, the cleaved ribose ring of UNA makes this molecule very flexible.
In the figure below, the chemical structure of UNA (“unlocked RNA”), RNA and LNA (“locked RNA”) monomers are shown.

 

 

 


In 1995 the research group of Jesper Wengel introduced the thymine UNA monomer as a modification in DNA oligonucleotides [P. Nielsen et al., Bioorg. Med. Chem., 1995, 3, 19-28]. Along with many other acyclic nucleotide modifications, UNA was shown to induce decreased binding affinity towards a complementary strand. UNA has subsequently been explored as a constituent in gap-mer antisense oligonucleotides, and compatibility with RNase H recognition and RNA cleavage has been reported [M. M. Mangos et al., J. Am. Chem. Soc., 2003, 125, 654-661].


UNA enables fine tuning of duplex thermodynamic stabilities

 

Their antipodal structural characteristics make UNA and LNA complementary with respect to effect on binding affinity towards a DNA or RNA target:

 

UNA:   Tm decrease of 5-10 0C per UNA monomer

LNA:   Tm increase of 3-10 0C per LNA monomer

 

We have recently published our first report on UNA hybridization [Jensen, T. B. et al., Nucleic Acid Res. Symp. Series, 2008, 133-133;  http://nass.oxfordjournals.org/cgi/reprint/52/1/133].


As the effect of UNA monomers is additive, a selected number of UNA monomers can be incorporated into DNA or RNA oligonucleotides to gradually decrease the thermodynamic stabilities of duplexes. Because of its acyclic ribose ring, UNA can also be applied to introduce local structural flexibility in a single or double stranded nucleic acid. It should however be noted that our mismatch studies have shown that UNA monomers form Watson-Crick hydrogen bonds with complementary bases.

 

UNA improves siRNA gene silencing

 

UNA monomers are very useful to improve siRNA mediated gene silencing in cell cultures or in vivo. In the EU-FP6 project RIGHT, we and our partners have found the following key characteristics of UNA modified siRNAs:

  • One or two UNA monomers in the 3’-overhangs stabilize towards degradation by nucleases
  • One UNA monomer positioned in the antisense strand leads to very potent gene silencing
  • One UNA monomer in position 6 or 7 in the antisense strand alleviates miRNA-type off-target effects
  • UNA monomers in the antisense strand can be combined with other modifications in the overhangs or in other positions in the two strands

RiboTask offers advice on the design of UNA oligonucleotides. Please contact info@ribotask.com

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