A reliable and convenient method for determining the configuration and conformation of the furanose ring in carbohydrates and nucleosides by vibrational circular dichroism (VCD) spectroscopy is described. Diastereomeric pairs of several furanose monosaccharides and nucleosides were prepared, and their VCD spectra were analyzed. The results revealed that VCD spectroscopy elucidates the equibrated state of the furanose ring puckers, which is often difficult to study by other techniques.
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http://dx.doi.org/10.1021/acs.orglett.6b03626 | DOI Listing |
NAR Genom Bioinform
December 2024
Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
We have subjected several analogs of DNA that have been widely used as antisense oligonucleotide (ASO) inhibitors of gene expression to comparative molecular dynamics (MD) calculations of their ability to form duplexes with DNA and RNA. The analogs included in this study are the phosphorothioate (PS), peptide nucleic acid (PNA), locked nucleic acid (LNA), morpholino nucleic acid (PMO), the 2'-OMe, 2'-F, 2'-methoxyethyl (2'-MOE) and the constrained cET analogs, as well as the natural phosphodiester (PO) as control, for a total of nine structures, in both XNA-DNA and XNA-RNA duplexes. This is intended as an objective criterion for their relative ability to duplex with an RNA complement and their comparative potential for antisense applications.
View Article and Find Full Text PDFJ Am Chem Soc
November 2024
Department of Physics, Hong Kong University of Science and Technology, Hong Kong 999077, China.
How life started on Earth is an unsolved mystery. There are various hypotheses for the location ranging from outer space to the seafloor, subseafloor, or potentially deeper. Here, we applied extensive ab initio molecular dynamics simulations to study chemical reactions between NH, HO, H, and CO at pressures () and temperatures () approximating the conditions of Earth's upper mantle (i.
View Article and Find Full Text PDFAMB Express
September 2024
Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.
The GDS(L)-like lipase from the Basidiomycota Pleurotus sapidus (PSA_Lip) was heterologously expressed using Trichoderma reesei with an activity of 350 U L. The isoelectric point of 5.0 was determined by isoelectric focusing.
View Article and Find Full Text PDFJ Phys Chem A
March 2024
ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
This study presents a comprehensive analysis of the vibrational spectra of methyl-β-D-ribofuranoside. Employing a combination of inelastic neutron scattering, Raman, and infrared spectroscopy allows for the observation of all modes regardless of the selection rules. The experimental techniques were complemented by density functional theory computational methods using both gas-phase () and solid-state (, ) approaches to provide an unambiguous assignment of the defining vibrational features.
View Article and Find Full Text PDFCurr Protoc
September 2023
Graduate School of Pharmaceutical Science, Tokushima University, Shomachi, Tokushima, Japan.
Cyclic diadenosine monophosphate (c-di-AMP) is a bacterial cyclic dinucleotide (CDN) comprising two adenosine monophosphates covalently linked by two 3',5'-phosphodiester bonds. c-di-AMP works as a second messenger, regulating many biological processes in bacteria such as cell wall homeostasis, DNA integrity, and sporulation via specific protein and/or RNA receptors. Moreover, c-di-AMP can function as an immunomodulatory agent in eukaryote cells via the stimulator of interferon genes (STING) signaling pathway.
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