Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number

Area of Science:

• Biophysics
• Molecular Biology
• Polymer Science

Background:

• Ribonucleic acids (RNA) are crucial for cellular functions.
• RNA's hydrodynamic behavior significantly influences its biological roles.
• Predicting RNA behavior is essential for understanding molecular mechanisms.

Purpose of the Study:

• To establish a predictive model for the hydrodynamic behavior of single-stranded RNA (ssRNA).
• To correlate RNA size with its hydrodynamic radius and diffusion coefficient.
• To validate empirical models with experimental data for conserved and unevolved RNAs.

Main Methods:

• Atom-level shell-modelling of high-resolution RNA structures.
• Calculation of hydrodynamic radius (R(H)) and diffusion coefficient (D) based on nucleotide count (N).
• Comparison of calculated parameters with experimental measurements in solution.

Main Results:

• Established empirical laws: D = 4.56 × 10⁻¹⁰ N⁻⁰.³⁹ m²/s and R(H) = 5.00 × 10⁻¹⁰ N⁰.³⁸ m.
• Calculated an average ratio of radius of gyration to hydrodynamic radius of 0.98 ± 0.08.
• Demonstrated high consistency between model predictions and experimental data for conserved ssRNA.

Conclusions:

• Empirical models accurately predict translational diffusion and molecular size of short ssRNA based on polymer size.
• The findings provide a valuable tool for analyzing RNA structure-function relationships.
• This approach is applicable to both evolutionarily conserved and unevolved RNA molecules.