Ribose Sugar Alters Conformational Sampling of G⋅T Mismatched Duplex DNA.

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• DNA polymerases can introduce Guanine-Thymine (dG⋅dT) mismatches.
• Ribonucleotide incorporation, particularly rG⋅dT, is a frequent error that challenges DNA repair fidelity.
• The rG⋅dT mismatch is notably stable, prompting investigation into its structural and dynamic effects.

Purpose of the Study:

• To investigate the structural and dynamic consequences of a single rG⋅dT mismatch in a DNA duplex.
• To compare the effects of rG⋅dT with the canonical dG⋅dT mismatch and an rA-dT mismatch.
• To elucidate the impact of ribose incorporation on DNA fidelity and repair recognition.

Main Methods:

• Solution-state Nuclear Magnetic Resonance (NMR) spectroscopy.
• Partial anisotropic measurements.
• Molecular dynamics (MD) simulations.
• Dodecanucleotide DNA duplex model system.

Main Results:

• The rG⋅dT mismatch exhibits increased flexibility in both base-pairing and sugar dynamics compared to the dG⋅dT mismatch.
• These perturbations are more pronounced in rG⋅dT than in a ribose-incorporated adenine-thymine (rA-dT) pair.
• Structural differences between rG⋅dT and dG⋅dT offer insights into repair enzyme recognition.

Conclusions:

• Ribose incorporation significantly alters DNA duplex dynamics and base-pair stability.
• The enhanced flexibility of rG⋅dT may influence the efficiency and mechanisms of DNA repair pathways, including ribonucleotide excision repair (RER) and mismatch repair (MMR).
• Understanding these structural consequences is crucial for comprehending genome integrity maintenance.