Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications

Area of Science:

• Biochemistry
• Computational Biology
• Pharmacology

Background:

• Antisense oligonucleotides (ASOs) are engineered nucleic acids with therapeutic potential for genetic diseases.
• Chemical modifications, such as phosphorothioate (PS) backbones, enhance ASO stability and binding affinity.
• Accurate molecular dynamics (MD) simulations require reliable force field parameters for modified nucleic acids.

Purpose of the Study:

• To develop and validate force field parameters for simulating ASOs with phosphorothioate (PS) backbone modifications.
• To investigate the effects of PS modifications on the conformational dynamics of DNA, RNA, and DNA/RNA hybrid duplexes.
• To understand how PS modifications influence ASO target recognition and protein interactions.

Main Methods:

• Development of novel force field parameters for PS-modified nucleic acids.
• Extensive all-atom molecular dynamics (MD) simulations of B-DNA, RNA, and DNA/RNA hybrid duplexes with single PS substitutions.
• Validation of simulation results against experimentally derived structural data.

Main Results:

• Single PS substitutions had minimal impact on ordered DNA/RNA duplex structures.
• Substantial effects of phosphorothioation were observed in single-stranded RNA and B-DNA, consistent with experimental data.
• PS modifications induced shifts between high and low twist states in NAs, potentially affecting target binding and protein interactions.
• Conformational sampling was significantly altered in PS-modified ssRNA, suggesting sequence-dependent effects on duplex formation.

Conclusions:

• The developed force field parameters enable accurate MD simulations of PS-modified ASOs.
• Phosphorothioation significantly impacts the conformational dynamics of certain nucleic acid structures, particularly single-stranded forms.
• These findings provide crucial insights into the structure-function relationships of therapeutic ASOs, aiding in drug design and development.