Liquid crystal ordering of nucleic acids

Area of Science:

• Biophysics
• Materials Science
• Computational Chemistry

Background:

• Liquid crystal (LC) ordering is typically observed in rod-like molecules with high aspect ratios.
• Recent experiments show LC ordering in short nucleic acids (NAs) that lack significant shape anisotropy.
• End-to-end adhesion and stacking mechanisms are proposed for NA LC ordering.

Purpose of the Study:

• To explicitly verify end-to-end stacking of double-stranded RNA (dsRNA) using all-atom molecular dynamics (MD) simulations.
• To demonstrate and quantify liquid crystal (LC) ordering in dsRNA systems at the microscopic level.
• To investigate the inter-NA interaction potential and ordering behavior compared to double-stranded DNA (dsDNA).

Main Methods:

• All-atom molecular dynamics (MD) simulations to observe dsRNA stacking.
• Umbrella sampling (US) calculations to determine the potential of mean force (PMF) between dsRNAs.
• Analysis of MD simulations under varying initial configurations and physiological conditions.

Main Results:

• Explicit verification of end-to-end stacking in dsRNA molecules.
• Demonstration of liquid crystal (LC) ordering in dsRNA systems.
• PMF profiles indicate anisotropic inter-NA interactions, with preferred end-to-end stacking over sideways repulsion.
• Formation of supra-molecular columns and stable nematic ordering at high NA volume fractions.
• Ordering behavior remains consistent across different initial configurations and external conditions.

Conclusions:

• Double-stranded RNA (dsRNA) exhibits end-to-end stacking and liquid crystal (LC) ordering, consistent with proposed mechanisms.
• The observed anisotropic interactions and supra-molecular column formation are key to LC ordering in dsRNA.
• MD simulations provide a robust method for quantifying NA interactions and ordering phenomena.