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Concept

Ribose

Related publications (15)

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

A New Strategy Coupling Ion-Mobility-Selective CID and Cryogenic IR Spectroscopy to Identify Glycan Anomers

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Eduardo Carrascosa Casado, Priyanka Bansal, Robert Paul Pellegrinelli, Lei Yue

Determining the primary structure of glycans remains challenging due to their isomeric complexity. While high-resolution ion mobility spectrometry (IMS) has recently allowed distinguishing between many glycan isomers, the arrival-time distributions (ATDs) ...

2022

Identification of Mobility-Resolved N-Glycan Isomers

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Priyanka Bansal, Robert Paul Pellegrinelli

Glycan analysis has evolved considerably during the last decade. The advent of high-resolution ion-mobility spectrometry has enabled the separation of isomers with only the slightest of structural differences. However, the ability to separate such species ...

AMER CHEMICAL SOC2022

Combining multi-stage ion mobility spectrometry with cryogenic infrared spectroscopy for glycan analysis

Priyanka Bansal

Structural analysis of biomolecules is essential to understanding biological processes. Among the various classes of biomolecules, glycans have gained significant attention recently due to their ubiquitous roles in biological systems. However, study of gly ...

EPFL2022

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Francesco Piazza, Daniel Maria Busiello, Shiling Liang

The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...

Nature Research2021

Combining cryognic ion spectroscopy with ion mobility for the study of glycan fragmentation

Robert Paul Pellegrinelli

The importance of glycans in biological processes are matched by their structural complexity. Coating the surface of most living cells, glycans play key roles in many biological processes, and the role they play is closely related to their structures. Stru ...

EPFL2021

Revealing Single-Bond Anomeric Selectivity in Carbohydrate-Protein Interactions

Oleg Boyarkine, Aleksandr Pereverzev, Ruslan Yamaletdinov, Viktoriia Aladinskaia

The noncovalent binding of proteins to glycans is amazingly selective to the isoforms of carbohydrates, including alpha/beta anomers that coexist in solution. We isolate in the gas phase and study at the atomic level the simplest model system: noncovalent ...

AMER CHEMICAL SOC2020

The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution

Benjamin Marcel Daniel Rothé

Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the abil ...

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER2019

Bioconversion of pentose sugars to value added chemicals and fuels: Recent trends, challenges and possibilities

Edgard Gnansounou

Most of the crop plants contain about 30% of hemicelluloses comprising D-xylose and D-arabinose. One of the major limitation for the use of pentose sugars is that high purity grade D-xylose and D-arabinose are yet to be produced as commodity chemicals. Res ...

Elsevier2018

Selective detection of epimeric pentose saccharides at physiological pH using a fluorescent receptor

Joao Pedro De Almeida Neres

Epimerisation between ribofuranose and arabinofuranose sugars is crucial in several biosynthetic pathways, but is typically challenging to monitor. Here, we have screened for fluorescent boronic acids that can be used as molecular probes for the specific d ...

Elsevier Sci Ltd2014

Toward Quantitative Measurements of Enzyme Kinetics by Dissolution Dynamic Nuclear Polarization

Geoffrey Bodenhausen, Sami Jannin, Aurélien Bornet, Jonas Milani

Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which ...

2014

Modeling proton-induced damage on 2-deoxy-D-ribose. Conformational analysis

Pablo Lopez Tarifa

Modeling proton-induced damage in biological systems, in particular in DNA building blocks, is of major concern in studies on cancer proton therapy. This is indeed an extremely complex process and analysis of the mechanism at the molecular level is of cruc ...

Springer2014

Synthesis and Conformational Analysis of (alpha-D-Galactosyl)phenylmethane and alpha-,beta-Difluoromethane Analogues: Interactions with the Plant Lectin Viscumin

Pierre Vogel, Maria Kolympadi

alpha-D-Galactosyl)phenylmethane (1). (alpha- and beta-D-galactosyl)-(difluoro)phenylmethane (2 and 3) have been prepared and their conformations in solution were described by using a combination of force-field calculations and NMR spectroscopic studies. G ...

2009

Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein–RNA complexes

Luc Reymond, Philipp Wenter

We report an optimized synthesis of all canonical 2'-O-TOM protected ribonucleoside phosphoramidites and solid supports containing [13C5]-labeled ribose moieties, their sequence-specific introduction into very short RNA sequences and their use for the stru ...

Oxford University Press2006

Synthesis and evaluation of 2'-O-substituted oligoribonucleotide analogues with new properties

Luc Reymond

During a previous, exploratory project in our group, it was observed that duplexes formed by oligonucleotides modified with polar 2'-O-substituents were more tolerant towards the addition of 1,2-dimethoxyethane (DME) than RNA and DNA duplexes [1]. Inspired ...

EPFL2006