Publications related to Nucleic acid notation

Stimulus-responsive assembly of nonviral nucleocapsids

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

Nature Portfolio2024

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes

Maartje Martina Cornelia Bastings, Cem Tekin, Diana Kornelia Morzy, Vincenzo Caroprese

Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electr ...

ROYAL SOC CHEMISTRY2023

Core-shell Structured Chitosan-polyethylenimine Nanoparticles for Gene Delivery: Improved Stability, Cellular Uptake, and Transfection Efficiency

Sandrine Gerber, Laura Camille Louise Nicolle, Perrine Agnes Edith Robin

Gene therapy emerged as a promising treatment option for acquired and inherited diseases. The delivery of nucleic acids relies on vectors that condense and encapsulate their cargo. Especially non-viral gene delivery systems are of increasing interest. Howe ...

2022

Ring-Opening Reactions of Aminocyclopropanes and Aminocyclobutanes

Mingming Wang

Nitrogen-containing compounds are an important class of molecules in medicinal chemistry, chemical biology, biochemistry, material sciences or environmental sciences. Organic nitrogen occurs in many forms, ranging from small building blocks such as urea, a ...

EPFL2022

Electronic and structural dynamics in DNA single strands

Benjamin Bauer

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA ...

EPFL2021

Regulation of cGAS- and RLR-mediated immunity to nucleic acids

Andrea Ablasser

Pathogen-derived nucleic acids are crucial signals for innate immunity. Despite the structural similarity between those and host nucleic acids, mammalian cells have been able to evolve powerful innate immune signaling pathways that originate from the detec ...

NATURE PUBLISHING GROUP2020

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

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

AMER CHEMICAL SOC2019

A sequence-dependent coarse-grain model of B-DNA with explicit description of bases and phosphate groups parametrised from large scale Molecular Dynamics simulations

Alessandro Samuele Patelli

We introduce a sequence-dependent coarse-grain model of double-stranded DNA with an explicit description of both the bases and the phosphate groups as interacting rigid-bodies. The model parameters are trained on extensive, state-of-the-art large scale mol ...

EPFL2019

Computation and Visualization in Multiscale Modelling of DNA Mechanics

Jaroslaw Glowacki

Amongst the substances found in any living organism one of the most central in the workings of each living cell is deoxyribonucleic acid (DNA). For that reason it has been the subject of research in many of its aspects. These range from DNA sequencing to a ...

EPFL2016

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

Matteo Dal Peraro, Andrea Cavalli, Giulia Palermo

Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, ...

Amer Chemical Soc2015

Modulation of mitophagy and use thereof

Didier Trono, Isabelle Barde

The present invention relates to an agent or composition comprising at least one of: (i) a micro-RNA targeting a mitophagy-associated gene or a variant thereof, (ii) a vector comprising a nucleic acid encoding said micro-RNA or variant thereof, (iii) an in ...

2014

Analyzing ion distributions around DNA

John Maddocks, Marco Pasi

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordin ...

Oxford University Press2014

Controlled hydrogel photopolymerization inside live systems by X-ray irradiation

Giorgio Margaritondo

We successfully demonstrate the in situ formation by X-ray irradiation induced polymerization of a three-dimensional (3D) hydrogel based on poly(ethylene glycol) (PEG) diacrylate (PEG DA), with the option of heparin incorporation to enhance cell adhesion. ...

Royal Society of Chemistry2012

Striking Influence of the Catalyst Support and Its Acid–Base Properties: New Insight into the Growth Mechanism of Carbon Nanotubes

Arnaud Magrez, Gabor Laurenczy, Endre Horvath, Jin Won Seo, Rita Smajda, Donatello Acquaviva, Juan Carlos Andresen

In the accepted mechanisms of carbon nanotube (CNT) growth by catalytic chemical vapor deposition (CCVD), the catalyst support is falsely considered as a passive material whose only role is to prevent catalytic particles from coarsening. The chemical chang ...

2011

Stacking and spreading interaction in N-heteroaromatic systems

Jeremy Samuel Arey, Brijesh Kumar Mishra

π−π interactions in heteroaromatic systems are ubiquitous in biological systems. In the present study, stabilization energies of stacked and hydrogen-bonded dimers of N-heteroaromatic systems (pyridine, pyrazine, sym-triazine, and sym-tetrazine) have been ...

American Chemical Society2010

Surface optofluidics

Demetri Psaltis, Andreas Vasdekis, Wuzhou Song, Jae-Woo Choi, Julien Cuennet, Luciano De Sio

Surfaces -defined as the interfaces between solids and liquids- have attracted much attention in optics and biology, such as total internal reflection imaging (TIRF) and DNA microarrays. Within the context of optofluidics however, surfaces have received li ...

Spie-Int Soc Optical Engineering, Po Box 10, Bellingham, Wa 98227-0010 Usa2010

Preparation of templates for nucleic acid sequencing

Gerardo Turcatti

The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to ...

2009