Isothermal multiple displacement amplification of DNA templates in minimally buffered conditions using phi29 polymerase

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Generation of a Large Peptide Phage Display Library by Self-Ligation of Whole-Plasmid PCR Product

Kaycie Marie Butler, Christian Heinis, Xudong Kong, Vanessa Carle, Cristina Diaz Perlas

The success of phage display, used for developing target-specific binders based on peptides and proteins, depends on the size and diversity of the library screened, but generating large libraries of phage-encoded polypeptides remains challenging. New pepti ...

2020

Exploring on Protein-DNA interactions

Alexandra Styliani Kalantzi

A variety of DNA-binding proteins organizes the chromosomal DNA and regulates gene transcription, and DNA replication and recombination. In particular, for gene regulation there is a category of DNA-binding proteins, the transcription factors, which can de ...

EPFL2019

Experimenting with knots

Giovanni Dietler

Knots are interesting objects to experiment since their topological properties are combined with mechanical properties, fluid mechanics or dynamical properties like unknotting under the excitation of the thermal energy. Knots play also a role in biology be ...

SPRINGER HEIDELBERG2019

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

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

RADX: A novel single-stranded DNA-binding protein regulating telomere recombination

Anna-Sophia Briod

Telomeres are specialized nucleoprotein structures present at the ends of linear chromosome. The telomeric DNA part is comprised of 5-15 kilo base pairs of double stranded TTAGGG repeats and it contains at the 3' end a single-stranded G-rich overhang of 50 ...

EPFL2019

Engineering a stable future for DNA-origami as a biomaterial

Maartje Martina Cornelia Bastings, Eva Eugene Kurisinkal, Hale Bila

DNA as a biomaterial has evoked great interest as a potential platform for therapeutics and diagnostics and as hydrogel scaffolds due to the relative ease of programming its robust and uniform shape, site-specific functionality and controlled responsive be ...

ROYAL SOC CHEMISTRY2019

Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

Melanie Blokesch, Nicolas Jean Philippe Guex, Christian Iseli, Sandrine Stutzmann, Noémie Matthey, Candice Stoudmann

Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the ...

2019

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

Two nanomachines drive evolution in diverse Vibrio species

Noémie Matthey

Horizontal gene transfer (HGT) has a major impact on bacterial evolution, leading to acquisition or deletion of genes and gene clusters, including those encoding antibiotic resistances and virulence factors. HGT therefore contributes to pathogen emergence, ...

EPFL2019

Detecting topological variations of DNA at single-molecule level

Aleksandra Radenovic, Georg Fantner, Adrian Pascal Nievergelt, Ke Liu

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electro ...

Nature Research2019

Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies

Vytautas Navikas

The DNA Curtains assay is a recently developed experimental platform for protein-DNA interaction studies at the single-molecule level that is based on anchoring and alignment of DNA fragments. The DNA Curtains so far have been made by using chromium barrie ...

AMER CHEMICAL SOC2019