[Simulation of interactions in the co-planar nucleic acid base pairs using atom-atom potential functions]

Area of Science:

• Biophysics
• Computational Chemistry
• Molecular Biology

Context:

• Understanding nucleic acid base pairing is crucial for DNA/RNA structure and function.
• Previous models often simplified the complex interactions governing base positioning.

Purpose:

• To computationally determine stable configurations of nucleic acid base pairs.
• To investigate the role of hydrogen bonding and van der Waals forces in base pairing energetics.

Summary:

• Atom-atom potential functions were used to calculate interaction energies for base pairs in a plane.
• Identified 27 energy minima corresponding to co-planar pairs with multiple hydrogen bonds (N--H...O, N--H...N).
• Found additional minima involving C-H...O/N bonds, and results align with experimental and quantum mechanical data.

Impact:

• Provides a detailed energetic map of nucleic acid base interactions.
• Explains the observed positions of bases in various nucleic acid structures (crystals, polynucleotides, tRNA).
• Enhances understanding of molecular recognition and stability in genetic materials.