Search results for "computational"
showing 10 items of 5884 documents
Analysis of pseudouridines and other RNA modifications using hydraPsiSeq protocol
2021
Detection of RNA modified nucleotides using deep sequencing can be performed by several approaches, including antibody-driven enrichment and natural or chemically induced RT signatures. However, only very few RNA modified nucleotides generate natural RT signatures and antibody-driven enrichment heavily depends on the quality of antibodies used and may be highly biased. Thus, the use of chemically-induced RT signatures is now considered as the most trusted experimental approach. In addition, the use of chemical reagents allows inclusion of simple "mock-treated" controls, to exclude spontaneous RT arrests, SNPs and other misincorporation-prone sites. Hydrazine is a well-known RNA-specific rea…
Mapping and Quantification of tRNA 2′-O-Methylation by RiboMethSeq
2018
Current development of epitranscriptomics field requires efficient experimental protocols for precise mapping and quantification of various modified nucleotides in RNA. Despite important advances in the field during the last 10 years, this task is still extremely laborious and time-consuming, even when high-throughput analytical approaches are employed. Moreover, only a very limited subset of RNA modifications can be detected and only rarely be quantified by these powerful techniques. In the past, we developed and successfully applied alkaline fragmentation-based RiboMethSeq approach for mapping and precise quantification of multiple 2'-O-methylation residues in ribosomal RNA. Here we descr…
AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-guanosine (m7G) and 3-Methyl-cytosine (m3C) in RNAs by Hi…
2021
Epitranscriptomics is an emerging field where the development of high-throughput analytical technologies is essential to profile the dynamics of RNA modifications under different conditions. Despite important advances during the last 10 years, the number of RNA modifications detectable by next-generation sequencing is restricted to a very limited subset. Here, we describe a highly efficient and fast method called AlkAniline-Seq to map simultaneously two different RNA modifications: 7-methyl-guanosine (m7G) and 3-methyl-cytosine (m3C) in RNA. Our protocol is based on three subsequent chemical/enzymatic steps allowing the enrichment of RNA fragments ending at position n + 1 to the modified nu…
Application of headspace analysis to the study of aroma compounds-lipids interactions
1998
Taking into account interactions between aroma compounds and food components is necessary to better manage the flavoring of food products. These interactions occur at a molecular level and reflect changes, at a macroscopic level, in thermodynamic equilibria, such as solubility or volatility. The rate of transfer of an aroma compound from the liquid to the vapor phase can be affected as well. The behavior of aroma compounds in water and lipid solutions was studied in two complementary ways, a thermodynamic and a kinetic approach (head-space analysis). The transfer rate of volatiles at the liquid-water interface does not only depend on the hydrophobicity of the aroma compounds. Vapor-liquid p…
An analysis of the regioselectivity of 1,3-dipolar cycloaddition reactions of benzonitrile n-oxides based on global and local electrophilicity and nu…
2009
The regioselectivity of the 1,3-dipolar cycloaddition (13DC) reactions of benzonitrile N-oxides (BNOs) with electrophilic and nucleophilic alkenes has been analyzed by using global and local nucleophilicity and electrophilicity reactivity indices defined within the conceptual DFT. The BNOs react with electron-deficient and electron-rich ethylenes, but the regioselectivities of these polar reactions are different. Whereas the reactions with electron-rich ethylenes are completely regioselective, yielding 5-isoxazolines, a change in the regioselectivity is observed in the reactions with electron-deficient ethylenes, which yield a mixture of 4- and 5-isoxazolines. Analysis of the energies, geom…
Function of biomolecules as a probe for studying the effects of organic co-solvents on their conformations
1980
Abstract Conformation changes associated with the function of biomolecules can bring out variations of the extent and specific structure of their hydrophobic areas exposed to solvent, with consequent local rearrangements of the solvent. This is one of the channels through which the solvent exerts its role in the functional equilibria of biomolecules. The function of biological macromolecules in perturbed aqueous solvent can therefore be a suitable probe for studying the response of macromolecule-solvent systems to perturbations caused by organic co-solvents. We shall discussed the effects that the presence of some monohydric alcohols and some amides in the aqueous medium have on some thermo…
Coordination chemistry of N,N′-bis(coordinating group substituted)oxamides: a rational design of nuclearity tailored polynuclear complexes
1999
Abstract The coordinating properties of N , N ′-bis(coordinating group substituted)oxamides have been thoroughly investigated both in aqueous solution and in the solid state. The easy cis – trans isomerization equilibria that they exhibit together with the great variety of N , N ′-substituents which can be used to play on the overall charge, complexing ability and polarity, make them very suitable ligands in designing homo- and heterometallic species. The knowledge of their complex formation in aqueous solution by potentiometry and using the hydrogen ion concentration as a probe, allowed us to settle the basis of a rational design of oxamidate-containing polynuclear species whose nuclearity…
On the tautomerization process of glycine in aqueous solution
2000
The experimental activation energy for the tautomerization of glycine zwitterion neutral form has been reported to be 14.6 kcalrmol. It has been generally assumed that this energy barrier is needed for proton transfer to occur. However, previous theoretical results do not support this interpretation. In the present work, we examine this question using density functional calculations, extended basis sets and a polarizable continuum solvent model. Our results suggest that the limiting step for the tautomerization process corresponds basically to H-atom reorientation in the -COOH group. This could be a general feature in the tautomerization of amino acids. q 2000 Elsevier Science B.V. All righ…
Interaction of Alkyltin(IV) Compounds with Ligands of Interest in the Speciation of Natural fluids: Complexes of (CH3)2Sn2+ with Carboxylates
1997
Complex formation by (CH3)2Sn 2+ with acetate (ac), malonate (mal), 1,2,3-propanetricarboxylate (tricarballylate, tca) and 1,2,3,4-butanetetracarboxylate (btc) ligands in aqueous solution is reported. The study has been performed by potentiometry ([H + ]‐glass electrode) at T = 25 °C, and in the 0 < I < 1 mol dm 2 3 ionic strength range. In order to evaluate the salt effects on the formation constants of the complex species, and to contribute to the definition of the chemical speciation of diorganotin(IV) compounds in natural waters where carboxylic ligands are naturally present, interactions of NaCl (which is the major component of all natural fluids), with the components of the systems un…
A detailed MSn study for the molecular identification of a dimer formed from oxidation of pinene
2016
Abstract Dimeric products formed in the oxidation of α- and β-pinene have been frequently observed in laboratory and field studies of biogenic SOA formation. While their existence is undoubted, their exact chemical structures remain unclear. This study uses a combined two step approach aiming on the molecular identification of the most important of the various dimers that have been observed in biogenic secondary organic aerosol formation, a dimer with the molecular weight 358 g mol−1. The first step is the application of a functional group derivatization technique (esterification) to quantify the number of carboxylic acid groups in the target molecule. Based on the detailed interpretation o…