Conformational landscape of 2-aminopurine-substituted RNA oligonucleotides from machine-learning-driven enhanced...

Area of Science:

• Biophysics
• Computational Chemistry
• Molecular Biology

Background:

• Fluorescent base analogs, such as 2-aminopurine (2AP), are crucial tools for studying nucleic acid dynamics via fluorescence spectroscopy.
• Understanding base-stacking interactions and conformational dynamics is key to elucidating RNA function.

Purpose of the Study:

• To comprehensively explore the free-energy landscapes of RNA dinucleotides and trinucleotides with and without 2AP substitution.
• To investigate how 2AP substitution affects RNA stacking propensity and conformational populations.
• To correlate 2AP conformations with experimentally observed emissive and dark states.

Main Methods:

• Application of explainable machine-learning-derived surrogate-model collective variables.
• Enhanced-sampling molecular dynamics simulations.
• Analysis of free-energy landscapes for substituted and unsubstituted RNA oligomers.

Main Results:

• 2AP substitution does not significantly alter the intrinsic stacking propensity of RNA.
• 2AP substantially modulates the free-energy landscape, leading to a redistribution of populations among stacking modes.
• The fraction of stacked 2AP conformations correlates with experimentally observed "dark state" populations.

Conclusions:

• Base stacking in 2AP-substituted RNA quenches fluorescence and promotes dark state formation.
• This study establishes a link between specific structures in the free-energy landscape and observed 2AP states.
• Future studies will extend these findings to larger, physiologically relevant RNA systems.