How DNA polymerases catalyse replication and repair with contrasting fidelity

WJ Wu, W Yang, MD Tsai - Nature Reviews Chemistry, 2017 - nature.com
DNA polymerases were named for their function of catalysing DNA replication, a process
that is necessary for growth and propagation of life. DNA involving Watson–Crick base …

Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology

I Geronimo, P Vidossich, E Donati… - Wiley Interdisciplinary …, 2021 - Wiley Online Library
DNA and RNA polymerases (Pols) are central to life, health, and biotechnology because
they allow the flow of genetic information in biological systems. Importantly, Pol function and …

A transient and flexible cation− π interaction promotes hydrolysis of nucleic acids in DNA and RNA nucleases

V Genna, M Marcia, M De Vivo - Journal of the American Chemical …, 2019 - ACS Publications
Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great
efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for …

Exploring the catalytic mechanism of Cas9 using information inferred from endonuclease VII

H Yoon, LN Zhao, A Warshel - ACS catalysis, 2018 - ACS Publications
Elucidating the nature of the gene editing mechanism of CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats) is an important task in view of the role of this …

Metal fluorides: Tools for structural and computational analysis of phosphoryl transfer enzymes

Y Jin, RW Molt, GM Blackburn - Phosphate Labeling and Sensing in …, 2017 - Springer
Abstract The phosphoryl group, PO 3–, is the dynamic structural unit in the biological
chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much …

Theoretical insights into the E1cB/E2 mechanistic dichotomy of elimination reactions

DE Ortega, R Ormazábal-Toledo… - Organic & …, 2019 - pubs.rsc.org
E1cB and E2 eliminations have been described as competing mechanisms that can even
share a common pathway when the E1cB/E2 borderline mechanism operates. A suitable …

Capturing a mammalian DNA polymerase extending from an oxidized nucleotide

AM Whitaker, MR Smith, MA Schaich… - Nucleic acids …, 2017 - academic.oup.com
Abstract The oxidized nucleotide, 8-oxo-7, 8-dihydro-2΄-deoxyguanosine (8-oxoG), is one of
the most abundant DNA lesions. 8-oxoG plays a major role in tumorigenesis and human …

Meisenheimer complexes as hidden intermediates in the aza-S N Ar mechanism

R Ormazábal-Toledo, S Richter… - Organic & …, 2020 - pubs.rsc.org
In this work we report a computational study about the aza-SNAr mechanism in fluorine-and
chlorine-containing azines with the aim to unravel the physical factors that determine the …

Exploring the identity of the general base for a DNA polymerase catalyzed reaction using QM/MM: the case study of human translesion synthesis polymerase η

KA Wilson, PA Fernandes, MJ Ramos… - ACS Catalysis, 2019 - ACS Publications
DNA replication is a fundamental process for life. Despite previous experimental and
computational studies of the reaction pathway catalyzed by a variety of DNA polymerases …

Unveiling the Mechanism of Deprotonation and Proton Transfer of DNA Polymerase Catalysis via Single‐Molecule Conductance

L Zhao, Y Xu, Z Yang, W Liu, S Zhong, J Bai… - Advanced …, 2025 - Wiley Online Library
DNA polymerases (Pols) play important roles in the transmission of genetic information.
Although the function and (de) regulation of Pols are linked to many human diseases, the …