Position-Dependent Stabilization of DNA/RNA Duplexes by Site-Specific Incorporation of LNA Nucleosides

Owing to their enhanced functional properties, 2 ^',4 ^'-bridged nucleic acids/locked nucleic acids (2 ^',4 ^'-BNAs/LNAs) are considered promising candidates for antisense oligonucleotide therapeutics. The spatial arrangement of LNA residues within the oligonucleotide sequence is a key determinant of binding affinity to the target RNA. In this study, a series of antisense oligonucleotides containing LNA at different positions was synthesized, and their binding affinities toward the target RNA were systematically evaluated. Oligonucleotides with LNA modifications at the terminal regions exhibited approximately 100-fold lower affinity than those modified near the central region. These results offer valuable insights for the rational design of LNA-based antisense oligonucleotides.