Avance 3 hd spectrometer

Manufactured by Bruker

Sourced in Germany, United States, Canada, Switzerland, United Kingdom

The Avance III HD spectrometer is a high-performance nuclear magnetic resonance (NMR) instrument designed for laboratory applications. The core function of the Avance III HD is to provide accurate and precise measurements of the chemical and physical properties of samples through the detection and analysis of nuclear magnetic resonances.

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Close spelling variants of this product

AVANCE III HD 400 NMR spectrometer A8 Avance III HD 800 MHz NMR spectrometer Avance III HD Ascend 400 MHz spectrometer Avance III HD 600 MHz NMR spectrometer AVANCE™ III HD 300 MHz spectrometer Avance III HD 14.1 T spectrometer Avance III HD 800 MHz NMR spectrometer Avance III HD Nanobay spectrometer Avance III HD 500 spectrometer AVANCE III HD 600 spectrometer

198 protocols using avance 3 hd spectrometer

NMR Characterization of Amyloid-Beta Tetramer

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All experiments were carried out at 37 °C on a 900 MHz Bruker Avance III HD spectrometer equipped with a 5-mm CP-TCI cryogenic probe, or an 800 MHz Bruker Avance III HD spectrometer equipped with a 3-mm CP-TCI cryogenic probe, both instruments located at the Swedish NMR Centre in Gothenburg, or an 800 MHz Bruker Avance III HD spectrometer equipped with a 5-mm CP-TCI cryogenic probe, located at IECB in Bordeaux.
For the resonance assignment of backbone atoms of the Aβ(1-42) tetramer prepared in DPC micelles, experiments from the standard Bruker library were recorded (HNCA, HNCACB, HNCO, and HN-NH NOESY). For the resonance assignment of methyl groups, experiments from the standard Bruker library were recorded (Hme)Cme([C]CA)CO, (Hme)Cme([C]CA)NH, Hme(Cme[C]CA)NH^{44 (link)} and complemented with (H)C-TOCSY-C-TOCSY-(C)H experiments⁴⁵. Additionally, four 3D SOFAST-NOESY-HMQC experiments^{44 (link)} were recorded to obtain NOE correlation between methyl groups (Hm-HmCm and Cm-HmCm) and between methyl and amide protons (Hm-NH and Cm-HN) of the Aβ(1-42) tetramer in DPC micelles. The acquisition parameters for all the NMR experiments carried out are summarized in Supplementary Table 5. All these experiments were acquired using non-uniform sampling (NUS) using TopSpin 3.5, processed with MDDNMR 2.5 software^{45 ,46 (link)}, and analyzed using CCPNmr Analysis 2.4.2.

Ciudad S., Puig E., Botzanowski T., Meigooni M., Arango A.S., Do J., Mayzel M., Bayoumi M., Chaignepain S., Maglia G., Cianferani S., Orekhov V., Tajkhorshid E., Bardiaux B, & Carulla N. (2020). Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. Nature Communications, 11, 3014.

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NMR Spectroscopy Protocol for Protein Structure Characterization

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Two sets of NMR experiments were recorded. The first was done at 25° C on a 700MHz Bruker AVANCE III-HD spectrometer equipped with 5mm CP-TCI probe. The second was performed at 20° C on an 800MHz Bruker AVANCE III-HD spectrometer equipped with 3mm CP-TCI probe. At both temperatures, the TA procedure was implemented using the non-uniformly sampled best-TROSY experiments (Favier and Brutscher, 2011 (link)): 3D HNCO, 3D HNCOCA, 3D HNCA, 3D HNCACO, 3D HNCOCACB and 3D HNCACB. The latter two experiments were optimized for detection of cross peaks of ¹³C^β nuclei, and all these spectra were recorded with a relaxation delay of 0.2 s. The experimental parameters for the 3D experiments are summarised in Supplementary Table 1.

Agback P., Dominguez F., Pustovalova Y., Lukash T., Shiliaev N., Orekhov V.Y., Frolov I., Agback T, & Frolova E.I. (2019). Structural characterization and biological function of bivalent binding of CD2AP to intrinsically disordered domain of chikungunya virus nsP3 protein. Virology, 537, 130-142.

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High-Field NMR Spectroscopic Protocols

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All the ¹H-detected NMR measurements were performed at 23.5 T (1 GHz ¹H frequency) on a Bruker Avance Neo spectrometer or using a 18.8 T (800 MHz ¹H frequency) Bruker Avance III HD spectrometer, equipped with cryogenically cooled x, y, and z pulsed-field gradient triple-resonance probes. The ¹⁹F-detected NMR measurements were performed at 11.7 T (500 MHz ¹H frequency) on a Bruker Avance III HD spectrometer equipped with a liquid nitrogen-cooled z pulsed-field gradient triple-resonance probe. All measurement and analysis details are as described previously (13 ).

Toyama Y., Rangadurai A.K., Forman-Kay J.D, & Kay L.E. (2022). Surface electrostatics dictate RNA-binding protein CAPRIN1 condensate concentration and hydrodynamic properties. The Journal of Biological Chemistry, 299(1), 102776.

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Structural Characterization of PACT-D3 Mutant

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NMR samples were prepared by dialysis into 20 mM MES pH 6.5, 50 mM NaCl, 5–10 mM TCEP followed by the addition of 10% D₂O and 50 μM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). The 2D (¹H, ¹⁵N) HSQC and EXSY spectra, and 3D experiments for assignment of PACT-D3 L273R, were recorded using a Bruker Avance II 700 MHz spectrometer with a triple-resonance room temperature probe. Spectra for backbone assignment of wild-type (WT) PACT-D3 were recorded on a Bruker 600 MHz Avance II+ spectrometer with triple-resonance cryoprobe, while spectra for side-chain assignment was collected on a Bruker 800 MHz Avance III HD spectrometer with triple-resonance cryoprobe. The ¹³C filter-edit NOESY experiment was recorded on a 50:50 mixture of [¹³C,¹⁵N]- and [¹⁵N]-labelled WT PACT-D3 using a Bruker 700 MHz Avance III HD spectrometer with quadruple-resonance cryoprobe. The high pressure 2D (¹H, ¹⁵N) HSQC NMR experiments were recorded using a Bruker 800 MHz Avance I spectrometer, equipped with a triple-resonance room temperature probe. The sample was inserted into a ceramic tube (rated to 2.5 kbar) and pressurized with paraffin oil (Sigma) using a high-pressure syringe pump (Daedalus Innovations LLC, PA).

Heyam A., Coupland C.E., Dégut C., Haley R.A., Baxter N.J., Jakob L., Aguiar P.M., Meister G., Williamson M.P., Lagos D, & Plevin M.J. (2017). Conserved asymmetry underpins homodimerization of Dicer-associated double-stranded RNA-binding proteins. Nucleic Acids Research, 45(21), 12577-12584.

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NMR Spectroscopy Protocol for Metabolomics

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NMR spectra was acquired as described by Mercier et al.^{50 (link)}. In brief, ¹H-NMR spectra were recorded at 300 K on a 600-MHz Avance III HD Bruker spectrometer (Bruker Biospin Inc, Billerica, MA) equipped with a triple resonance inverse detection TCI cryoprobe operating at 600.13 MHz. Sample preparation and data acquisition for NMR based metabolomics are detailed in the Supplementary methods section.

Bahado-Singh R., Poon L.C., Yilmaz A., Syngelaki A., Turkoglu O., Kumar P., Kirma J., Allos M., Accurti V., Li J., Zhao P., Graham S.F., Cool D.R, & Nicolaides K. (2017). Integrated Proteomic and Metabolomic prediction of Term Preeclampsia. Scientific Reports, 7, 16189.

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Metabolite Profiling of Seaweed Extracts using NMR Spectroscopy

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Five hundred microliters of methanol-d4, 400 μL of 0.2 M phosphate buffer solution (0.2 M of sodium hydrogen phosphate, 0.2 M sodium dihydrogen phosphate in D₂O, pH 7.0 ± 0.1), and 100 μL of 5 mM TSP (3-trimethylsilyl propionic-2, 2, 3, 3-d4 acid sodium salt) were added into an Eppendorf tube containing 50 ± 0.5 mg of each seaweed extract. ¹H-NMR experiments were carried out on Ascend 800 MHz, Avance III HD Bruker spectrometer (Bruker Biospin AG, Fällanden, Switzerland) equipped with 5 mm CPTIC ¹H-¹³C/15 N/D Z-GRD Z119427/0011 cryogenic probe. ¹H-NMR spectra were processed and analysed using Chenomx NMR Suite 8.4 (Chenomx, Edmonton, AB, Canada). All ¹H-NMR spectra were calibrated, phased and baseline-corrected manually using the processor module of Chenomx NMR Suite. The concentration and profiling of metabolites were estimated using the profiler module of Chenomx NMR Suite. The detail procedures of such analyses has been reported in a previous article Choi et al.^{23 (link)}.

Choi Y., Lee S.J., Kim H.S., Eom J.S., Jo S.U., Guan L.L., Seo J., Kim H., Lee S.S, & Lee S.S. (2021). Effects of seaweed extracts on in vitro rumen fermentation characteristics, methane production, and microbial abundance. Scientific Reports, 11, 24092.

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NMR Metabolomics Profiling of Serum Samples

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A total of 250 μL of serum was combined with 500 μL of saline solution (10% D₂O for lock signal, NaCl 0.9%, 500 mM sodium phosphate buffer in D₂O containing 0.05 trimethylsilylpropanoic acid [TSP] 0.05% for chemical shift calibration, and concentration reference, pH 7.0). After centrifuging the samples at 12,000× g for 10 min, 600 μL aliquots of the supernatant were transferred to 5-mm nuclear magnetic resonance (NMR) tubes for analysis. An ASCEND 800-MHz AVANCE III HD Bruker spectrometer was used, outfitted with a 5-mm CPTIC 1H-13C/15N/DZ-GRD Z1194227/0011 cryogenic probe. The NMR sequence (Carr-Purcell-Meiboom-Gill [CPMG] condition: total T2 relaxation time of 60, 4 K data points, 128 scans, four dummy scans, 8-s delay time) used was a CPMG spin-echo pulse. The Chenomx program performed baseline correction on the 1D data obtained from the NMR analysis. Binning was then performed in units of 0.05 ppm, followed by spectral alignment using the COW algorithm in MATLAB. SIMCA −P++ was used for the multivariate analysis of the data organized using MATLAB.
TSP was used as an internal standard for quality control. The TSP peak was used as a reference to correct for chemical shifts and quantify the metabolites.

Kim C.H., Lee Y.U., Kim K.H., Kang S., Kang G.H., Chu H, & Lee S. (2022). Comparison of Metabolites and Gut Microbes between Patients with Ulcerative Colitis and Healthy Individuals for an Integrative Medicine Approach to Ulcerative Colitis—A Pilot Observational Clinical Study (STROBE Compliant). Diagnostics, 12(8), 1969.

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NMR Spectroscopic Analysis of Samples

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The samples were analyzed using an Ascend 800 MHz, AVANCE III HD Bruker spectrometer (Bruker BioSpin AG, Fällanden, Switzerland). Proton nuclear magnetic resonance spectra were acquired at 25°C using the first transient the Carr-Purcell-Meiboom-Gill pulse sequence with the following parameters: temperature = 25°C, repetition number = 128, acquisition time = 2.0 s. The free induction decay was acquired with a spectral width of 20 ppm and collected to 64 k data points.

Kim H.S., Eom J.S., Lee S.J., Choi Y., Jo S.U., Lee S.S., Kim E.T, & Lee S.S. (2023). Blood and milk metabolites of Holstein dairy cattle for the development of objective indicators of a subacute ruminal acidosis. Animal Bioscience, 36(8), 1199-1208.

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NMR Spectroscopy of 15N-labeled CnGRASP

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¹⁵N-CnGRASP was expressed in minimum medium supplemented with ¹⁵N labeled ammonium chloride (Sigma Aldrich) and purified using the same procedure for the unlabeled sample. The protein was dissolved in 10% deuterium oxide in phosphate buffer pH 7.4 at a final concentration of 180 μM for NMR measurements. Glycerol (5% V/V) and beta-mercaptoethanol (5 mM) were present in the sample. NMR experiments were conducted in an AVANCE III HD Bruker spectrometer (Germany) operating at 600 MHz for ¹H equipped with a triple resonance cryoprobe. The regular 1D spectrum was first obtained using the water suppression by excitation sculpting pulse sequence with gradients. A spectral width of 16 ppm and acquisition time of 3.4 s were set. A recycle delay of 2 seconds and delay for gradient recovery of 200 μs were used and 256 scans were recorded. For ¹H -¹⁵N Heteronuclear Single Quantum Coherence (HSQC), the spectra were collected in increasing urea concentration (0, 2 and 4 M). For each experiment, 256 complex increments of 2048 complex data points were collected using 16 scans. The spectral widths were set to 14 ppm (¹H) and 32 ppm (¹⁵N) and a relaxation delay of 2 seconds and delay for gradient recovery of 200 μs were used between scans.

Mendes L.F., Garcia A.F., Kumagai P.S., de Morais F.R., Melo F.A., Kmetzsch L., Vainstein M.H., Rodrigues M.L, & Costa-Filho A.J. (2016). New structural insights into Golgi Reassembly and Stacking Protein (GRASP) in solution. Scientific Reports, 6, 29976.

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Characterization of Organic Compounds

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Reagents, chemicals, starting materials and solvents were obtained from commercial sources and used without further purification. Melting points were determined on an Microquímica MQAPF-302 apparatus. IR spectra were recorded on Perkin-Elmer Spectrum 100 FT-IR spectrometer with a Universal ATR sampling accessory. NMR spectra were recorded on a Avance III HD Bruker spectrometer with chemical shifts values (δ) in ppm relative to TMS using the residual DMSO-d6 signal as an internal standard. High-resolution mass spectra (HRMS) were recorded on an LTQ Orbitrap Discovery mass spectrometer (Thermo Fisher Scientific, Bremen, Germany). This system combines an LTQ XL linear ion-trap mass spectrometer and an Orbitrap mass analyser. The analyses were performed by direct infusion of the sample in MeOH/CH₃CN (1:1) with 0.1% formic acid (flow rate of 10 µL/min) in positive-ion mode using electrospray ionisation (ESI). For the elemental composition, the calculations used the specific tool included in the Qual Browser module of Xcalibur (Thermo Fisher Scientific, release 2.0.7) software.

Czeczot A.D., Roth C.D., Ducati R.G., Pissinate K., Rambo R.S., Timmers L.F., Abbadi B.L., Macchi F.S., Pestana V.Z., Basso L.A., Machado P, & Bizarro C.V. (2021). 8-Mercaptoguanine-based inhibitors of Mycobacterium tuberculosis dihydroneopterin aldolase: synthesis, in vitro inhibition and docking studies. Journal of Enzyme Inhibition and Medicinal Chemistry, 36(1), 847-855.

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