Publications related to Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Related publications (32)

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology

Sarah Emmert

Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

EPFL2024

Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features

Luciano Andres Abriata

Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discov ...

Royal Soc Chemistry2024

Green hydrogen production using Shewanella oneidensis MR-1 bioanode and cuprous oxide-based photocathode

Michele Morgante

In recent years, many efforts have been made to find alternative renewable energy sources that can ideally replace the use of fossil fuels in all aspects. One of the new emerging energy technologies is the bioelectrochemical system, of which two types are ...

EPFL2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

Chromosome organization shapes replisome dynamics in Caulobacter crescentus

Suliana Manley, Chen Zhang

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial specie ...

Nature Portfolio2024

Room-Temperature Quantum Optomechanics and Free-Electron Quantum Optics

Guanhao Huang

Quantum optics studies how photons interact with other forms of matter, the understanding of which was crucial for the development of quantum mechanics as a whole. Starting from the photoelectric effect, the quantum property of light has led to the develop ...

EPFL2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Realization of Organocerium-Based Fullerene Molecular Materials Showing Mott Insulator-Type Behavior

Pragati Pandey

Electron-rich organocerium complexes (C5Me4H)(3)Ce and [(C5Me5)(2)Ce(ortho-oxa)], with redox potentials E-1/2 = -0.82 V and E-1/2 = -0.86 V versus Fc/Fc(+), respectively, were reacted with fullerene (C-60) in different stoichiometries to obtain molecular m ...

Amer Chemical Soc2024

Telomere protection against oxidative stress

Thu Trang Nguyen

Telomeres are nucleoprotein structures at the ends of linear chromosomes, being essential for the maintenance of genomic integrity. Telomeres have a unique structure which distinguishes chromosome termini from DNA damage sites. Shelterin complexes are the ...

EPFL2023

Regulation and impact of TERRA R-loops at human telomeres

Rita Valador Fernandes

Telomeres are the nucleoprotein structures found at the ends of linear chromosomes. They ensure that the termini of chromosomes are not inappropriately recognized as sites of DNA damage, and are therefore crucial for genome stability. In spite of the heter ...

EPFL2023

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Sandrine Gerber, Mounir Driss Mensi, Perrine Agnes Edith Robin, Lucas Mayoraz, Alireza Kavand

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring

Jonathan Selz, Sebastian Maerkl

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

WILEY2023

Multielectron Redox Chemistry of Uranium by Accessing the plus II Oxidation State and Enabling Reduction to a U(I) Synthon

Rosario Scopelliti, Marinella Mazzanti, Ivica Zivkovic, Anne-Sophie Chauvin, Megan Renee Keener, Maxime Christian Gérard Tricoire

Thesynthesis of molecular uranium complexes in oxidation stateslower than +3 remains a challenge despite the interest for their multielectrontransfer reactivity and electronic structures. Herein, we report theone- and two-electron reduction of a U(III) com ...

2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Spatially Explicit Linkages Between Redox Potential Cycles and Soil Moisture Fluctuations

Andrea Rinaldo, Rizlan Bernier-Latmani, Paolo Benettin, Manon Frutschi, Mitra Asadollahi, Simiao Wang, Filippo Miele

Reduction-oxidation cycles measured through soil redox potential (Eh) are associated with dynamic soil microbial activity. Understanding changes in the composition of, and resource use by, soil microbial communities requires Eh predictability under shiftin ...

American Geophysical Union2023

Chemical Trend of Nonradiative Recombination in Cu(In,Ga)Se2 Alloys

Stefano Falletta

Nonradiative recombination in Cu(In,Ga)Se2 (CIGS) solar cells has long been attributed to the antisite defects MCu (M = In, Ga), but the underlying mechanism is still elusive. Using rigorous first-principles calculations, we demonstrate that the antisites ...

American Physical Society (APS)2023

Unit-cell-thick zeolitic imidazolate framework films for membrane application

Kumar Varoon Agrawal, Luis Francisco Villalobos Vazquez de la Parra, Heng-Yu Chi, Shaoxian Li, Qi Liu, Deepu Joseph Babu, Shuqing Song, Jian Hao

Zeolitic imidazolate frameworks (ZIFs) are a subset of metal-organic frameworks with more than 200 characterized crystalline and amorphous networks made of divalent transition metal centres (for example, Zn2+ and Co2+) linked by imidazolate linkers. ZIF th ...

NATURE PORTFOLIO2023