Dynamical transition and heterogeneous hydration dynamics in RNA.

Area of Science:

• Biophysics
• Structural Biology
• Computational Chemistry

Background:

• Enhanced dynamical fluctuations of RNAs are critical for cellular signal response.
• Water molecules strongly interact with RNA, influencing its dynamics.

Purpose of the Study:

• To investigate the dynamics of water molecules interacting with purine and preQ1 sensing riboswitch aptamers.
• To understand how RNA structure influences local water dynamics and hydration.
• To explore the relationship between hydration dynamics and RNA functional activities.

Main Methods:

• Atomically detailed molecular dynamics simulations at various temperatures.
• Analysis of hydrogen bond lifetimes, relaxation times, and mean-square fluctuations.
• Investigated purine and preQ1 sensing riboswitch aptamers.

Main Results:

• Water dynamics near RNA are structure-dependent and exhibit slow, heterogeneous relaxation times, deviating from bulk water.
• Surface-bound water hydrogen bonds show significantly longer lifetimes than bulk water.
• Both RNAs exhibit a dynamic transition around 200 K, correlated with hydration dynamics.

Conclusions:

• Complex interplay between water dynamics and RNA local environment dictates RNA functional activities.
• Slow hydration dynamics and heterogeneous water motion are key features of RNA-water interactions.
• A universal dynamic transition in RNA is linked to hydration dynamics, suggesting conserved mechanisms.