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23 protocols using icon nmr

1

NR, NAR, NRH, and NARH Characterization in Biofluids

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NRH, NAR and NARH were custom synthesized as described previously [29 (link)]. Twelve individual solutions of NR, NAR, NRH, and NARH were prepared in water, DMEM, and blood plasma. The concentration of NR, NAR, and NRH stock solutions in water and DMEM was 55 mM, while the concentration of the NARH stock solution in water and DMEM was 30 mM. In plasma, the stock solution was ten times diluted (5.5 and 3.0 mM, respectively) as compared to water and DMEM media. A 450 mL volume of solution was mixed with 50 μL of D2O, and the resulting mixture was vortexed three times. NMR spectral acquisition (ns = 8) was then performed in water suppression mode using a Bruker Avance III HD NMR spectrometer equipped with a 400 MHz magnet Ultrashield Plus, with temperature fixed to 300 K for all NMR measurements. TopSpin 3.2 (Bruker BioSpin (Billerica, MA, USA)) was used for all NMR spectral acquisition and preprocessing, and the automation of sample submission was performed using ICON-NMR (Bruker BioSpin). All samples were automatically shimmed. The FID was processed automatically using ICON-NMR (Bruker BioSpin), and phasing was refined manually. The solutions were examined at 1, 12, and 24 h by 1H NMR analysis. Chemical shift allocations for the individual compounds are shown in Figure S5.
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2

NRH Quantification in Cell Culture

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The supernatants were examined at 0, 1, and 24 h by 1H NMR analysis for the presence of any remaining NRH after supplementation at 100 μM in HEK293T and HepG3. Samples were prepared as follows: 450 μL of cell culture supernatant was mixed with 50 μL of D2O, and the resulting mixture was vortexed three times. NMR spectral acquisition (ns = 2048) was then performed using a Bruker Avance III HD NMR spectrometer equipped with 400 MHz magnet Ultrashield Plus, with temperature fixed to 300 K for all NMR measurements. TopSpin 3.2 (Bruker BioSpin) was used for all NMR spectral acquisition and preprocessing, and the automation of sample submission was performed using ICON-NMR (Bruker BioSpin). All samples were automatically shimmed. The FID were processed automatically using ICON-NMR (Bruker BioSpin), and phasing was refined manually. NRH, NR, and nicotinamide were all detected (S1 Fig). NRH is oxidized to NR in aqueous solution over time, while nicotinamide is present at ~16 μM in DMEM. Nicotinamide accumulates in the media over time as NRH is consumed by the cells.
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3

NMR Spectroscopy for Metabolite Identification

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All measurements were performed on a Bruker Avance III 600 Ascend NMR spectrometer (Bruker, Ettlingen, Germany), operating at 600.13 MHz for 1H observation, equipped with a TCI cryoprobe incorporating a z axis gradient coil and automatic tuning-matching (ATM). Experiments were acquired at 300 K in automation mode after loading individual samples by a Bruker Automatic Sample Changer, interfaced with the software IconNMR (Bruker). For each sample a 1D sequence with pre-saturation and composite pulse for selection (zgcppr Bruker standard pulse sequence) was acquired, with 16 transients, 16 dummy scans, 5 s relaxation delay, size of fid of 64K data points, a spectral width of 12019.230 Hz (20.0276 ppm) and an acquisition time of 2.73 s. The resulting FIDs were multiplied by an exponential weighting function corresponding to a line broadening of 0.3 Hz before Fourier transformation, automated phasing and baseline correction. Metabolite identification were based on 1H and 13C assignment by 1D and 2D omo and eteronuclear experiments and by comparison with literature data [19 (link),26 (link),47 (link),48 (link),49 (link)]. NMR data processing was performed by using TopSpin 3.5 (Bruker). All spectra were referenced to the TSP signal (δ = 0.00 ppm).
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4

NMR Stability Analysis of Aqueous NRH

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NRH was dissolved in water and kept in single-use aliquots at −80ºC. After 2 months, the samples were tested for their stability. The samples were prepared for NMR analysis as follows: aqueous NRH solution (450 μl) was mixed with D2O (50 μl), and the resulting mixture was vortexed three times. NMR spectral acquisition (ns = 16) was then performed using a Bruker Avance III HD NMR spectrometer equipped with 400 MHz magnets Ultrashield Plus, with temperature fixed to 300 K NMR measurements. TopSpin 3.2 (Bruker BioSpin) was used for NMR spectral acquisition and preprocessing, and the automation of sample submission was performed using ICON-NMR (Bruker BioSpin). The samples were automatically shimmed.
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5

NMR Spectral Monitoring of Monomer Concentration

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The monomer concentration was estimated from the decrease of the NMR spectrum signal. A sample was placed in a glass tube with an inner diameter of 5 mm and incubated at 25 °C. NMR spectra were measured using AVANCE III HD with a superconducting magnet with a Larmor frequency of 400.13 MHz (Bruker, Germany). The spectrometer was controlled using the programs of Topspin 1.5 and IconNMR (Bruker). High homogeneity of the magnetic field was achieved by Topspim, a routine tool built by Topspin 1.5, and a pulse program, zgesgp, was used for spectral measurements.
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6

Quantitative 1H NMR Metabolite Analysis

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1H NMR spectra were acquired using a Bruker 600 or 900 MHz spectrometer equipped with a TCI H/F-cryogenic probe. Samples (pH 6.9 ± 0.1) were mixed 1:1 (v/v) with D2O containing TSP (1.0 mM [22 (link)]). Each spectrum represents the average of 64 spectra acquired using a 1D pulse sequence that included a 4.0 s relaxation delay and 2.73 s acquisition time. Water suppression was accomplished using Excitation Sculpting [23 ]. Samples were equilibrated, and spectra were acquired at 298 ± 2 °K. 600 MHz spectra were collected using the Bruker automated acquisition software ICON-NMR and SampleJet. Peaks were fit to a Lorentzian peak shape using TopSpin3.5 [24 (link)]. Metabolite concentrations were determined by normalizing their peak areas to that of the TSP signal [24 (link)].
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7

NMR Spectroscopy of Lipid Extracts

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All measurements were performed on a Bruker Avance III 600 Ascend NMR spectrometer (Bruker, Hamburg, Germany) operating at 600.13 MHz for 1H observation, equipped with a z axis gradient coil and automatic tuning-matching (ATM). Experiments were acquired at 300 K in automation mode after loading individual samples on a Bruker Automatic Sample Changer, interfaced with the software IconNMR (Bruker). For each lipid extract a one-dimensional experiment (zg Bruker pulse program) was run with 64 scans, 64 K time domain, spectral width 20.0276 ppm (12,019.230 Hz), 3 s delay, p1 10 µs and 2.73 s acquisition time. All spectra were referenced to the tetramethylsilane (TMS) signal (δ = 0.00 ppm). 31P NMR spectra (zg0pg Bruker pulse program) were acquired with a spectral width of 50.1172 ppm (12,175.324 Hz), p1 11 µs, 3 s delay and 1.34 s acquisition time and referenced to H3PO4 as external standard. The metabolites were assigned on the basis of 2D NMR spectra analysis (2D 1H JRES, 1H COSY, 1H-13C HSQC and HMBC) and comparison with published data [18 (link),23 (link),37 (link),38 (link)].
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8

NMR Analysis of Promising Fraction

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1H NMR analysis of the promising fraction (F6) was performed using a Bruker Ascend system (1H operating frequency of 400 MHz) equipped with a sample changer and a gradient inverse triple-resonance 5 mm probe-head (Bruker Biospin). NMR sample was prepared by dissolving appx. 5 mg of CH-F6 in 0.7 mL D2O containing 0.05 wt. % TMSP-d4 sodium salt as an internal standard. IconNMR (version 4.2, Bruker Biospin) was used for controlling automated acquisition of NMR data (temperature equilibration to 300 K, optimization of lock parameters, gradient shimming, and setting of receiver gain), and processing of NMR data was performed using Topspin (version 3.0, Bruker Biospin). The one-dimensional 1H NMR spectra were acquired using 30° pulses, 4 s acquisition time, 1 s relaxation delay and 32 K data points. The data points were zero-filled to 64 K and multiplied with an exponential function (line-broadening = 0.3 Hz) prior to Fourier transformation.
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9

Phosphorolysis of NR+ Cl- Compounds

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Phosphorolysis of NR+ Cl and its glycine conjugate (12a, Gly-NR) by PNP (Purine Nucleoside Phosphorylase, Sigma Aldrich) was performed in HEPES buffer, containing KH2PO4 and 10% D2O at 25 °C and was monitored by 1H NMR. All spectra were obtained at 300 K on a Bruker AscendTM 400 MHz ultra-shielded spectrometer (Bruker Biospin) operating at 400.13 MHz for protons. TopSpin 3.2 (Bruker BioSpin) was used for all NMR spectral acquisition and pre-processing. The automation of sample submission was performed using ICON-NMR (Bruker BioSpin). Incubations were conducted in the NMR tube which contained a final volume of 505 μl : 450 μl HEPES buffer (100.0 mM, pH 7.0), containing 100 mM KH2PO4, 50.0 μl NR-Cl or NR glycine conjugate (50.0 mM in 1 mL D2O) and when appropriate 5 μl PNP (1 mg dissolved in 50 μl HEPES buffer) and measurements taken at t = 0, 20 min and 6 h (ns = 128). For each independent experiment, freshly prepared solutions of NR-Cl and NR glycine conjugate in HEPES buffer, containing 100 mM KH2PO4 and 50 μl D2O, were used.
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10

NMR Characterization of Compounds

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All compounds were characterized by nuclear magnetic resonance (NMR) spectroscopy to confirm their molecular identity. 1H spectra were recorded with a Bruker 600 MHz NEO600 spectrometer operating at room temperature. Spectra were observed from compounds dissolved in deuterated chloroform (CDCl3). Spectral analysis is carried out in ICONNMR (Bruker) and Mestre Nova (Version 12.0.0–2 000 080, Metrelab Research).
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