scholarly journals Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA

2017 ◽  
Vol 53 (96) ◽  
pp. 12938-12941 ◽  
Author(s):  
J. Kremser ◽  
E. Strebitzer ◽  
R. Plangger ◽  
M. A. Juen ◽  
F. Nußbaumer ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Stable Isotope ◽  
Chemical Synthesis ◽  
Structural Biology

A synthetic access to stable isotope modified large RNAs for structural biology is introduced.

scholarly journals Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy

Molecules ◽  
2019 ◽  
Vol 24 (19) ◽  
pp. 3476 ◽  
Author(s):  
Owen Becette ◽  
Lukasz T. Olenginski ◽  
Theodore K. Dayie
Keyword(s):  
Nmr Spectroscopy ◽  
Stable Isotope ◽  
Chemical Synthesis ◽  
Rna Structure ◽  
Solid Phase ◽  
Rna World ◽  
Dynamic Studies ◽  
Labeled Rna ◽  
Spectroscopy Studies ◽  
Phase Chemical

RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.

Controlling Gas Selectivity in Molecular Porous Liquids by Tuning the Cage Window Size

2019 ◽  
Author(s):  
Benjamin Egleston ◽  
Konstantin V. Luzyanin ◽  
Michael C. Brand ◽  
Rob Clowes ◽  
Michael E. Briggs ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Synthesis ◽  
Field Gradient ◽  
Window Size ◽  
Standard Approach ◽  
Porous Solids ◽  
Pulsed Field Gradient Nmr ◽  
Pulsed Field ◽  
Cage Molecules ◽  
Gas Selectivity

Control of pore window size is the standard approach for tuning gas selectivity in porous solids. Here, we present the first example where this is translated into a molecular porous liquid formed from organic cage molecules. Reduction of the cage window size by chemical synthesis switches the selectivity from Xe-selective to CH<sub>4</sub>-selective, which is understood using <sup>129</sup>Xe, <sup>1</sup>H, and pulsed-field gradient NMR spectroscopy.

Controlling Gas Selectivity in Molecular Porous Liquids by Tuning the Cage Window Size

2019 ◽  
Author(s):  
Benjamin Egleston ◽  
Konstantin V. Luzyanin ◽  
Michael C. Brand ◽  
Rob Clowes ◽  
Michael E. Briggs ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Synthesis ◽  
Field Gradient ◽  
Window Size ◽  
Standard Approach ◽  
Porous Solids ◽  
Pulsed Field Gradient Nmr ◽  
Pulsed Field ◽  
Cage Molecules ◽  
Gas Selectivity

Control of pore window size is the standard approach for tuning gas selectivity in porous solids. Here, we present the first example where this is translated into a molecular porous liquid formed from organic cage molecules. Reduction of the cage window size by chemical synthesis switches the selectivity from Xe-selective to CH<sub>4</sub>-selective, which is understood using <sup>129</sup>Xe, <sup>1</sup>H, and pulsed-field gradient NMR spectroscopy.

scholarly journals Radical Dehalogenation and Purine Nucleoside Phosphorylase E. coli: How Does an Admixture of 2′,3′-Anhydroinosine Hinder 2-fluoro-cordycepin Synthesis

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 539
Author(s):  
Alexey L. Kayushin ◽  
Julia A. Tokunova ◽  
Ilja V. Fateev ◽  
Alexandra O. Arnautova ◽  
Maria Ya. Berzina ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Synthesis ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Preparative Synthesis ◽  
Nucleoside Phosphorylase ◽  
E Coli ◽  
First Time

During the preparative synthesis of 2-fluorocordycepin from 2-fluoroadenosine and 3′-deoxyinosine catalyzed by E. coli purine nucleoside phosphorylase, a slowdown of the reaction and decrease of yield down to 5% were encountered. An unknown nucleoside was found in the reaction mixture and its structure was established. This nucleoside is formed from the admixture of 2′,3′-anhydroinosine, a byproduct in the preparation of 3-′deoxyinosine. Moreover, 2′,3′-anhydroinosine forms during radical dehalogenation of 9-(2′,5′-di-O-acetyl-3′-bromo- -3′-deoxyxylofuranosyl)hypoxanthine, a precursor of 3′-deoxyinosine in chemical synthesis. The products of 2′,3′-anhydroinosine hydrolysis inhibit the formation of 1-phospho-3-deoxyribose during the synthesis of 2-fluorocordycepin. The progress of 2′,3′-anhydroinosine hydrolysis was investigated. The reactions were performed in D2O instead of H2O; this allowed accumulating intermediate substances in sufficient quantities. Two intermediates were isolated and their structures were confirmed by mass and NMR spectroscopy. A mechanism of 2′,3′-anhydroinosine hydrolysis in D2O is fully determined for the first time.

A Solid-State NMR Approach to Structure Determination of Membrane-Associated Peptides and Proteins

1997 ◽  
Author(s):  
S.J. Opella ◽  
L.E. Chirlian
Keyword(s):  
Nmr Spectroscopy ◽  
Membrane Proteins ◽  
Structural Biology ◽  
Experimental Studies ◽  
Globular Proteins ◽  
Biological Properties ◽  
Cellular Functions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Form And Function

Structural biology relies on detailed descriptions of the three-dimensional structures of peptides, proteins, and other biopolymers to explain the form and function of biological systems ranging in complexity from individual molecules to entire organisms. NMR spectroscopy and X-ray crystallography, in combination with several types of calculations, provide the required structural information. In recent years, the structures of several hundred proteins have been determined by one or both of these experimental methods. However, since the protein molecules must either reorient rapidly in samples for multidimensional solution NMR spectroscopy or form high quality single crystals in samples for X-ray crystallography, nearly all of the structures determined up to now have been of the soluble, globular proteins that are found in the cytoplasm and periplasmof cells and fortuitously have these favorable properties. Since only a minority of biological properties are expressed by globular proteins, and proteins, in general, have evolved in order to express specific functions rather than act as samples for experimental studies, there are other classes of proteins whose structures are currently unknown but are of keen interest in structural biology. More than half of all proteins appear to be associated with membranes, and many cellular functions are expressed by proteins in other types of supramolecular complexes with nucleic acids, carbohydrates, or other proteins. The interest in the structures of membrane proteins, structural proteins, and proteins in complexes provides many opportunities for the further development and application of NMR spectroscopy. Our understanding of polypeptides associated with lipids in membranes, in particular, is primitive, especially compared to that for globular proteins. This is largely a consequence of the experimental difficulties encountered in their study by conventional NMR and X-ray approaches. Fortunately, the principal features of two major classes of membrane proteins have been identified from studies of several tractable examples. Bacteriorhodopsin (Henderson et al., 1990), the subunits of the photosynthetic reaction center (Deisenhofer et al., 1985), and filamentous bacteriophage coat proteins (Shon et al., 1991; McDonnell et al., 1993) have all been shown to have long transmembrane hydrophobic helices, shorter amphipathic bridging helices in the plane of the bilayers, both structured and mobile loops connecting the helices, and mobile N- and C-terminal regions.

Chemical synthesis of GDP-fucose analogs and their utilization by the Lewis *A(1 → 4) fucosyltransferase

1990 ◽  
Vol 68 (7) ◽  
pp. 1063-1071 ◽  
Author(s):  
Uday B. Gokhale ◽  
Ole Hindsgaul ◽  
Monica M. Palcic
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Synthesis ◽  
Human Milk ◽  
Immunosorbent Assay ◽  
Spectrophotometric Assay ◽  
Enzyme Linked Immunosorbent Assay ◽  
Elisa Assay ◽  
Oligosaccharide Synthesis ◽  
H Nmr ◽  
Nucleotide Analog

Chemical syntheses are reported for GDP-fucose (5), GDP-3-deoxy-fucose (6), and GDP-arabinose (7), the demethyl analog of 5. All three sugar nucleotides were found to act as donor substrates for an α(1 → 4) fucosyltransferase isolated from human milk when *BDGal(1 → 3)*BDGlcNAc-O(CH2)8COOMe (1) was used as the acceptor. The rate of transfer of sugar residues to 1 was measured using a coupled spectrophotometric assay and was found to be 100% (5), 2.3% (6), and 5.9% (7). The product Lea-active oligosaccharide analogs were identified by both an enzyme-linked immunosorbent assay (ELISA) and by 1H NMR spectroscopy. Keywords: glycosyltransferase, oligosaccharide synthesis, sugar-nucleotide analog, ELISA assay, fucosyltransferase.

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