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Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair

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Related publications (35)

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Designing Complexes of f-elements Capable of Multielectron Transfer Reactivity

Fang-Che Hsueh

Over the past few decades, low oxidation state f-element molecular complexes, including those of lanthanide, uranium, and thorium, have demonstrated high reactivity towards small molecules such as N2 and CO2 due to their unique chemical properties. However ...

EPFL2025

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

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

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

Instabilities in Elastic and Magneto-Elastic Beams and Shells: from Shell Buckling to the Design of a Programmable Braille Reader

Arefeh Abbasi

In this thesis, we conduct a comprehensive investigation into structural instabilities of both elastic and magneto-elastic beams and shells, resulting in a creative proposal to design a programmable braille reader. Methodologically, we combine numerical si ...

EPFL2024

Positive Streamer Initiation in SF6/CO2 Based on Zener's Field Ionization

Guang-Yu Sun

In this study, experiments were performed to measure the inception and breakdown voltages of SF6/CO2 mixed gases with varying mixing ratios at two different pressures (1 and 2 bar). Using the preliminary data obtained from the experiments, a 3D particle mo ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023

Electrical spectroscopy of defect states and their hybridization in monolayer MoS2

Andras Kis, Oleg Yazyev, Ahmet Avsar, Zhenyu Wang, Yanfei Zhao, Mukesh Kumar Tripathi, Kristians Cernevics, Juan Francisco Gonzalez Marin, Cheol Yeon Cheon, Hyungoo Ji

Defects in solids are unavoidable and can create complex electronic states that can significantly influence the electrical and optical properties of semiconductors. With the rapid progress in the integration of 2D semiconductors in practical devices, it is ...

Nature Research2023

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

koopmans: An Open-Source Package for Accurately and Efficiently Predicting Spectral Properties with Koopmans Functionals

Nicola Marzari, Nicola Colonna, Edward Baxter Linscott, Ngoc Linh Nguyen, Giovanni Borghi, Riccardo De Gennaro

Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity conditio ...

Amer Chemical Soc2023

Nonlinear interactions of ion acoustic waves explored using fast imaging decompositions

Simon Pierre Henri Vincent

Fast camera imaging is used to study ion acoustic waves propagating azimuthally in a magnetized plasma column. The high-speed image sequences are analyzed using proper orthogonal decomposition and 2D Fourier transform, allowing to evaluate the assets and d ...

2023

Self-Interaction and Polarons in Density Functional Theory

Stefano Falletta

The electron self-interaction is a long-standing problem in density functional theory and is particularly critical in the description of polarons. Polarons are quasiparticles involving charge localization coupled with self-induced lattice distortions. Sinc ...

EPFL2023

Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes

Maartje Martina Cornelia Bastings, Cem Tekin, Vincenzo Caroprese, Diana Kornelia Morzy

Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electr ...

ROYAL SOC CHEMISTRY2023

Metal-Free Molecular Catalysts for the Oxygen Reduction Reaction: Electron Affinity as an Activity Descriptor

Ganna Gryn'ova, Juliette Veronique Schleicher

Heteroatom-doped polyaromatic hydrocarbons (or nanographenes) are promising molecular electrocatalysts for the oxygen reduction reaction (ORR). Here, we use density functional theory to investigate the first step of the ORR pathway (chemisorption) for a se ...

AMER CHEMICAL SOC2023

Hierarchy of quasisymmetries and degeneracies in the CoSi family of chiral crystal materials

Philip Johannes Walter Moll, Yi-Chiang Sun, Chunyu Guo

In materials, certain approximated symmetry operations can exist in a lower-order approximation of the effective model but are good enough to influence the physical responses of the system, and these approximated symmetries were recently dubbed "quasisymme ...

AMER PHYSICAL SOC2023

Machine-learning the electronic density of states: electronic properties without quantum mechanics

Chiheb Ben Mahmoud

The electronic density of states (DOS) quantifies the distribution of the energy levels that can be occupied by electrons in a quasiparticle picture and is central to modern electronic structure theory. It also underpins the computation and interpretation ...

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

Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds

Gordanna Pistoletti Blanchet, Aleksandra Radenovic, Georg Fantner, Sanjin Marion, Vytautas Navikas, Samuel Mendes Leitão, Barney Frederick Drake, Simon Finn Mayer, Helena Miljkovic

In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to ...

2023

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

Preomic profile of BxPC-3 cells after treatment with BRC4

Andrea Cavalli

BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the ...

ELSEVIER2023