Publications related to Nanocapillaries combined with optical tweezers as a single molecule technique for studying DNA-protein complexes

Related publications (37)

Mitochondrial control of ciliary gene expression and structure in striatal neurons

Maria del Carmen Sandi Perez, Olivia Zanoletti, Dogukan Hazar Ülgen, Alessandro Chioino

Mitochondria play essential metabolic roles and are increasingly understood to interact with other organelles, influencing cellular function and disease. Primary cilia, as sensory and signalling organelles, are crucial for neuronal communication and functi ...

WILEY2025

Quantum interference observed in state-resolved molecule-surface scattering

Rainer Beck, Christopher Scott Reilly, Liang Zhang

Although the dynamics of collisions between a molecule and a solid surface are ultimately quantum mechanical, decohering effects owing to the large number of interacting degrees of freedom typically obscure the wavelike nature of these events. However, a p ...

American Association for the Advancement of Science (AAAS)2025

Quantifying Interaction of Single Molecules with Surfaces using Label-Free Microscopy

Jenny Sülzle

Label-free microscopy is a rapidly advancing field that allows for imaging and tracking of objects without the need for (fluorescent) labels. One technique is interferometric scattering (iSCAT) microscopy, which allows the detection and quantification of s ...

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

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

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

Advancing Cell-Free Synthetic Biology: From sustained PURE protein synthesis to an isothermal one-pot DNA replication system

Laura Sophie Grasemann

One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

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

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

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

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

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento Ribeiro De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

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

Lumped Drag Model Identification and Real-Time External Force Detection for Rotary-Wing Micro Aerial Vehicles

Alcherio Martinoli, Lucas Cédric Wälti

This work focuses on understanding and identifying the drag forces applied to a rotary-wing Micro Aerial Vehicle (MAV). We propose a lumped drag model that concisely describes the aerodynamical forces the MAV is subject to, with a minimal set of parameters ...

IEEE2024

Characterisation of EIF5A perturbations on ribosome dynamics with single-molecule imaging

Irene Lamberti

The development of protein-tagging techniques such as SunTag has given unprecedented opportunities to measure translation dynamics in living cells. In this study we leveraged the SunTag system to investigate the regulatory role of translation elongation in ...

EPFL2024

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

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

Experimental demonstration of attosecond pump-probe spectroscopy with an X-ray free-electron laser

Christoph Bostedt, Jun Wang, Zhaoheng Guo

Pump-probe experiments with subfemtosecond resolution are the key to understanding electronic dynamics in quantum systems. Here we demonstrate the generation and control of subfemtosecond pulse pairs from a two-colour X-ray free-electron laser. By measurin ...

Nature Publishing Group2024