Publications related to The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study

Related publications (37)

Exploring New Nanopore Sensors from the Aerolysin Family

Julian Andrew Barry, Matteo Dal Peraro, Maria Josefina Marcaida Lopez, Juan Francisco Bada Juarez

Aerolysin‐like proteins are a family of pore‐forming toxins with potential biotechnological applications as nanopore sensors for biomolecular detection and sequencing. Despite their conserved structural fold, the low sequence identity complicates sequence ...

Wiley2025

2D Metalorganic Ferromagnets

Diego Radillo Ochoa, Céline Hensky, Christian Wäckerlin, Quy Hien Le

Low-dimensional materials exhibiting stable magnetic ordering are interesting from a fundamental point of view as well as for future application in information technologies. Metalorganic magnets, created by linking metal atoms with specific organic molecul ...

WILEY2025

Engineering Spin Interaction Channels of FePc on Au(111)

Wolf-Dieter Schneider

We demonstrate the reversible control of interactions between a local molecular spin, hosted within an iron phthalocyanine (FePc) molecule, and the conduction electrons of a supporting Au(111) surface. Using the tip of a scanning tunneling microscope, we d ...

American Chemical Society (ACS)2025

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations

Marcos Penedo Garcia

The invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and princi ...

Wiley-V C H Verlag Gmbh2024

Structural heterogeneity of the ion and lipid channel TMEM16F

Horst Arthur Vogel

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

Nature Portfolio2024

Composition-tunable transition metal dichalcogenide nanosheets via a scalable, solution-processable method

Kevin Sivula, Andras Kis, Victor Carle Adrien Boureau, Zhenyu Wang, Yanfei Zhao, Simon Nussbaum, Rebekah Anne Wells, Marina Caroline Michèle Caretti, Nicolas Johannes Diercks

The alloying of two-dimensional (2D) transition metal dichalcogenides (TMDs) is an established route to produce robust semiconductors with continuously tunable optoelectronic properties. However, typically reported methods for fabricating alloyed 2D TMD na ...

Royal Soc Chemistry2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

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

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

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

Marta Di Fabrizio

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the prot ...

MDPI2023

Selectively Exciting and Probing Radiative Plasmon Modes on Short Gold Nanorods by Scanning Tunneling Microscope-Induced Light Emission

Olivier Martin

We study the plasmon modes of gold nanorods (as short as similar to 100 nm) on a nonmetallic conductive substrate using scanning tunneling microscope-induced light emission (STM-LE) with a nonplasmonic tungsten tip at room temperature in high vacuum (10-7 ...

AMER CHEMICAL SOC2023

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Andreas Füglistaler, Ana Paola Rico Villarreal, Patrick Daniel Barth, Mahdi Hijazi, Aurélien Laurent Jean-Charles Oggier, Robert Everett Jefferson

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Nature Research2023

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

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023