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14 results for “Nucleobase”
Supplementary Material for "Route Efficiency Assessment and Review of the Synthesis of β-Nucleosides via N-Glycosylation of Nucleobases"
<p>This is the external Supplementary Material for our publication "Route Efficiency Assessment and Review of the Synthesis of β-Nucleosides via <em>N</em>-Glycosylation of Nucleobases", which has been released as a preprint on <em>ChemRxiv </em>(https://doi.org/10.26434/chemrxiv.12753413.v1). The files in this record are additionally available from <em>ChemRxiv</em>.</p>
Research data supporting "Plasmonic chirality imprinting on nucleobase-displaying supramolecular nanohelices via metal-nucleobase recognition"
<p>This file contains the raw research data supporting the publication:</p> <p>Y. Lin<em> et al</em>., Plasmonic chirality imprinting on nucleobase-displaying supramolecular nanohelices via metal-nucleobase recognition, Angew. Chem. Int. Ed. 2017, DOI: 10.1002/anie.201610976.</p> <p> </p>
Supporting Information for Gas-phase formation of interstellar nucleobases from dehydrogenated radicals of formamide and vinyl cyanide
<p>Supporting Information for Gas-phase formation of interstellar nucleobases from dehydrogenated radicals of formamide and vinyl cyanide, including:</p> <p>1. Comparison between results obtained using M06 and MP2 methods.</p> <p>2. Energy diagrams of the reaction for transforming the reactants via H migration.</p> <p>3. Atomic coordinates data.</p>
A High-Level Quantum Chemical Study of the Thermodynamics Associated with Chlorine Transfer between N-Chlorinated Nucleobases
<p>Geometries of the isomers of the N-Chlorinated nucleobases (adenine, guanine and thymine) as well as the lowest energy structures of the DNA bases (adenine, cytosine, guanine and thymine) obtained at the B3LYP/6-31G(2df,p) level of theory (in Cartesian Coordinates).</p> <p> </p> <p><strong>ABSTRACT: </strong>The relative free energies of the isomers formed upon <em>N</em>-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the <em>N</em>-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy <em>N</em>-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from <em>N</em>-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from an <em>N</em>-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from <em>N</em>-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with D<em>G</em><sup>o</sup> values of ­–50.3 (cytosine), –28.0 (guanine), and –6.7 (adenine) kJ mol<sup>–1</sup>. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In an aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from <em>N</em>-chlorothymine to the three other nucleobases: –58.4 (cytosine), –26.4 (adenine), and –18.7 (guanine) kJ mol<sup>–1</sup>. Therefore, our calculations, whether in the gas phase or in an aqueous solution, clearly indicate that chlorine transfer from any of the <em>N</em>-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in <em>N</em>-chlorinated cytidine than in other <em>N</em>-chlorinated nucleosides.</p>
Characterising conical intersections in DNA/RNA nucleobases with multiconfigurational wave functions of varying active space size. Supplementary Information.
<p>Supplementary information that contains several files with the Cartesian coordinates for each one of the conical intersections optimized for each nucleobase at every active space studied. </p>
Supplementary Material for "Updating and Extending an UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases"
<p>This is the supplementary material for our publication "Updating and Extending an UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases".</p> <p> </p> <p><strong>For a detailed description of this material, please see the "Notes on the Supporting Material".</strong></p> <p> </p> <p>Naturally, this publication builds on previous work. The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publication (10.3390/mps2030060, 10.5281/zenodo.3333469). Applications of this methodology are described in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858).</p> <p>I wish to thank all authors of this publication for their contribution, using the method and generously sharing your experience and your data with me. This helped us develop robust protocols, learn about the potential and limits of the method and ultimately made this update article possible. While I have been the primary user of the method, your applications, questions and problems have spurred us to think outside of the box and find solutions that helped us expand our repertoire of "unmixable" reactions. This Supplementary Information contains some of our shared data and I thank each of you for contributing to this work.</p> <p> </p>
Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases
<p>Additional supporting simulation data for "Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases". Includes starting coordinates, topologies, and trajectories, as well as all files needed to reproduce the simulations.</p>
Base-resolution analysis of deoxyuridine at genome scale based on artificial incorporation modified nucleobase
GEO Series GSE142071. Homo sapiens. 3 samples. Type: Other.
Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
GEO Series GSE263194. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing nucleobase modification
GEO Series GSE197166. Mus musculus. 44 samples. Type: Expression profiling by array.
High resolution mapping of modified nucleobases in DNA using excision repair enzymes
GEO Series GSE51361. Saccharomyces cerevisiae; Escherichia coli. 11 samples. Type: Other.
Nucleobase adducts bind MR1 and stimulate MR1-restricted T cells
GEO Series GSE160366. Homo sapiens. 14 samples. Type: Other.
Reprogramming deaminase substrate specificity for single nucleobase editing
GEO Series GSE294219. Homo sapiens. 40 samples. Type: Other.
An Experimental and Theoretical Mass Spectrometric Quantification of Non–covalent Interactions in High Order Homogeneous Self–associates of Nucleobases and Nucleosides - experimental mass spectrometric dataset
<p>Experimental mass spectrometric dataset of APCI and ESI spectra to a chapter.</p>
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OpenNeuro
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