Variable helix elongation as a tool to modulate RNA alignment and motional couplings

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Residual dipolar couplings (RDCs) are powerful tools for RNA structure and dynamics studies.
• Interactions between collective helix motions and overall molecular alignment complicate RDC analysis.
• Modulating molecular alignment independently of the ordering medium is challenging.

Purpose of the Study:

• To investigate if variable helix elongation can alter overall alignment and collective motion couplings in RNA.
• To provide guidelines for assessing and mitigating motional coupling effects in RDC studies.
• To explore new strategies for characterizing RNA structural dynamics.

Main Methods:

• Utilized a 27-nucleotide TAR RNA construct with varying helix elongation.
• Measured changes in overall alignment and residual dipolar couplings (RDCs).
• Performed PALES simulations using a three-state dynamic ensemble model.

Main Results:

• Helix elongation modulated both overall alignment and couplings to collective helix motions.
• Different elongation lengths shifted the RNA between motional coupling and decoupling limits.
• Simulation results rationalized the observed trends in alignment and dynamics.

Conclusions:

• Variable helix elongation offers a semi-predictable method to control RNA alignment and dynamics.
• This approach provides insights into motional couplings and their impact on RDC measurements.
• Helix elongation enables access to independent RDC datasets for enhanced structural characterization.