Stacking interactions of ApA analogues with modified backbones

Area of Science:

• Biochemistry
• Oligonucleotide Chemistry
• Antisense Therapeutics

Background:

• Oligonucleotides with modified backbones are investigated as antisense agents for viral therapeutics.
• Understanding base stacking interactions is crucial for designing effective oligonucleotide-based drugs.

Purpose of the Study:

• To investigate the base stacking behavior of ApA analogues with modified backbones.
• To determine the impact of backbone modifications on oligonucleotide structure and stability.
• To evaluate the potential of these modified oligonucleotides as antisense agents.

Main Methods:

• Circular Dichroism (CD) spectroscopy was used to measure spectra as a function of temperature.
• Singular value decomposition (SVD) was applied to analyze spectral data.
• Taylor series decomposition was employed to quantify base stacking interactions.
• The van't Hoff equation was utilized to calculate thermodynamic parameters.

Main Results:

• Oligonucleotides with uncharged backbones (carbonyl for phosphate) and sugar or morpholino substitution showed no base stacking.
• Morpholino group substitution for sugar, with an uncharged phosphate, resulted in strong base stacking.
• Phosphorus-linked morpholino analogues exhibited stacking interactions comparable to or stronger than d(ApA).
• CD spectral analysis indicated two-state stacking behavior.

Conclusions:

• Backbone modification significantly influences base stacking in oligonucleotides.
• Morpholino-phosphorus linkages promote robust base stacking, essential for antisense activity.
• These findings provide insights into the structural requirements for effective antisense oligonucleotide design.