"False" thymine-1H-Enol guanine base pair. low misinsertion rate by DNA polymerase explained by computational...

Area of Science:

• Molecular Biology
• Biochemistry
• Computational Chemistry

Background:

• Accurate DNA replication is crucial for genetic stability.
• Base pairing fidelity during nucleotide insertion is a key determinant of replication accuracy.
• Understanding the energetics of correct and incorrect base pairs is essential for predicting DNA synthesis errors.

Purpose of the Study:

• To investigate the role of specific base pairs, including a novel false pair (thymine-1H-enol guanine), in controlling DNA nucleotide insertion.
• To quantify the thermodynamic contributions (Gibbs free energy) to base pairing in aqueous solution.
• To estimate the error probability of nucleotide insertion based on calculated base pairing energies.

Main Methods:

• Utilized the semi-empiric MNDO/PM3 method to calculate base pairing energies in a vacuum.
• Employed the Boundary Element Method (BEM) to account for hydration effects on base pairing energetics.
• Calculated changes in Gibbs free energy (DeltaDeltaG) for correct (TA, GC) and false (thymine-1H-enol guanine) base pairs.

Main Results:

• Calculated DeltaDeltaG values indicate similar insertion rates for correctly formed TA and GC base pairs.
• The thymine-1H-enol guanine false base pair was identified as a significant contributor to replication errors.
• An error probability of 10^-3 to 10^-4 for false nucleotide insertion was estimated, primarily driven by the TGenol pair.

Conclusions:

• The study provides thermodynamic insights into the fidelity of DNA base pairing during replication.
• The thymine-1H-enol guanine base pair represents a critical misincorporation event that can lead to DNA sequence errors.
• Michaelis-Menten kinetics at low substrate concentrations, modulated by base pairing stability, govern nucleotide insertion accuracy.