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Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations.

Mallikarjunachari V N Uppuladinne1, Uddhavesh B Sonavane1, Ramesh Ch Deka2

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Antisense therapies utilize modified nucleic acids like LNA and MOE for enhanced stability and binding. Molecular dynamics simulations reveal LNA

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2′-O-methoxyehtyl RNAMD simulationsantisense oligonucleotideschemically modified nucleic acidsfree-energygapmer

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Antisense technology is rapidly advancing with increasing clinical trials.
  • Phosphorothioate (PS) modification enhances nuclease resistance.
  • 2'-4' conformationally restricted nucleosides (LNA, MOE) offer improved binding affinity and toxicity profiles.

Purpose of the Study:

  • To investigate the structural dynamics, stability, and solvation properties of various antisense gapmer/target-RNA duplexes using molecular dynamics (MD) simulations.
  • To compare the effects of different nucleoside modifications (LNA, MOE, PS-DNA) on duplex stability and binding affinity.
  • To correlate structural properties with potential therapeutic efficacy and toxicity.

Main Methods:

  • Classical molecular dynamics (MD) simulations.
  • Analysis of six different antisense gapmer/target-RNA oligomer duplexes.
  • Calculation of helical parameters, free energy, and solvent accessible surface area (SASA).

Main Results:

  • LNA and MOE nucleotides exhibit A-form helix structures, while PS-DNA resembles a B-form helix.
  • Free energy calculations indicate stronger RNA binding for LNA-containing oligomers compared to other modifications.
  • MOE modifications showed lower binding affinity but higher SASA, potentially influencing toxicity.

Conclusions:

  • LNA modifications provide superior binding affinity to target RNA, aligning with experimental findings.
  • MOE modifications, despite lower binding affinity, may contribute to favorable toxicity profiles, as seen in Mipomersen.
  • MD simulations provide valuable insights into the structure-function relationships of modified antisense oligonucleotides.