Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity

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dc.citation.articleNumber102938
dc.citation.issueNumber3
dc.citation.journalTitleJournal of Biological Chemistry
dc.citation.volumeNumber299
dc.contributor.authorChang, Caleb
dc.contributor.authorLee Luo, Christie
dc.contributor.authorEleraky, Sarah
dc.contributor.authorLin, Aaron
dc.contributor.authorZhou, Grace
dc.contributor.authorGao, Yang
dc.date.accessioned2023-03-10T19:04:10Z
dc.date.available2023-03-10T19:04:10Z
dc.date.issued2023
dc.description.abstractDNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2′-endo to C3′-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.
dc.identifier.citationChang, Caleb, Lee Luo, Christie, Eleraky, Sarah, et al.. "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity." <i>Journal of Biological Chemistry,</i> 299, no. 3 (2023) Elsevier: https://doi.org/10.1016/j.jbc.2023.102938.
dc.identifier.digitalPIIS0021925823000704
dc.identifier.doihttps://doi.org/10.1016/j.jbc.2023.102938
dc.identifier.urihttps://hdl.handle.net/1911/114494
dc.language.isoeng
dc.publisherElsevier
dc.rightsThis is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/).
dc.titlePrimer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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