Glen Report 34-23: New Products — LA CPGs

Locked Nucleic Acid (LNA) is a modified ribonucleic acid containing a methylene bridge connecting the 2’-oxygen and 4’-carbon atoms. LNA is a very popular backbone modification.^{1, 2} The bicyclic structure introduces conformationally restrained units, locking the modified ribose into a C3’-endo conformation (Figure 1).³ LNA-modified oligos are increasingly prominent for hybridization assays and probes due to enhanced thermal stability towards complementary oligos, without compromising base pairing specificity.² Each LNA modification can increase the melting temperature of a duplex by 2-8 °C.⁴

^{Figure 1. Sugar pucker conformations}

The improved binding of LNA oligos have been crucial for the detection of difficult samples, such as microRNA (miRNA).⁵ DNA- or RNA-based technologies for miRNA analysis is complicated because the melting temperature is highly dependent on the GC content of the sequence. The T_m of a duplex can be designed by varying the LNA content, regardless of the presence of GC base pairs in a miRNA sequence. LNA probes can be used for detecting other challenging targets, including low-abundance, short, or highly similar sequences.⁶

Figure 2. ASO design

Third generation antisense oligonucleotides (ASOs) containing chemical modifications, such as phosphorodiamidate morpholino oligomers (PMO), have gained FDA approval as early as 2016. LNA modifications have also found their place in these types of therapeutics.^{7, 8} The enzymatic stability against RNase H1 of the constrained nucleotides provides more control when designing ASOs with LNAs. LNAs are commonly employed in ASOs as gapmers or mixers (Figure 2). Gapmers feature a block of DNA sandwiched between two terminal blocks made of a very stable backbone. LNA-DNA-LNA designs consist of at least four LNA nucleotides at the 5’- and 3’- ends.⁶ In recent years, several LNA-based ASOs have been in or are currently in clinical trials (Table 1).^7,8  

Table 1. Clinical trials on LNA-based ASOs

PS = phosphorothioate linkages

More research is coming out about the effects of using LNA-featured ASOs, especially when combined with other modifications such as phosphorothioate (PS) linkages. While gapmer ASOs offer enhanced nuclease resistance, they may come with the caveat of hepatotoxicity. It was very recently reported that gapmer ASO-mediated hepatotoxicity was reduced when combined with certain nucleobase modifications.9 This was particularly true for 5-hydroxy-dC (10-1063), 8-bromo-dG (10-1027), 8-amino-dG (10-1079), and 2-thio-dT (10-1036), modifications that are also available at Glen Research.

LNA Supports

Our locked analog, or LA, phosphoramidite products have been discussed in previous Glen Reports (Figure 3).^{1, 2} We often receive inquiries about LNA supports. Until now, a universal support was required to synthesize a 3’-LNA modified oligonucleotide. We are pleased to introduce LA CPGs (Figure 3). LA CPGs negate the need for Universal Supports, which typically require special cleavage conditions. As is the case for LA phosphoramidites, the pyrimidine bases are thymidine and 5-methylcytosine, rather than uracil and cytosine, respectively.

Figure 3. LA Products

These supports are available as 1000Å CPG. LA CPGs are cleaved with standard protocols. It is advisable to avoid the use of methylamine when deprotecting oligos containing Bz-5-Me-C-LA, since this can result in introduction of an N4-methyl modification. 

LNA oligonucleotides are water soluble, can be separated by gel electrophoresis and precipitated by ethanol. LA-containing oligonucleotides can be purified and analyzed using the same methods employed for standard DNA. LNA can be mixed with DNA and RNA, as well as other nucleic acid analogs, modifiers, and labels.

References

1. The Glen Report, 2003, 16.2, 5. 

2. The Glen Report, 2018, 30.2, 8-9.

3. M. Petersen, et al., J Mol Recognit, 2000, 13, 44-53.

4. D.A. Braasch; D.R. Corey, Chem Biol, 2001, 8, 1-7.

5. T. Ouyang; Z. Liu; Z. Han; Q. Ge, Anal Chem, 2019, 91, 3179-3186.

6. S. Mishra, et al., Nano Lett, 2021, 21, 9061-9068.

7. K. Dhuri, et al., J Clin Med, 2020, 9, 2004-2028.

8. A.M. Quemener; M.L. Centomo; S.L. Sax; R. Panella, Molecules, 2022, 27, 536-562.

9. T. Yoshida, et al., Nucleic Acids Res, 2022, 50, 7224-7234.

Product Information

Locked Analog Phosphoramidites and Supports