Publications de Aleksandre Japaridze

Structural and DNA binding properties of mycobacterial integration host factor mIHF

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

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

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

Giovanni Dietler, Aleksandre Japaridze, Sylvain Renevey

Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring pro ...

American Society for Biochemistry & Molecular Biology (ASBMB)2017

Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization

Giovanni Dietler, Paolo De Los Rios, Giovanni Longo, Fabrizio Benedetti, Aleksandre Japaridze

Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understan ...

American Chemical Society2017

Spatial confinement induces hairpins in nicked circular DNA

Giovanni Dietler, Aleksandre Japaridze, Enzo Orlandini

In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of ...

Oxford University Press (OUP)2017

Preparation of Well-Defined DNA Samples for Reproducible Nanospectroscopic Measurements

Giovanni Dietler, Aleksandre Japaridze, Ewelina Wioletta Lipiec

Wiley-Blackwell2016

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

Giovanni Dietler, Dusan Vobornik, Aleksandre Japaridze, Andrea Cerreta, Ewelina Wioletta Lipiec

DNA adopts different conformations based on its environment. We reveal conditions that either preserve the DNA's physiological B-conformation, even upon its placement in UHV, or lead to a partial B-form to A-form reorganization upon DNA's deposition on a s ...

American Chemical Society2016

Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis

Stewart Cole, Florence Pojer, Jérémie Piton, Aleksandre Japaridze

Mycobacterium tuberculosis secretes multiple virulence factors during infection via the general Sec and Tat pathways, and via specialized ESX secretion systems, also referred to as type VII secretion systems. The ESX-1 secretion system is an important viru ...

Elsevier2015

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Giovanni Dietler, Julien Dorier, Fabrizio Benedetti, Yannis Burnier, Aleksandre Japaridze, Andrzej Stasiak, Robert Sebastian Kwapich

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from ...

Oxford University Press2015

Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

Giovanni Dietler, Aleksandre Japaridze, Aleksandr Benke, Sylvain Renevey

Fluorescent dyes are widely used for staining and visualization of DNA in optical microscopy based methods. Even though for some dyes the mechanism of binding is known, how this binding affects DNA remains poorly understood. Here we present a novel experim ...

American Chemical Society2015

From polymers to gene regulation : a bottom up approach to the bacterial chromatin

Aleksandre Japaridze

DNA molecule is the fundamental component of every living organism, since it encodes the hereditary information. Although the genetic code of almost 200 species has been sequenced, the direct connection between gene sequence, DNA structure and biological f ...

EPFL2015