Publications related to RNA world

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

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

Francesco Aquilante

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) al ...

Amer Chemical Soc2023

Construction of sequencing libraries from a ribonucleic acid (rna) using tailing and ligation of cdna (tlc)

Didier Trono, Christina Ernst

The present invention provides a method for preparing a sequencing library from a ribonucleic acid (RNA) sample. ...

2023

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Didier Trono, Julien Léonard Duc, Christina Ernst

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

2023

Regulation and impact of TERRA R-loops at human telomeres

Rita Valador Fernandes

Telomeres are the nucleoprotein structures found at the ends of linear chromosomes. They ensure that the termini of chromosomes are not inappropriately recognized as sites of DNA damage, and are therefore crucial for genome stability. In spite of the heter ...

EPFL2023

RNA-based nanomedicines and their clinical applications

Yi Wang

RNA-based nanomedicines encompass a range of therapeutic approaches that utilize RNA molecules or molecules that target RNAs for the treatment or prevention of diseases. These include antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), endo ...

Tsinghua Univ Press2023

Recycling of Polymerase Chain Reaction (PCR) Kits

Francesco Stellacci, Yong Zhu, Weina Liu

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginn ...

AMER CHEMICAL SOC2023

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Felix Naef, Cédric Gobet, Benjamin Dieter Weger, Clémence Yumie Syloun Hurni

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of ...

PUBLIC LIBRARY SCIENCE2022

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...

EPFL2021

Small peptide diversification through photoredox-catalyzed oxidative C-terminal modification

Jérôme Waser, Eliott Hugo Joran Le Du, Marion Marie-Agnès Garreau

A photoredox-catalyzed oxidative decarboxylative coupling of small peptides is reported, giving access to a variety of N,O-acetals. They were used as intermediates for the addition of phenols and indoles, leading to novel peptide scaffolds and bioconjugate ...

2021

Shear Stress-Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates

Esther Amstad, Antoine Claude Jean Vian

Some marine plankton called dinoflagellates emit light in response to the movement of surrounding water, resulting in a phenomenon called milky seas or sea sparkle. The underlying concept, a shear-stress induced permeabilisation of biocatalytic reaction co ...

Wiley-VCH Verlag GmbH2021

The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity

Didier Trono, Matteo Dal Peraro, Suliana Manley, Maria Josefina Marcaida Lopez, Jenny Sülzle, Annamaria Kauzlaric, Alice Duperrex

Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological fun ...

2020

RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops

Joachim Lingner, Thomas Frédéric Lunardi, Marianna Feretzaki, Rita Valador Fernandes

Telomeres-repeated, noncoding nucleotide motifs and associated proteins that are found at the ends of eukaryotic chromosomes-mediate genome stability and determine cellular lifespan1. Telomeric-repeat-containing RNA (TERRA) is a class of long noncoding RNA ...

2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020

Mitochondrial RNA granules are fluid condensates positioned by membrane dynamics

Suliana Manley, Mary-Claude Croisier-Coeytaux, Timo Henry René Rey

Phase separation concentrates mitochondrial RNA granules. Here Rey et al., show that mitochondrial RNA granules (MRGs) behaviour is consistent with liquid-liquid phase separation (LLPS) and their fusion coincides with mitochondrial remodelling. Mitochondri ...

2020

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Daniel Darbellay, Anamaria Necsulea

The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon l ...

OXFORD UNIV PRESS2020

Revisiting the Urech Synthesis of Hydantoins: Direct Access to Enantiopure 1,5-Substituted Hydantoins Using Cyanobenziodoxolone

Jérôme Waser, Franck Le Vaillant, Nina Declas

A method for the synthesis of enantiopure 1,5-substituted hydantoins was developed using a hypervalent iodine cyanation reagent (cyanobenziodoxolone, CBX) as a source of electrophilic carbon. Starting from inexpensive commercially available enantiopure pro ...

2019

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

Didier Trono, Priscilla Turelli, Christian Axel Wandall Thorball, Julien Léonard Duc, Michaël Imbeault, Andrea Coluccio, Julien Paul André Pontis, Pierre-Yves Joseph Laurent Helleboid, Cécile Piot, Ruedi Aebersold

Krüppel‐associated box (KRAB)‐containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin‐inducing KAP1 as repressors of transposable elements (TEs) during early embryogene ...

2019

Palladium-Catalyzed Synthesis of Ketenimines from Isocyanides and Synthetic Studies Towards the Total Synthesis of Mersilongine

Mathias Mamboury

In the first chapter of this thesis, the development of two new reactions for the synthesis of vinyl ketenimines and alpha-oxo-ketenimines from isocyanides is presented. These palladium-catalyzed transformations both feature an isocyanide insertion / beta- ...

EPFL2019

Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases

Michele Ceriotti, David Mark Wilkins, Andrea Grisafi, Yang Yang

While density functional theory (DFT) is often an accurate and efficient methodology for evaluating molecular properties such as energies and multipole moments, this approach often yields larger errors for response properties such as the dipole polarizabil ...

2019