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34 protocols using topspin version 3

1

NMR Spectroscopy of Metabolites in D2O

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Deuterium oxide (D2O, 99.9% D) and 3-trimethylsilyl-2H4-propionic acid sodium salt (TSP) were purchased from Cambridge Isotope Laboratories, Inc. (Miami, U.S.A.) and from Sigma-Aldrich (St. Louis, MO). Spectra were obtained from solutions in D2O (580 µL plus 20 µL of TSP 1 mg/mL at 30 °C, using TSP as reference (δ = 0.00 ppm), using a Bruker AVANCE III NMR spectrometer operating at 14.1 Tesla (600.13 MHz for 1H) equipped with a QXI probe with gradient on the z-axis (Bruker Biospin, Germany). 2D 13C/1H multiplicity-edited HSQC NMR experiments were carried out using heteronuclear correlation via double inept transfer with decoupling during acquisition, using trim pulses in inept transfer with multiplicity editing during the selection step (hsqcedetgpsisp2.2). The 2D HSQC experiments were recorded for quadrature detection in the indirect dimension, using 8 scans per series of 2 K × 256 W data points with zero filling in F1 (4 K) prior to Fourier transformation42 (link). Data processing and integration were performed using the software Topspin version 3.1 (Bruker Biospin, Rheinstetten, Germany). 13C/1H correlations were assigned according to Nascimento et al.11 (link).
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2

NMR Analysis of Polysaccharide Samples

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Vacuum dried polysaccharide samples were solubilized in 0.65 mL of deuterium oxide (99.9 % atom D, Sigma Aldrich) to reach a final concentration ranging from 8 to 15 mg/mL and transferred to 5-mm NMR tubes (Wilmad). 1H and 13C NMR spectra were acquired using a 5-mm broadband probe on Bruker Avance III 400 or 500 MHz spectrometers, equipped with a high precision temperature controller. Data acquisition and processing were performed using TopSpin version 3.1 (Bruker).
1H NMR experiments were acquired at 25 +/- 0.1 °C using a mono-dimensional standard pulse-program with 32k data points over a 10 ppm spectral width, accumulating 128 scans. The spectra were weighted with 0.2 Hz line broadening and Fourier-transformed. The transmitter was set at the water frequency, which was used as the reference signal (4.79 ppm).
To obtain 13C spectra with adequate signal-to-noise ratio, all data were acquired using distortionless enhancement by polarization transfer (DEPT). DEPT experiments were collected at pulse angle of 3π/4 at 25 ± 0.1 °C, accumulating a number of scans > 16,384. The transmitter was set at the ethanol frequency which was used as the reference signal (17.47 ppm). All mono-dimensional proton NMR spectra were obtained in quantitative manner using a total recycle time to ensure full recovery of each signal (5 x Longitudinal Relaxation Time T1).
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3

NMR-based Determination of Pectin Methylation

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Mono-dimensional 1H-NMR measurements were performed at 353 °K on a Bruker AVANCE I instrument equipped with a 5-mm probe operating at 400.2 MHz (Bruker, Billerica, MA, USA). A total of 3 mg of polymer was dissolved in 0.5 mL of D2O, and 32 scans were recorded. Chemical shifts of the protons were expressed as δ (ppm) using H2O at 4.25 ppm at 80 °C as reference. The data were collected and processed using the Software TOPSPIN, version 3.1 (Bruker Biospin, Rheinstetten, Germany).
The degree of methyl-esterification (DM) values was determined by 1H-NMR spectroscopy, integrating the hydrogen areas corresponding to -CH3 at 3.9 ppm, H-1 (5.1–5.3 ppm), H-5 of unesterified α-D-GalAp units at 4.7 ppm, and H-5′ of esterified α-D-GalAp units at 5 ppm, as discussed by Grasdalen, Bakøy, and Larsen [21 (link)]. The hydrogen from -CH3 around 3.9 ppm gives DM, using H-1 integral as reference [22 (link)]. Nevertheless, the H-1 signal of Gal-A units is very near the H-1 of arabinogalactan. The DM % is also determined by the ratio of -CH3 using (H-5 + H-5′) integrals or from the ratio H-5′/(H-5 + H-5′) with a relatively good accordance.
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4

NMR Spectroscopy of Polysaccharide Characterization

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Mono-dimensional ( 1 H-) and bi-dimensional (HSQC) NMR spectra were acquired at 70 °C with a Bruker AVANCE III 400 MHz or Bruker AVANCE III HD 600 MHz spectrometers, equipped with a BBI 5 mm probe (400 MHz) or with a 5 mm CPP-TCI probe (600 MHz) (Bruker, Billerica, Massachusetts, USA).
The samples were solubilized in D2O and the chemical shifts of the polysaccharide were expressed as δ (ppm), using the resonances of -CH3 groups of acetone ( 1 H at δ 2.22; 13 C at δ 30.20) as internal references. The data were collected and processed using the Software TOPSPIN, version 3.1 (Bruker Biospin, Rheinstetten, Germany).
Complementary 1 H NMR measurements were performed at 353 K on a Bruker AVANCE I instrument equipped with a 5 mm probe operating at 400.2 MHz. An amount of 3 mg of polymer was dissolved in 0.5 mL of D2O, and 32 scans were recorded. Chemical shifts are expressed using H2O at 4.25 ppm at 80 °C as reference.
The values of degree of methyl-esterification (DM) were determined by 1 H-NMR spectroscopy integrating the hydrogen areas corresponding to H-1, H-5 of unesterified α-D-GalAp units and H-5 of esterified α-D-GalAp units as discussed by Grasdalen, Bakøy, & Larsen, 1988 (link). The hydrogen from -CH3 around 3.76 ppm gives DM using H-1 integral as reference (Patova et al., 2019) (link).
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5

NMR Spectroscopy of Glycosidic Compound

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1H-NMR and 13C NMR spectroscopy of about 3 mM Q3O-(Glc)-Gal in d6-DMSO was performed at 600 MHz 1H frequency. Chemical shifts were referenced to tetramethylsilane. Data was processed using Topspin version 3.2 (Bruker, Karlsruhe, Germany).
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6

NMR Structural Characterization Protocol

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NMR experiments were performed using a 600 MHz (1H) Bruker Avance III spectrometer with a 5 mm QCI-F cryoprobe. Assignments were completed using DQF-COSY, TOCSY (20 ms and 80 ms mixing times), NOESY (500 ms mixing time), 13C-HSQC-TOCSY, 13C,1H-HSQC and 13C,1H-HMBC experiments with WaterGATE or excitation sculpting water suppression on 0.1-1 mM samples dissolved in deuterium oxide. All 13C data was obtained using natural isotopic abundance. Data were processed and analysed using Bruker Topspin version 3.2 and CCPN analysis. 1H Chemical shift referencing was based on the position of the water resonance, 13C referencing used 1H/13C gyromagnetic ratios to define indirect carrier position (Wishart and Case, 2001 (link)) and all data were obtained at 25°C.
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7

HRMS and 2D NMR Characterization Protocol

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HRMS data were obtained by a LC-HRMS system that by all practical means was identical to the Agilent-system described above, a Bruker micrOTOF-Q II mass spectrometer equipped with an electrospray ionization source (Bruker Daltonik GmbH, Bremen, Germany) operated in the positive ionization mode at 200 °C with a corona potential of 4 kV, a nebulizer pressure of 2.0 bar, and a drying gas flow of 7 L/min. Two-dimensional COSY, ROESY, HSQC, H2BC and HMBC NMR spectra (Bruker’s standard pulse sequences, 600.13 for 1H, 150.90 for 13C) were recorded on the above-mentioned instrument with 1H spectral widths of 12 ppm, and either 170 (HSQC, H2BC) or 240 ppm (HMBC) for 13C. The number of data points was 2 k in F2 and 128 (HMBC, H2BC, and ROESY), 256 (HSQC), or 512 (COSY) in F1. ROESY was obtained with 300 ms spinlock, HMBC with 62.5 ms evolution delay for nJCH of 8 Hz, H2BC with 22 ms for evolution of JHH and HSQC was optimized for a 1JCH of 145 Hz. Relaxation delays were set to 1.0 s, except for the ROESY experiment, where the relaxation delay was set to 2.0 s. Data processing was performed using Topspin, version 3.2 (Bruker BioSpin, Rheinstetten, Germany), and spin simulations were performed in NMR-SIM (Bruker BioSpin, Rheinstetten, Germany).
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8

NMR Spectroscopy of G-Quadruplex RNA

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The one-dimensional 1H NMR spectra were mostly recorded at 308 K on Bruker 700-MHz spectrometers equipped with a regular probe. RNA samples were dissolved in 5 mM Potassium Cacodylate (Kcaco) (pH 6.5), 50 mM KCl, and 10% D2O at a final concentration of 300 μM. The NMR data were processed with Bruker TopSpin Version 3.2 and MestReNova. Formation of the G4 structure was demonstrated by the presence of an imino proton peak in the 10–11.5 ppm region of the 1H NMR spectrum, which is highly characteristic of the Hoogsteen hydrogen bonds of G4 (42 (link)).
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9

NMR Study of VIN3 Proteins Binding to Histone H3

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For NMR spectroscopy, A. thaliana VIN3150-208 and P. dactilyfera VIN3123-326 were expressed in M9 minimal medium supplemented with 0.4% glucose, antibiotics, trace elements, 25 ml overnight culture, and 2 g of 15N-H4Cl per liter of expression culture. Cultures were grown and processed essentially as described before. NMR samples containing 50 μM 15N-labeled VIN3150-208 or VIN3123-326 were prepared in aqueous buffer (25 mM Tris pH 8, 150 mM NaCl, and 1 mM DTT). The 50 μM 15N-labeled VIN3150-208 or VIN3123-326 was incubated with 0.5 mM histone H3 peptides resuspended in 25 mM Tris pH 8, 150 mM NaCl, and 1 mM DTT for >30 min before measurement. Spectra were recorded on a Bruker Avance-III spectrometer operating at 600 MHz 1H frequency and equipped with a 5 mm inverse detection cryogenic probe. BEST-TROSY shift correlation experiments (45 (link)) were acquired with 256 × 1024 points in t1 and t2, respectively. Spectra were processed in TopSpin version 3.2 (Bruker), with linear prediction in t1, giving a digital resolution of 2.2 and 8.2 Hz/point in the processed data.
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10

Nuclear Magnetic Resonance Spectroscopy Protocol

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Proton and 13C spectra were measured using a Bruker Avance III 400 MHz NMR instrument (Bruker, Billerica, Massachusetts, USA). Samples were dissolved in 500 μL D2O in 5 mm NMR tubes. Analysis of spectra was performed using the TopSpin version 3.2 software package (Bruker, Billerica, Massachusetts, USA).
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