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Avance 1 nmr spectrometer

Manufactured by Bruker

The Avance I NMR spectrometer is a compact and efficient nuclear magnetic resonance (NMR) instrument designed for routine analytical applications. It provides high-resolution NMR spectroscopy capabilities for the characterization and identification of organic and inorganic compounds.

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10 protocols using avance 1 nmr spectrometer

1

Structural Characterization of Nucleic Acid Duplexes

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NMR experiments were collected on a 600 MHz Bruker AVANCE I NMR spectrometer equipped with a room temperature, triple resonance (i.e., 1H, 13C, and 15N) TXI probe.
Initially, a standard 1D 1H experiment was acquired using a water flip-back Watergate for water suppression. The imino 1H region, 10.0–15.0 ppm, was inspected to assure that the duplex was properly formed. Duplex formation is ascertained from qualitatively visualizing peak shape (30±10 Hz imino linewidth) and counting the appropriate number of peaks. Imino resonances from terminal base pairs are known to exchange rapidly with solvent and are usually not observed. For duplex oligonucleo-tides, most other imino resonances from the Watson–Crick pairs should be observed.
A 2D nuclear Overhauser effect spectroscopy (NOESY) experiment also employing a water flip-back Watergate for solvent suppression was then collected at typically two different mixing times (e.g., 100 and 300 ms). This standard experiment allows the user to map sequential correlations of imino resonances along the length of the sequences. This assignment process has been reviewed extensively (Flinders & Dieckmann, 2006 ).
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2

Quantification of Trimethylamine by NMR

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For analysis of TMAO reduction, trimethylamine (TMA) concentrations in supernatant samples were quantified by 1H-NMR. To 800 μl of sample 10 μl of 100 mM trimethylsilyl propionate (TSP) was added as a 0 ppm chemical shift and quantitation reference. 450 μl of the mixture was transferred to NMR tubes, 50 μl of D2O was added and spectra acquired as described by Sellars et al.17 (link). Integration of the single peak of TMA at 2.88–2.89 ppm and comparison with the TSP peak allowed TMA concentrations to be calculated. The 13C chemical shifts of succinate and pyruvate were obtained from a 2D 1H−13C HSQC spectrum, acquired with the standard Bruker pulse program, hsqcetgpsisp2, on an 800 MHz Avance I NMR spectrometer. The data were acquired with 2048 points in the direct dimension and 300 complex points in the indirect dimension, 64 transients per indirect point and a SW of 100 ppm for 13C.
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3

High-Field NMR Spectroscopy Protocols

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All experiments were performed
with a wide bore Bruker Avance I NMR spectrometer operating at a 1H Larmor frequency of 600 MHz (14.1 T), using either a standard
bore 3.2 mm HFCN MAS probe or a 3.2 mm EFree HCN MAS probe from Bruker
Biospin. The sample temperature was controlled using a constant flow
of cooled gas. Spectra were acquired with the Bruker Topspin software
but processed and analyzed with NMRPipe, Sparky, and CCPNMR/Analysis.
External referencing to 4,4-dimethyl-4-silapentane-1-sulfonic acid
(DSS) was done indirectly via the 13C signals of adamantane.50 (link) For all spectra shown, additional experimental
details can be found in Table S1 of the Supporting
Information
.
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4

Metabolomic Analysis of Bacterial Stress Response

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Five millitres of mid-exponential phase bacterial cultures (grown in LB and M9 minimal salt medium at salinities ranging from 0.25 to 2.5 M NaCl) was harvested and centrifuged at 3000 g for 10 min. After the supernatant was discarded, the resulting pellets were washed twice in 1 ml sterile distilled water and vortexed for 1 min at room temperature. The washed cells were then transferred into 1.5 ml Eppendorf tubes and sonicated twice for 20 s with 10 s breaks between each 20 s of sonication to allow cooling of the sample. Samples were centrifuged at 6000 g for 10 min, and the resulting supernatant was transferred into 1.5 ml Eppendorf tubes, and stored at –80 °C. After a minimum of 2 h at −80 °C, the samples were freeze-dried and stored at room temperature until required for NMR analysis. The dried samples were prepared for NMR analysis by dissolving them in 500 µl of D2O, adding 5 µl of 100 mM trimethyl silyl propionate (TSP; standard) using 1.5 ml Eppendorf tubes. The dissolved samples were transferred into 5 mm NMR tubes for analysis. Samples were run on a Bruker Avance-I NMR spectrometer operating at 500 MHz, at 298 K. All spectra used 90° pulses and long relaxation delays for accurate quantitation.
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5

Solid-state NMR of Labeled Peptides

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All ssNMR spectra were recorded on a 9.4 Tesla Bruker Avance I NMR spectrometer, operating at frequencies of 400 MHz (1H) and 100 MHz (13C). Magic angle spinning (MAS) frequency was 10 kHz for all experiments.
Labelled peptides were packed into kevlar inserts (Bruker) which in turn fit into standard zirconia 4 mm rotors (Bruker).
13C and 15N cross polarization (13C CP) experiments: The standard CP sequence in the Bruker pulse program library was used with 1H 90° pulse length 2.5 μs, contact time 2.5 ms; during the contact pulse a ramped pulse was applied on 1H with average spin lock field of 70 kHz. During acquisition, SPINAL64 decoupling at field strength 100 kHz was applied on 1H. Chemical shifts were referenced to external glycine (α polymorph), using the methylene signal at 43.1 ppm relative to TMS (13C).
Variable temperature experiment: using a Bruker Variable Temperature Unit, the temperature of the sample was varied from 242 K to 342 K in steps of 5 K. At each temperature, the sample was allowed to equilibrate for up to 10 minutes before a standard 13C CP-MAS spectrum was recorded.
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6

Polymer Vesicle Characterization Protocol

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All organics solvents and chemicals were purchased from Sigma-Aldrich (Sigma-Aldrich Chimie, Saint Quentin Fallavier, France) and Thermo Scientific (Waltham, MA, USA). 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (Rhodamine-PE) were obtained from Avanti Polar Lipids Inc. (Alabaster, AL, USA). Poly(dimethylsiloxane)-nitrobenzoxadiazole (PDMS-NBD) and poly(dimethylsiloxane)-block-poly(ethylene oxide) (PDMS36-b-PEO23, Mn 4000 g.mol-1) were synthesized as previously described [20 (link)]. This copolymer is known to spontaneously form polymersomes with a membrane thickness of 9.9 ± 1.6 nm. Cationic switchable lipid (CSL) was synthesized as previously described [16 (link)]. Sucrose, calcein and all other chemicals were purchased from Sigma-Aldrich (Saint Quentin Fallavier, France). 1H Nuclear Magnetic Resonance spectra were acquired at 298 K on a Bruker Avance I NMR spectrometer operating at 400 MHz, using trimethylsilane (TMS) as the internal standard and deuterated chloroform as solvent. Data were treated with TopSpin 4.0.7 (Bruker BioSpin, Wissembourg, France).
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7

400 MHz NMR Spectrometer Protocol

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Avance I NMR spectrometer operating at 400 MHz, and equipped with a Bruker multinuclear zgradient direct probe head capable of producing gradients in the z direction with 53.5 G.cm -1 strength. 1 H NMR spectra were recorded with a D1 of 2 sec and 64 scans.
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8

NMR Spectroscopy Protocol for 400.2 MHz

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NMR spectra were acquired in D 2 O or CDCl 3 at 298 K on a Bruker Avance I NMR spectrometer operating at 400.2 MHz and equipped with a Bruker multinuclear z-gradient direct probe head capable of producing gradients in the z direction with 53.5 G.cm -1 strength. The relaxation time was fixed to 3 seconds for homonuclear correlation spectroscopy (COSY) measurements.
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9

Precise NMR Characterization of Aqueous Solutions

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Experiments were carried out on an 11.7 T NMR Bruker Avance I spectrometer (Bruker BioSpin) operating at 500.19 MHz for 1H, and 132.3 MHz for 23Na, using a 5 mm double resonance broadband probe. The test tubes with different samples under investigation (aqueous solutions with different NaCl concentrations, agarose gel, ex vivo tissues) were placed inside the spectrometer where the sample temperature could be controlled using gas flow and a temperature sensor providing a precise, stable and reliable temperature regulation. After each desired temperature was reached, a standard free induction decay (FID) pulse sequence was used with a 90° pulse. The duration of the pulse is 11 and 9 μs for 1H and 23Na, respectively, and 8 averages were used with TR = 15 s for 1H, and 0.5 s for 23Na, dwell time dw = 100 μs, spectral width sw = 5 kHz, 16,384 data points per spectrum. Complex FIDs were acquired in digital quadrature detection (DQD) mode, a simultaneous acquisition mode in Bruker systems resulting in sw=12dw . All experiments were performed with the following exact spectrometer reference frequencies: f0H=500.2031765MHz , f0Na=132.3120951MHz (fixed ratio f0H/f0Na=3.7804796 ).
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10

Precise NMR Characterization of Aqueous Solutions

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Experiments were carried out on an 11.7 T NMR Bruker Avance I spectrometer (Bruker BioSpin) operating at 500.19 MHz for 1H, and 132.3 MHz for 23Na, using a 5 mm double resonance broadband probe. The test tubes with different samples under investigation (aqueous solutions with different NaCl concentrations, agarose gel, ex vivo tissues) were placed inside the spectrometer where the sample temperature could be controlled using gas flow and a temperature sensor providing a precise, stable and reliable temperature regulation. After each desired temperature was reached, a standard free induction decay (FID) pulse sequence was used with a 90° pulse. The duration of the pulse is 11 and 9 μs for 1H and 23Na, respectively, and 8 averages were used with TR = 15 s for 1H, and 0.5 s for 23Na, dwell time dw = 100 μs, spectral width sw = 5 kHz, 16,384 data points per spectrum. Complex FIDs were acquired in digital quadrature detection (DQD) mode, a simultaneous acquisition mode in Bruker systems resulting in sw=12dw . All experiments were performed with the following exact spectrometer reference frequencies: f0H=500.2031765MHz , f0Na=132.3120951MHz (fixed ratio f0H/f0Na=3.7804796 ).
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