Towards Zwitterionic Oligonucleotides with Improved Properties: the NAA/LNA‐Gapmer Approach

Abstract

Oligonucleotides (ON) are promising therapeutic candidates, for instance by blocking endogenous mRNA (antisense mechanism). However, ON usually require structural modifications of the native nucleic acid backbone to ensure satisfying pharmacokinetic properties. One such strategy to design novel antisense oligonucleotides is to replace native phosphate diester units by positively charged artificial linkages, thus leading to (partially) zwitterionic backbone structures. Herein, we report a "gapmer" architecture comprised of one zwitterionic central segment ("gap") containing nucleosyl amino acid (NAA) modifications and two outer segments of locked nucleic acid (LNA). This NAA/LNA-gapmer approach furnished a partially zwitterionic ON with optimised properties: i) the formation of stable ON-RNA duplexes with base-pairing fidelity and superior target selectivity at 37°C; and ii) excellent stability in complex biological media. Overall, the NAA/LNA-gapmer approach is thus established as a strategy to design partially zwitterionic ON for the future development of novel antisense agents.

Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design

“…Its base pairing specificity and mismatch sensitivity make it attractive for use in many applications, such as polymerase chain reaction (PCR) detection and diagnosis, − high binding diagnostic probes, − stability improvement and hybridization efficiency in loop-mediated isothermal amplification (LAMP) detection, improvement of targeting, specificity and stability in antisense oligonucleotides (ASOs), − aptamers, − and siRNA approaches. , LNA is also used in DNAzymes and LNAzymes to improve targeting and cleavage efficiency, − molecular beacons, and as enhancers to RNA in situ hybridization , and as direct antagonist in miRNA silencing. − …”