Why nature really chose phosphate

SCL Kamerlin, PK Sharma, RB Prasad… - Quarterly reviews of …, 2013 - cambridge.org
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and
maintaining the integrity of the genetic material. On the surface, it would appear to be a …

Base excision repair and cancer

SS Wallace, DL Murphy, JB Sweasy - Cancer letters, 2012 - Elsevier
Base excision repair is the system used from bacteria to man to remove the tens of
thousands of endogenous DNA damages produced daily in each human cell. Base excision …

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

BD Freudenthal, WA Beard, L Perera, DD Shock, T Kim… - Nature, 2015 - nature.com
Oxidative stress promotes genomic instability and human diseases. A common oxidized
nucleoside is 8-oxo-7, 8-dihydro-2′-deoxyguanosine, which is found both in DNA (8-oxo …

Nucleic acid polymerases use a general acid for nucleotidyl transfer

C Castro, ED Smidansky, JJ Arnold… - Nature structural & …, 2009 - nature.com
Nucleic acid polymerases catalyze the formation of DNA or RNA from nucleoside-
triphosphate precursors. Amino acid residues in the active site of polymerases are thought to …

Structure and mechanism of DNA polymerase β

WA Beard, SH Wilson - Biochemistry, 2014 - ACS Publications
DNA polymerase (pol) β is a small eukaryotic DNA polymerase composed of two domains.
Each domain contributes an enzymatic activity (DNA synthesis and deoxyribose phosphate …

DNA polymerase family X: function, structure, and cellular roles

J Yamtich, JB Sweasy - Biochimica et Biophysica Acta (BBA)-Proteins and …, 2010 - Elsevier
The X family of DNA polymerases in eukaryotic cells consists of terminal transferase, and
DNA polymerases β, λ, and μ. These enzymes have similar structural portraits, yet different …

The empirical valence bond model: theory and applications

SCL Kamerlin, A Warshel - Wiley Interdisciplinary Reviews …, 2011 - Wiley Online Library
Recent years have seen an explosion in computer power, allowing for the examination of
ever more challenging problems. For instance, a recent simulation study, which was the first …

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

J Kottur, DT Nair - Nucleic Acids Research, 2018 - academic.oup.com
DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the
genome in all living organisms. dPols catalyze the formation of a phosphodiester bond …

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 …

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

SCL Kamerlin, A Warshel - Faraday discussions, 2010 - pubs.rsc.org
Recent years have seen dramatic improvements in computer power, allowing ever more
challenging problems to be approached. In light of this, it is imperative to have a quantitative …