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Updated: Jun 6, 2026

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives
Published on: January 19, 2016
Replacing the 2'-oxygen with an exocyclic methylene group reverses the stabilization effects of α-L-LNA
Punit P Seth1, Charles R Allerson, Andres Berdeja
1Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc, 1891 Rutherford Road, Carlsbad, CA 92008, United States. pseth@isisph.com
Abstract:
The synthesis and hybridization properties of an α-L-LNA analog where the 2'-oxygen atom is replaced with an exocyclic methylene group is reported. Contrary to the β-D series where the exocyclic methylene group is extremely well tolerated, this group was very poorly tolerated in the α-L-series and lead to duplex destabilization. Modeling studies showed that the exocyclic methylene group results in a steric clash with the nucleobase 3' to the modified residue. Based on this structural model one can anticipate that replacing the 2'-oxygen atom of α-L-LNA with larger groups is likely to be detrimental to duplex stability. The model also provides insights into what type of 2',4'-bridges are most likely to be tolerated in α-L-LNA modified oligonucleotide duplexes.
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