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  UNA Oligonucleotides: A Flexible RNA Mimic

TriLink is proud to offer unlocked nucleic acid (UNA) oligonucleotides, flexible RNA mimics that enable modulation of affinity and specificity. UNA is an acyclic ­RNA analogue also known as 2’,3’-seco-RNA, where the C2’-C3’ bond is absent, making the molecule very flexible.

This gives UNA the property of decreased binding affinity towards a complementary strand. A 5-10°C decrease in melting temperature (Tm) is seen per UNA insertion with additive effect, allowing a gradual decrease in the thermostability by introduction into DNA or RNA oligonucleotides. UNA modifications can be strategically placed to induce either a lack of mismatch discrimination or an increase in mismatch discrimination.(1)UNA

Due to these unique properties, UNA monomer substitution in an oligonucleotide permits modulation of the thermodynamic stability of various nucleic acid structures such as RNA:DNA duplexes, quadruplexes, aptamers and i-motifs. UNA has demonstrated utility in antisense oligonucleotide therapeutics, including single strand and gapmer oligonucleotides due to compatibility with RNase H activity.

 

Nuclease Resistance

One or two modifications near the 3’ end of the oligonucleotide increases stability to 3’ exonuclease degradation.(2) However, UNA is not as nuclease resistant as phosphorothioates or methylphosphonates.

 

Melting Temperature

Duplexes: The effect of UNA on Tm is highly dependent upon construct, sugar type and location. However, in general UNA reduces Tm by 5-10°C per replacement. Caution: Too many UNA modifications in an oligonucleotide can impede duplex hybridization. In general, phosphorothioates slightly decrease the Tm of an RNA duplex, methylphosphonates decrease Tm more and UNA will have the largest effect. To further explore this property of UNA, a list of references can be found here or submit your inquiry to Ask An Expert.
ΔPS ≈ 1-2°C/link; ΔMP ≈ 2-3°C/link; ΔUNA ≈ 5-10°C/link

Aptamers: A well placed UNA modification can increase or decrease the Hoogsteen base pairing effect. This is best demonstrated in aptamers, where a UNA insertion can inhibit or assist G-quadruplex formation based on location. Agarwal, T. et. al. explored this phenomenon in their publication Unlocking G-quadruplex: Effect of unlocked nucleic acid on G-quadruplex stability.(3)

 

Thermostability

UNA modified duplexes are energetically more unfavorable to duplex formation compared to unmodified as demonstrated by Wengel et. al., in their publication UNA (unlocked nucleic acid): a flexible RNA mimic that allows engineering of nucleic acid duplex stability.(4) The same result is seen with both RNA and DNA duplexes.

 

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