Publications related to Immunoprecipitation

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

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

Site-Specific Protein Conjugation onto Fluorescent Single-Walled Carbon Nanotubes

Ardemis Anoush Boghossian, Shang-Jung Wu, Vitalijs Zubkovs, Nils Schürgers

Semiconducting single-walled carbon nanotubes (SWCNTs) are among the few photostable optical emitters that are ideal for sensing, imaging, drug delivery, and monitoring of protein activity. These applications often require strategies for immobilizing prote ...

2020

Development of microfluidic tools and methods for the biochemical characterization of scFv and Cas9 affinity reagents and their applications in molecular detection

Ekaterina Emilova Petrova

Recent progress in protein engineering, empowered by the rapidly evolving fields of synthetic biology and DNA synthesis, has enabled the generation of various custom-designed proteins. Their thorough analysis has led to applications in areas including medi ...

EPFL2018

Tandem affinity purification of AtTERT reveals putative interaction partners of plant telomerase in vivo

Jana Majerská

The life cycle of telomerase involves dynamic and complex interactions between proteins within multiple macromolecular networks. Elucidation of these associations is a key to understanding the regulation of telomerase under diverse physiological and pathol ...

Springer Wien2017

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

Sebastian Maerkl, Ekaterina Emilova Petrova, Bruno Emanuel Ferreira De Sousa Correia, Matthew Christopher Blackburn

The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full adva ...

Oxford Univ Press2016

Dose-response curve of a microfluidic magnetic bead-based surface coverage sandwich assay

Martinus Gijs, Thomas Lehnert, Matteo Cornaglia, Raphaël Etienne Jean Trouillon, Hüseyin Cumhur Tekin

Magnetic micro-and nanoparticles ('magnetic beads') have been used to advantage in many microfluidic devices for sensitive antigen (Ag) detection. Today, assays that use as read-out of the signal the number count of immobilized beads on a surface for quant ...

Elsevier2015

Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, Philipp Bucher, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

A random-walk based model to explain ultrasensitive magnetic bead-based immunoassays

Martinus Gijs, Thomas Lehnert, Matteo Cornaglia, Raphaël Etienne Jean Trouillon, Hüseyin Cumhur Tekin

We introduce a new modeling approach for understanding the fundamental principle of bead-based surface coverage immunoassays that rely on the specific interaction between surface-bound “small” magnetic beads (1 μm in diameter) and a flow of “large” magneti ...

2014

RNA-Protein interactions at AU-rich elements

Ramona Pauchard-Batschulat

The expression of many proto-oncogenes, nuclear transcription factors and cytokines is regulated post-transcriptionally by specific interactions between distinct cis-elements within the mRNA and trans-acting factors that bind to these elements and thereby ...

EPFL2013

Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments

Yury Tsybin, Kristina Srzentic, Unige Anna Laskay

Mass spectrometry (MS)-based bottom-up proteomics (BUP) is currently the method of choice for large-scale identification and characterization of proteins present in complex samples, such as cell lysates, body fluids, or tissues. Technically, BUP relies on ...

Amer Chemical Soc2013

Development of Electrokinetically Based Two-Dimensional Separation Methodologies for Proteomic Studies

Mohammad Reza Pourhaghighi

Proteomic studies require analytical methods capable of separating, identifying and quantifying thousands of proteins. Consequently, developing separation methodologies with high resolving power necessary to separate complex protein samples prior to protei ...

EPFL2012

Computational analysis of protein-DNA interactions from ChIP-seq data

Felix Naef, Jacques Rougemont

Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps ...

2011

Bubble cell for magnetic bead trapping in capillary electrophoresis

Hubert Girault, Anne-Laure Gassner

A bubble cell capillary classically used to extend the optical path length for UV-vis detection is employed here to trap magnetic beads. With this system, a large amount of beads can be captured without inducing a strong pressure drop, as it is the case wi ...

Springer Verlag2011

Two Nucleus-Localized CDK-Like Kinases With Crucial Roles for Malaria Parasite Erythrocytic Replication Are Involved in Phosphorylation of Splicing Factor

The kinome of the human malaria parasite Plasmodium falciparum comprises representatives of most eukaryotic protein kinase groups, including kinases which regulate proliferation and differentiation processes. Despite extensive research on most plasmodial e ...

Wiley-Blackwell2011

Protein Microarrays Based on Polymer Brushes Prepared via Surface-Initiated Atom Transfer Radical Polymerization

Harm-Anton Klok, Raphaël Barbey, Markus Ehrat

Polymer brushes represent an interesting platform for the development of high-capacity protein binding surfaces. Whereas the protein binding properties of polymer brushes have been investigated before, this manuscript evaluates the feasibility of poly(glyc ...

American Chemical Society2010

Phototocatalytic Lithography of Poly(propylene sulfide) Block Copolymers: Toward High-Throughput Nanolithography for Biomolecular Arraying Applications

Jeffrey Alan Hubbell

Photocatalytic lithography (PCL) is an inexpensive, fast, and robust method of oxidizing surface chemical moieties to produce patterned substrates. This technique has utility in basic biological research as well as various biochip applications. We report o ...

2009

Magnetic beads retention device for sandwich immunoassay: comparison of off-chip and on-chip antibody incubation

Martinus Gijs, Caroline Vandevyver, Frédéric Lacharme

We use magnetic microbeads, which are magnetically self-assembled in chains in a microfluidic chip, as reaction substrates to implement two different sandwich immunoassay protocols for the detection of mouse monoclonal target antibodies. The magnetic chain ...

Springer-Verlag2009

Protein-binding microarray technology and ChIP-sequencing for the identification of novel targets of the human tumor suppressor AP2[alpha]

Jan Kerschgens

The mis-regulation of gene transcription in the living cell can be the cause of complex human diseases like cancer. One challenge of the post-genomic era of biomedical research is the development of in vitro techniques for the rapid and cost-effective anal ...

EPFL2009

The affinity precipitation for the isolation of biomolecules

Gisela Stocker Majd

Product isolation increasingly becomes a major bottleneck in molecular biotechnology. This is especially the case for the sensitive proteineous substances (recombinant proteins, antibodies) and lately also DNA, usually produced in low concentration. The cu ...

EPFL2007

New insight into cataract formation: Enhanced stability through mutual attraction

Nicolas Dorsaz, Giuseppe Foffi

Small-angle neutron scattering experiments and molecular dynamics simulations combined with an application of concepts from soft matter physics to complex protein mixtures provide new insight into the stability of eye lens protein mixtures. Exploring this ...

2007