Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains

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Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

Riccardo Dainese

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

EPFL2019

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair

Ursula Röthlisberger, Ivano Tavernelli, Polydefkis Diamantis

To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as ...

2019

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Paolo De Los Rios, Alessandro Barducci

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs i ...

2019

Periodic Motion of Sedimenting Flexible Knots

Giovanni Dietler, Krishnan Thyagarajan

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwi ...

APS2018

Evaluation of Auramine O staining and conventional PCR for leprosy diagnosis: A comparative cross-sectional study from Ethiopia

Stewart Cole, Charlotte Avanzi, Philippe Busso

Background ...

PUBLIC LIBRARY SCIENCE2018

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

Oxford University Press2018

Nuclear RNR-alpha antagonizes cell proliferation by directly inhibiting ZRANB3

Yimon Aye

Since the origins of DNA-based life, the enzyme ribonucleotide reductase (RNR) has spurred proliferation because of its rate-limiting role in de novo deoxynucleoside-triphosphate (dNTP) biosynthesis. Paradoxically, the large subunit, RNR-alpha, of this obl ...

2018

On chirality of toroidal embeddings of polyhedral graphs

Senja Dominique Barthel

We investigate properties of spatial graphs on the standard torus. It is known that nontrivial embeddings of planar graphs in the torus contain a nontrivial knot or a non-split link due to [2, 3]. Building on this and using the chirality of torus knots and ...

World Scientific Publishing2017

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

Roman Bulushev

Interactions of proteins with DNA are essential for carrying out DNA's biological functions and performing a cellular cycle. Such processes as DNA replication, expression and repair are performed by an organised action of various proteins. To better unders ...

EPFL2017

Spatial confinement induces hairpins in nicked circular DNA

Giovanni Dietler, Aleksandre Japaridze

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

DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation

Beat Fierz, Andreas Linus Bachmann

Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27 to mark genes for repression. We measured the dynamics of PRC2 binding on recombinant chromatin and free DNA at the single-molecule level using total internal reflection fluorescenc ...

Nature Research2017

Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA

Virginija Jovaisaite

Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a dou ...

Oxford University Press (OUP)2017