Publications associées à Toward an Effective Control of DNA's Submolecular Conformation on a Surface

Ru(II)-Arene Complexes of Curcumin and Bisdesmethoxycurcumin Metabolites

Paul Joseph Dyson, Farzaneh Fadaei Tirani, Mouna Hadiji

Curcuminoids and their complexes continue to attract attention in medicinal chemistry, but little attention has been given to their metabolic derivatives. Here, the first examples of (arene)Ru(II) complexes with curcuminoid metabolites, tetrahydrocurcumin ...

Amer Chemical Soc2024

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

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

Sebastian Maerkl, Jonathan Selz, Nicolas Rémi Adam

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

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

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

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

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

Thomas Lehnert, Martinus Gijs, Lin Sun

Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fa ...

ROYAL SOC CHEMISTRY2022

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

Thomas Lehnert, Martinus Gijs, Lin Sun

DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...

ROYAL SOC CHEMISTRY2022

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Nina Vesel

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022

2D MoS2 Nanopores: Wafer-scale Fabrication and Monolayer Stability for Long-term Single-Molecule Sensing

Mukeshchand Thakur

Biologically inspired solid-state nanopores are artificial openings or apertures in thin membranes similar to natural protein ion channels in a lipid bilayer of cell membranes. In solid-state nanopores, a thin insulating membrane with single or multiple po ...

EPFL2022

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

Directed evolution of DNA-wrapped single-walled carbon nanotube complexes for optical sensing

Benjamin Paul Johanès Gabriel Lambert

Single-walled carbon nanotubes (SWCNTs) have garnered significant interest for their applications in optical biosensing. SWCNTs exhibit a sensitive and photostable fluorescence in the near-infrared (NIR) range, allowing for the continuous monitoring of tar ...

EPFL2021

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Paolo Carloni, Marco Pasi, Rahul Sharma

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Springernature2021

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure

Himanshu Joshi, Diana Kornelia Morzy

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improveme ...

AMER CHEMICAL SOC2021

Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly

Tatiana Favez, Pierre Gönczy, Virginie Hamel, Santiago Harald Andany, Georg Fantner, Oliver Hantschel, Georgios Hatzopoulos, Niccolo Banterle

Centrioles are evolutionarily conserved multi-protein organelles essential for forming cilia and centrosomes. Centriole biogenesis begins with self-assembly of SAS-6 proteins into 9-fold symmetrical ring polymers, which then stack into a cartwheel that sca ...

Nature Research2021

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Shang-Jung Wu

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

EPFL2020

Electrochemical and morphological engineering of 2D materials for nanopore sensing

Martina Lihter

Nanopores are nanometer-sized holes that were initially proposed for DNA sequencing. Several years ago sequencing was made possible with biological nanopores. However, solid-state nanopores have plenty of advantages to offer compared to their biological co ...

EPFL2020

Structural and Photophysical Templating of Conjugated Polyelectrolytes with Single-Stranded DNA

Ursula Röthlisberger, Polydefkis Diamantis, Natalie Renuka Banerji

A promising approach to influence and control the photophysical properties of conjugated polymers is directing their molecular conformation by templating. We explore here the templating effect of single-stranded DNA oligomers (ssDNAs) on cationic polythiop ...

AMER CHEMICAL SOC2020

Structural and DNA binding properties of mycobacterial integration host factor mIHF

Giovanni Dietler, Stewart Cole, Aleksandre Japaridze, Rajkumar Singh, Luciano Andres Abriata, Nina Theres Odermatt, Jérémie Piton, David Lyndon Emsley, Moreno Lelli

In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted ...

Elsevier2020

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams

Tom Ian Battin, Paraskevi Pramateftaki, Hannes Markus Peter, Jade Brandani, Stylianos Fodelianakis, Susheel Bhanu Busi

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and ...

PEERJ INC2020