Molecular dynamics study of the base pair opening process in the self-complementary octanucleotide d(CTGATCAG)

Area of Science:

• Computational Biology
• Biophysics
• Molecular Modeling

Background:

• Understanding DNA base dynamics is crucial for molecular recognition and function.
• Oligonucleotide behavior is influenced by hydration and ionic environment.

Purpose of the Study:

• To analyze the base opening process in a double-stranded oligonucleotide using Molecular Dynamics.
• To investigate the rotational motion of Thymine 5 about the helix axis.

Main Methods:

• A 200 picosecond Molecular Dynamics simulation of d(CTGATCAG) with explicit water and Na+ ions.
• Analysis of autocorrelation functions and mean square displacements to study base rotational motion.

Main Results:

• The opening of Thymine 5 demonstrates Brownian character.
• A rotational diffusion coefficient of 4.7 rad²s⁻¹ was determined.
• The DNA torsional constant was estimated at 0.5 x 10⁻¹⁸ J.rad⁻², with an RMS angular displacement of 8.3 degrees.

Conclusions:

• Simulated base rotational motions are consistent with experimental data from fluorescence polarization.
• The study validates the use of Molecular Dynamics for analyzing DNA base dynamics at short timescales.