Translesion and repair DNA polymerases: diverse structure and mechanism

W Yang, Y Gao - Annual review of biochemistry, 2018 - annualreviews.org
The number of DNA polymerases identified in each organism has mushroomed in the past
two decades. Most newly found DNA polymerases specialize in translesion synthesis and …

Eukaryotic base excision repair: new approaches shine light on mechanism

WA Beard, JK Horton, R Prasad… - Annual review of …, 2019 - annualreviews.org
Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA
structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair …

Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates

B Liu, X Dong, C Zheng, D Keener, Z Chen… - Nature …, 2024 - nature.com
Reverse transcriptases, used in prime editing systems, exhibit lower fidelity, processivity and
dNTP affinity than many DNA-dependent DNA polymerases. We report that a DNA …

An open quantum systems approach to proton tunnelling in DNA

L Slocombe, M Sacchi, J Al-Khalili - Communications Physics, 2022 - nature.com
One of the most important topics in molecular biology is the genetic stability of DNA. One
threat to this stability is proton transfer along the hydrogen bonds of DNA that could lead to …

Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs

L Slocombe, JS Al-Khalili, M Sacchi - Physical Chemistry Chemical …, 2021 - pubs.rsc.org
Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but
biologically relevant point mutations that can further lead to gene mutation and, potentially …

Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM

SJ Amann, D Keihsler, T Bodrug, NG Brown… - Structure, 2023 - cell.com
Molecular machines, such as polymerases, ribosomes, or proteasomes, fulfill complex tasks
requiring the thermal energy of their environment. They achieve this by restricting random …

Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines

T Kubař, M Elstner, Q Cui - Annual review of biophysics, 2023 - annualreviews.org
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …

Two-metal-ion catalysis: Inhibition of DNA polymerase activity by a third divalent metal ion

J Wang, WH Konigsberg - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
Almost all DNA polymerases (pols) exhibit bell-shaped activity curves as a function of both
pH and Mg2+ concentration. The pol activity is reduced when the pH deviates from the …

Terminal deoxynucleotidyl transferase in the synthesis and modification of nucleic acids

I Sarac, M Hollenstein - ChemBioChem, 2019 - Wiley Online Library
The terminal deoxynucleotidyl transferase (TdT) belongs to the X family of DNA
polymerases. This unusual polymerase catalyzes the template‐independent addition of …

Evolution of a general RNA-cleaving FANA enzyme

Y Wang, AK Ngor, A Nikoomanzar… - Nature Communications, 2018 - nature.com
The isolation of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that
catalysis is not limited to natural biopolymers, but it remains unknown whether such systems …