Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

• DOI: 10.1016/j.omtn.2023.02.007
• Publication Date: 2023-02-14T21:57:34Z
• Authors: Farkhad Maksudov; Evgenii Kliuchnikov; Daniel Pierson; M.L. Ujwal; Kenneth A. Marx; Arani Chanda; Valeri Barsegov
• Keywords: Morpholino; Folding (DSP implementation)

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to lack of information about their structures. While PMOs have been approved by US Food and Drug Administration treatment Duchenne muscular dystrophy, no structural on these unique, charge-neutral, stable molecules available. We performed circular dichroism solution viscosity measurements combined with molecular dynamics simulations machine learning resolve structures 22-mer, 25-mer, 30-mer length PMOs. The PMO conformational are defined competition between non-polar nucleobases uncharged groups shielding from solvent exposure. form non-canonical, partially helical, folded a small 1.4- 1.7-nm radius gyration, low count three six base pairs nine stacks, characterized −34 −51 kcal/mol free energy, −57 −103 enthalpy, −23 −53 entropy folding. 4.5- 6.2-cm3/g intrinsic Huggins constant 4.5–9.9 indicative extended aggregating systems. results obtained highlight importance ensemble view structures, thermodynamic stability non-canonical concentration-dependent properties. These principles paradigm understand structure-properties-function relationship advance design new RNA-mimic-based drugs.