Conformational Dynamics of 8-Oxoguanine Mispairing Reveal a Mechanism of Polymerase λ Misincorporation

Abstract

Experimental evidence has shown the stability of oxygen-stress-damaged guanine, known as 8-oxoguanine. This common oxygen-damaged nucleobase is often found in the presence of reactive oxygen species and can result in the mispairing between adenine and 8-oxoguanine in a Hoogsteen pair. We have computationally investigated the role of 8-oxoguanine to support experimental results and focus the investigation towards the polymerase structure, identifying how 8-oxoguanine interacts in the polymerase environment. Quantum mechanical investigations show the Hoogsteen pairing of adenine and 8-oxoguanine is the most energetically favourable state compared to a Watson-Crick state, supporting experimental evidence. Molecular Dynamical calculation of 8-oxoguanine located in B-DNA provide an average C1' backbone spacing of 1.1 nm compared to adenine-thymine spacing of 1.05 nm but remains within the error margin, however when in the polymerase environment, 8-oxoguanine and the canonical adenine - thymine spacing match at 1.11-1.12nm spacing while 8-oxoguanine is located on the template strand, but is disrupted by tyrosine 251 while situated on the triphosphate strand. We observe that 8-oxoguanine, when paired with adenine in polymerase λ, can mimic the adenine-thymine structure, as predicted in experimental results, and thus would be misincorporated, but is strongly dependent on its conformation.

Magnesium cofactor missing from active site of polymerase lambda structure. Result sections 4.2 and 4.3 are no longer valid as they are based on results missing important cofactors. Conclusion from these results can no longer be confirmed as it is based on results including section 4.2 and 4.3. Our apologises for the inconvenience