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Concept

Base pair

Related publications (30)

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

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

Secondary structure of the human mitochondrial genome affects formation of deletions

Jacques Fellay, Konstantin Popadin

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

BMC2023

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Francesco Aquilante

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) al ...

Amer Chemical Soc2023

Electronic and structural dynamics in DNA single strands

Benjamin Bauer

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA ...

EPFL2021

Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs

Shaoline Sheppard

Homoeologs are pairs of genes or chromosomes in the same species that originated by speciation and were brought back together in the same genome by allopolyploidization. Bioinformatic methods for accurate homoeology inference are crucial for studying the e ...

OXFORD UNIV PRESS2021

Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution

Maartje Martina Cornelia Bastings, Alice Comberlato

DNA-based nanostructures are actively gaining interest as tools for biomedical and therapeutic applications following the recent development of protective coating strategies prolonging structural integrity in physiological conditions. For tailored biologic ...

AMER CHEMICAL SOC2021

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Structural transitions and mechanochemical coupling in the nucleoprotein filament explain homology selectivity and Rad51 protein cooperativity in cellular DNA repair

Daniel Migliozzi

The nucleoprotein filament (NPF) is the fundamental element of homologous recombination (HR), a major mechanism for the repair of double-strand DNA breaks in the cell. The NPF is made of the damaged DNA strand surrounded by recombinase proteins, and its se ...

AMER PHYSICAL SOC2020

Shear Stress-Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates

Esther Amstad, Antoine Claude Jean Vian

Some marine plankton called dinoflagellates emit light in response to the movement of surrounding water, resulting in a phenomenon called milky seas or sea sparkle. The underlying concept, a shear-stress induced permeabilisation of biocatalytic reaction co ...

Wiley-VCH Verlag GmbH2021

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Philipp Bucher, Giovanna Ambrosini, René Dreos, Romain Fernand Pietro Groux

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

Architecture of the centriole cartwheel‐containing region revealed by cryo‐electron tomography

Henning Paul-Julius Stahlberg, Paul Guichard, Virginie Hamel

Centrioles are evolutionarily conserved barrels of microtubule triplets that form the core of the centrosome and the base of the cilium. While the crucial role of the proximal region in centriole biogenesis has been well documented, its native architecture ...

2020

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Felix Naef, Frédéric Bruno Martin Gachon, Cédric Gobet, Benjamin Dieter Weger, Nagammal Neelagandan

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) pr ...

National Academy of Sciences2020

Statistical physics of interacting proteins: Impact of dataset size and quality assessed in synthetic sequences

Anne-Florence Raphaëlle Bitbol, Pierre Mergny

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...

2020

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Kristina Makasheva

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

2020

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

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) m ...

AMER CHEMICAL SOC2020

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

AMER CHEMICAL SOC2019

Exciton dynamics in DNA oligomers studied by broadband deep-UV transient absorption spectroscopy

Majed Chergui, Malte Oppermann, Benjamin Bauer

We report broadband transient absorption measurements of adenine strands in the deep-UV (250-370 nm). By varying the strand length we resolve the interplay between inter-base stacking and exciton formation and dynamics in DNA oligomers. ...

E D P SCIENCES2019

Detecting topological variations of DNA at single-molecule level

Aleksandra Radenovic, Georg Fantner, Adrian Pascal Nievergelt, Ke Liu

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electro ...

Nature Research2019

The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution

Benjamin Marcel Daniel Rothé

Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the abil ...

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER2019