The protonated guanine-cytosine base pair

Area of Science:

• Computational chemistry
• Molecular biology
• Biophysics

Background:

• Protonated base pairs are relevant to DNA proton transfer and charge migration.
• Understanding protonation effects on DNA structure is crucial for molecular biology.

Purpose of the Study:

• To investigate the structural and energetic effects of protonating different sites of the guanine-cytosine (GC) base pair.
• To compare the impact of protonation versus hydrogenation on the GC base pair structure.
• To identify the preferred protonation site in the GC base pair.

Main Methods:

• Utilized the DZP++ B3LYP density functional method for theoretical calculations.
• Optimized structures of protonated GC base pairs, parent GC, and the neutral hydrogenated GC radical (GCH).
• Calculated adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs).

Main Results:

• Proton and hydrogen-atom additions significantly alter GC base pair structure, with protonation causing less perturbation than hydrogenation.
• Protonation strengthens interstrand hydrogen bonds and increases base dissociation energies.
• The N7 site of guanine was identified as the preferred site for GC base pair protonation.

Conclusions:

• Protonation of GC base pairs significantly influences their structural integrity and stability.
• The N7 site of guanine is the primary target for protonation in GC base pairs.
• These findings contribute to understanding DNA proton transfer and charge migration mechanisms.