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Molecules (Basel, Switzerland) Sep 2022The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental DO. In this...
The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental DO. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between DO and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing DO proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and DO and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and DO. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules.
Topics: DNA, Single-Stranded; Deuterium; Deuterium Oxide; G-Quadruplexes; Spectrum Analysis, Raman
PubMed: 36144761
DOI: 10.3390/molecules27186023 -
Journal of Chromatography. A Jan 2023Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest...
Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest possible, the so-called quench conditions of low pH and low temperature. To retain maximum deuterium, separation must also be done as quickly as possible. The low temperature (0 °C) of quench conditions complicates the separation and leads primarily to a reduction in separation quality and an increase in chromatographic backpressure. To improve the separation in HDX MS, one could use a longer gradient, smaller particles, a different separation mechanism (for example, capillary electrophoresis), or multi-dimensional separations such as combining ion mobility separation with reversed-phase separation. Another way to improve separations under HDX MS quench conditions is to use a higher flow rate where separation efficiency at 0 °C is more ideal. Higher flow rates, however, require chromatographic systems (both pumps and fittings) with higher backpressure limits. We tested what improvements could be realized with a commercial UPLC/UHPLC system capable of ∼20,000 psi backpressure. We found that a maximum flow rate of 225 µL/min (using a 1 × 50 mm column packed with 1.8 µm particles) was possible and that higher flow rate clearly led to higher peak capacity. HDX MS analysis of both simple and particularly complex samples improved, permitting both shorter separation time, if desired, and providing more deuterium recovery.
Topics: Hydrogen Deuterium Exchange-Mass Spectrometry; Deuterium; Deuterium Exchange Measurement; Mass Spectrometry; Peptides; Hydrogen
PubMed: 36586285
DOI: 10.1016/j.chroma.2022.463742 -
International Journal of Medical... 2022Heavy water is an ideal contrast agent for metabolic activity and can be adapted to a wide range of biological systems owing to its non-invasiveness, universal... (Review)
Review
Heavy water is an ideal contrast agent for metabolic activity and can be adapted to a wide range of biological systems owing to its non-invasiveness, universal applicability, and cost-effectiveness. As a new type of probe, the heavy isotope of water has been widely used in the study of cell development, metabolism, tissue homeostasis, aging, and tumor heterogeneity. Herein, we review findings supporting the applications of and research on heavy water in monitoring of bacterial metabolism, rapid detection of drug sensitivity, identification of tumor cells, precision medicine, and evaluation of skin barrier function and promote the use of heavy water as a suitable marker for the development of detection and treatment methodologies.
Topics: Bacteria; Deuterium Oxide; Spectrum Analysis, Raman; Water
PubMed: 35928718
DOI: 10.7150/ijms.73150 -
Molecules (Basel, Switzerland) Apr 2022This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on... (Review)
Review
This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on chemical shifts can be used to elucidate the importance of either intra- or intermolecular hydrogen bonding in ionic liquids, of ammonium ions in a confined space, how isotope effects can help define dimers, trimers, etc., how isotope effects can lead to structural parameters such as distances and give information about ion pairing. Tautomerism is by advantage investigated by isotope effects on chemical shifts both in symmetric and asymmetric systems. The relationship between hydrogen bond energies and two-bond deuterium isotope effects on chemical shifts is described. Finally, theoretical calculations to obtain isotope effects on chemical shifts are looked into.
Topics: Deuterium; Hydrogen Bonding; Magnetic Resonance Spectroscopy
PubMed: 35458603
DOI: 10.3390/molecules27082405 -
Cancer Control : Journal of the Moffitt... 2021The effects of deuterium-depleted water (DDW) containing deuterium (D) at a concentration of 25 parts per million (ppm), 50 ppm, 105 ppm and the control at 150 ppm were...
The effects of deuterium-depleted water (DDW) containing deuterium (D) at a concentration of 25 parts per million (ppm), 50 ppm, 105 ppm and the control at 150 ppm were monitored in MIA-PaCa-2 pancreatic cancer cells by the real-time cell impedance detection xCELLigence method. The data revealed that lower deuterium concentrations corresponded to lower MiA PaCa-2 growth rate. Nuclear membrane turnover and nucleic acid synthesis rate at different D-concentrations were determined by targeted [1,2-C]-D-glucose fate associations. The data showed severely decreased oxidative pentose cycling, RNA ribose C labeling from [1,2-C]-D-glucose and nuclear membrane lignoceric (C24:0) acid turnover. Here, we treated advanced pancreatic cancer patients with DDW as an extra-mitochondrial deuterium-depleting strategy and evaluated overall patient survival. Eighty-six (36 male and 50 female) pancreatic adenocarcinoma patients were treated with conventional chemotherapy and natural water (control, 30 patients) or 85 ppm DDW (56 patients), which was gradually decreased to preparations with 65 ppm and 45 ppm deuterium content for each 1 to 3 months treatment period. Patient survival curves were calculated by the Kaplan-Meier method and Pearson correlation was taken between medial survival time (MST) and DDW treatment in pancreatic cancer patients. The MST for patients consuming DDW treatment (n = 56) was 19.6 months in comparison with the 6.36 months' MST achieved with chemotherapy alone (n = 30). There was a strong, statistically significant Pearson correlation (r = 0.504, p < 0.001) between survival time and length and frequency of DDW treatment.
Topics: Cell Proliferation; Deuterium; Female; Humans; Male; Nuclear Envelope; Pancreatic Neoplasms; RNA
PubMed: 33760674
DOI: 10.1177/1073274821999655 -
Philosophical Transactions of the Royal... Aug 2020To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty... (Review)
Review
To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty acid composition analyses. Compound-specific stable isotope analysis (CSIA) of fatty acids combines both of these tools into an even more powerful method with the capacity to broaden our understanding of food web ecology and nutritional dynamics. Here, we provide an overview of the potential that CSIA studies hold and their constraints. We first review the use of fatty acid CSIA in ecology at the natural abundance level as well as enriched physiological tracers, and highlight the unique insights that CSIA of fatty acids can provide. Next, we evaluate methodological best practices when generating and interpreting CSIA data. We then introduce three cutting-edge methods: hydrogen CSIA of fatty acids, and fatty acid isotopomer and isotopologue analyses, which are not yet widely used in ecological studies, but hold the potential to address some of the limitations of current techniques. Finally, we address future priorities in the field of CSIA including: generating more data across a wider range of taxa; lowering costs and increasing laboratory availability; working across disciplinary and methodological boundaries; and combining approaches to answer macroevolutionary questions. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
Topics: Carbon Isotopes; Deuterium; Ecology; Fatty Acids; Food Chain; Nitrogen Isotopes
PubMed: 32536315
DOI: 10.1098/rstb.2019.0641 -
Journal of Medicinal Chemistry Apr 2023Covalent ligands are generally filtered out of chemical libraries used for high-throughput screening, because electrophilic functional groups are considered to be...
Covalent ligands are generally filtered out of chemical libraries used for high-throughput screening, because electrophilic functional groups are considered to be pan-assay interference compounds (PAINS). Therefore, screening strategies that can distinguish true covalent ligands from PAINS are required. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for evaluating protein stability. Here, we report a covalent modifier screening approach using HDX-MS. In this study, HDX-MS was used to classify peroxisome proliferator-activated receptor γ (PPARγ) and vitamin D receptor ligands. HDX-MS could discriminate the strength of ligand-protein interactions. Our HDX-MS screening method identified LT175 and nTZDpa, which can bind concurrently to the PPARγ ligand-binding domain (PPARγ-LBD) with synergistic activation. Furthermore, iodoacetic acid was identified as a novel covalent modifier that stabilizes the PPARγ-LBD.
Topics: Hydrogen Deuterium Exchange-Mass Spectrometry; Deuterium; Ligands; PPAR gamma; Mass Spectrometry; Deuterium Exchange Measurement
PubMed: 36994595
DOI: 10.1021/acs.jmedchem.2c01986 -
Journal of Labelled Compounds &... Apr 2022Base catalysed exchange with sodium hydroxide, calcium oxide or N,N,N,N-tetramethylguanidine in deuterium oxide is a viable procedure for the preparation of terminally...
Base catalysed exchange with sodium hydroxide, calcium oxide or N,N,N,N-tetramethylguanidine in deuterium oxide is a viable procedure for the preparation of terminally deuterated alkynes for those alkynes stable to strong base. The use of silver perchlorate as a catalyst is an alternative practical option when labelling alkynes which are sensitive to base or contain functionalities which would lead to labelling elsewhere in the molecule. Labelling with this catalyst takes place smoothly at ambient temperature in a mixture of N,N-dimethylformamide and deuterium oxide.
Topics: Alkynes; Catalysis; Deuterium
PubMed: 35067956
DOI: 10.1002/jlcr.3963 -
Drug Discovery Today Aug 2020An original approach to drug discovery and development is now in clinical and preclinical trials. The approach is based on the 'kinetic isotope effect' (i.e., the effect... (Review)
Review
An original approach to drug discovery and development is now in clinical and preclinical trials. The approach is based on the 'kinetic isotope effect' (i.e., the effect of isotopic substitution on chemical reaction rates). By replacing selective hydrogen atoms with deuterium in essential and conditionally essential lipids, a novel class of potent drugs is being created that prevents cellular and vascular oxidative damage causing diverse pathologies, such as neurodegeneration, atherosclerosis and macular degeneration. This review describes the molecular mechanisms underlying the new treatment modalities in these diseases and the encouraging results of ongoing studies for candidate drugs. Also, the possible extension of this new drug platform to treatment of nonoxidative diseases by deuterium-reinforced amino acids and nucleobases is briefly discussed.
Topics: Animals; Atherosclerosis; Deuterium; Humans; Lipids; Nerve Degeneration; Retinal Degeneration
PubMed: 32247036
DOI: 10.1016/j.drudis.2020.03.014 -
International Journal of Molecular... Mar 2022Much of the work probing antimicrobial peptide (AMP) mechanisms has focussed on how these molecules permeabilize lipid bilayers. However, AMPs must also traverse a... (Review)
Review
Much of the work probing antimicrobial peptide (AMP) mechanisms has focussed on how these molecules permeabilize lipid bilayers. However, AMPs must also traverse a variety of non-lipid cell envelope components before they reach the lipid bilayer. Additionally, there is a growing list of AMPs with non-lipid targets inside the cell. It is thus useful to extend the biophysical methods that have been traditionally applied to study AMP mechanisms in liposomes to the full bacteria, where the lipids are present along with the full complexity of the rest of the bacterium. This review focusses on what can be learned about AMP mechanisms from solid-state NMR of AMP-treated intact bacteria. It also touches on flow cytometry as a complementary method for measuring permeabilization of bacterial lipid membranes in whole bacteria.
Topics: Antimicrobial Cationic Peptides; Antimicrobial Peptides; Bacteria; Cell Membrane; Deuterium; Lipid Bilayers
PubMed: 35269882
DOI: 10.3390/ijms23052740