Metal sensing by DNA

W Zhou, R Saran, J Liu - Chemical reviews, 2017 - ACS Publications
Metal ions are essential to many chemical, biological, and environmental processes. In the
past two decades, many DNA-based metal sensors have emerged. While the main …

Oxidative stress in bacteria and the central dogma of molecular biology

M Fasnacht, N Polacek - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
Ever since the “great oxidation event,” Earth's cellular life forms had to cope with the danger
of reactive oxygen species (ROS) affecting the integrity of biomolecules and hampering …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

[PDF][PDF] CheckMyMetal: a macromolecular metal-binding validation tool

H Zheng, DR Cooper, PJ Porebski… - … Section D: Structural …, 2017 - journals.iucr.org
Metals are essential in many biological processes, and metal ions are modeled in roughly
40% of the macromolecular structures in the Protein Data Bank (PDB). However, a …

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

DGJ Smethurst, N Shcherbik - Journal of Biological Chemistry, 2021 - ASBMB
Metal ions provide considerable functionality across biological systems, and their utilization
within biomolecules has adapted through changes in the chemical environment to maintain …

Characterizing metal-binding sites in proteins with X-ray crystallography

KB Handing, E Niedzialkowska, IG Shabalin… - Nature protocols, 2018 - nature.com
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical,
and diagnostic processes. Proper handling of metal-containing macromolecule samples for …

Pathway-controlled formation of mesostructured all-DNA colloids and superstructures

R Merindol, S Loescher, A Samanta… - Nature nanotechnology, 2018 - nature.com
DNA has traditionally been used for the programmable design of nanostructures by
exploiting its sequence-defined supramolecular recognition. However, control on larger …

Polarizable force field for RNA based on the classical drude oscillator

JA Lemkul, AD MacKerell Jr - Journal of computational …, 2018 - Wiley Online Library
RNA molecules are highly dynamic and capable of adopting a wide range of complex,
folded structures. The factors driving the folding and dynamics of these structures are …

On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules

S Muscat, G Martino, J Manigrasso… - Journal of Chemical …, 2024 - ACS Publications
RNA molecules play a vital role in biological processes within the cell, with significant
implications for science and medicine. Notably, the biological functions exerted by specific …

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

B Liu, DK Merriman, SH Choi, MA Schumacher… - Nature …, 2018 - nature.com
Abstract N 6-Methyladenosine (m6A) is an abundant post-transcriptional RNA modification
that influences multiple aspects of gene expression. In addition to recruiting proteins, m6A …