NMR experiments were performed on a Bruker Avance III HD 850 MHz system equipped with an inverse triple resonance cryo-probe. Samples contained either 90% H2O and 10% D2O or 100% D2O. A trace amount of DSS was added as a frequency standard. Assignment of the imino protons of guanine residues was obtained using 1D SOFAST experiments (38 (link)) (8% 15N labeling), which filter out proton signals not coupled to 15N. Assignment of H8 protons was partially obtained from an HMBC spectrum correlating H1 and H8 resonances (39 (link)). Spectral assignments were made using NOESY and TOCSY spectra at various temperatures and mixing times. Spectral analyses were performed using TOPSPIN (Bruker) and Sparky (40–41 ).
Avance 3 hd 850 mhz
Manufactured by Bruker
Sourced in Germany
The Avance III HD 850 MHz is a high-field nuclear magnetic resonance (NMR) spectrometer produced by Bruker. It is designed to provide high-resolution and high-sensitivity NMR analysis for a wide range of applications. The core function of this instrument is to perform advanced NMR spectroscopy experiments to investigate the structure and dynamics of molecules.
Automatically generated - may contain errors
Lab products found in correlation
Topspin 2 1 3 0 3, by Bruker (2 mentions)
Dipsi2ggpphpr, by Bruker (2 mentions)
Hsqcetgpsisp2, by Bruker (2 mentions)
Topspin, by Bruker (1 mentions)
Sparky, by Bruker (1 mentions)
Nmr suite, by Chenomx (1 mentions)
Avance 3 600 mhz, by Bruker (1 mentions)
Isolera one, by Biotage (1 mentions)
Inova 400 mhz, by Bruker (1 mentions)
Acquity ultra high performance liquid chromatography, by Waters Corporation (1 mentions)
11 protocols using avance 3 hd 850 mhz
1
NMR Characterization of Nucleic Acid Structures
2
Backbone Assignment of Disordered SRSF1
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
SRSF1 cultured in 2H,13C, 15N M9 media was concentrated to 370 µM in 100 mM ER4, 400 mM Arg/Glu, pH 6.4, 1 mM TCEP, 10% D2O, and 0.02% NaN3. Triple resonance assignment experiments HNCA, HNCACB, HN(CO)CA, HN(CO)CACB, HNCO, and HN(CA)CO were collected at 37 °C on a Bruker Avance III-HD 850 MHz spectrometer installed with a cryo-probe. Approximately 85% of the protein backbone region was assigned using this method. Another approximately 13% of backbone exists in the disordered state with highly degenerate sequences, which leads to heavy peak overlap. These RS and G-rich regions were grouped into clusters. Multiplicity selective in-phase coherence transfer (MUSIC) experiments were collected to further characterize the clusters and verify the assignment of the rest of the protein. MUSIC was performed on SRSF1 for the following amino acids: Ser, Arg, Thr, Asn, Ala, Tyr/His/Phe, Pro, Asn/Gln, Met, and Gly. When used in combination with analysis of the effect of paramagnetic tag placement, peak clusters were able to be assigned to locations on the disordered regions. The NMR data was processed using NMRPipe (Delaglio et al., 1995 (link)), and assignment was performed using NMRViewJ (Johnson, 2004 (link)). The assignment of the well dispersed regions (85% of the protein) has been submitted to BMRB (ID: 51299).
3
850 MHz NMR Metabolite Profiling Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A Bruker AVANCE III HD 850 MHz NMR spectrometer (Bruker BioSpin, ettlingen, Germany) was used to acquire one-dimensional (1D) 1H-NMR spectra at 25 °C using the NOESYGPPR1D pulse sequence, with a relaxation delay of 4 s, 32 scans, and a spectral width of 20 ppm. Resonance assignments of metabolites were performed by a combination of the Chenomx NMR Suite (version 8.3, Chenomx Inc., Edmonton, Canada), Human Metabolome Database (HMDB, http://www.hmdb.ca/ (accessed on 1 September 2022)), and relevant published sources. To confirm these assignments, several two-dimensional (2D) NMR spectra were acquired, including 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC).
4
NMR Characterization of PTP1B Catalytic and Full-Length Domains
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
NMR data of PTP1Bcat and PTP1B1-393 were collected at 298 K on Bruker Avance 500 and 800 MHz spectrometers and a Bruker AvanceIIIHD 850 MHz spectrometer all equipped with a TCI HCN z-gradient cryoprobe. All NMR spectra were processed with Topspin 2.1/3.0/3.1 (Bruker) and analyzed using Cara (http://cara.nmr.ch ). TROSY versions of a 3D HNCA, 3D HN(CO)CA, 3D HNCACB and 3D HN(CO)CACB were recorded on 1 mM [2H,15N,13C]-PTP1Bcat and 0.3 mM [2H,15N,13C]-PTP1B1-393 samples. A TROSY version of a 3D 15N-resolved [1H,1H] NOESY (Tm = 120 ms) was also recorded on 1 mM [2H,15N]-PTP1Bcat to verify assignments using sequential backbone 1HN-1HN NOEs. Additionally, 2D [1H,15N] TROSY spectra of single 15N-isotopically labeled amino acid samples (15N-Leu, 15N-Tyr, 15N-Phe or 15N-Val) were recorded.
5
NMR Spectroscopy of Organic Compounds
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
NMR spectra were collected at 298 K on a Bruker AVANCE III HD 850 MHz solution-state spectrometer equipped with a cryogenically cooled TCI probe. 1D 1H spectra (Bruker pulse program “zgesgppe”) were collected with 16,384 complex points for a measurement time of around 4 min. The spectral width was 13,587.0 Hz, and the number of scans was 32. 2D 1H-1H TOCSY spectra were collected (Bruker pulse program “dipsi2ggpphpr”) with 256 complex t1 and 2048 complex t2 points for a measurement time of 4 h. The spectral widths along the indirect and direct dimensions were 10,202.0 and 10,204.1 Hz and the number of scans per t1 increment was 14. 2D 13C-1H HSQC spectra (Bruker pulse program “hsqcetgpsisp2.2”) were collected with 512 complex t1 and 2048 complex t2 points for a measurement time of 16 h. The spectral widths along the indirect and direct dimensions were 34,206.2 and 9375.0 Hz and the number of scans per t1 increment was 32. The transmitter frequency offset values were 75 ppm in the 13C dimension and 4.7 ppm in the 1H dimension for all experiments. NMR data was zero-filled four-fold in both dimensions, apodized using a cosine squared window function, Fourier-transformed, and phase-corrected using NMRPipe55 (link).
6
NMR Characterization of PTP1B Catalytic and Full-Length Domains
7
NMR Spectroscopy for Protein-Ligand Interactions
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
2D 1H–15N HSQC
spectra were acquired
on both Bruker Avance III HD 850 MHz and Bruker Avance III 600 MHz
(Bruker, Billerica, Massachusetts) spectrometers equipped with a 13C/1H/15N cryoprobe. All HSQC experiments
were measured at 298 K in Shigemi NMR tubes (Shigemi Co., Ltd., Tokyo,
Japan) containing 350 μL of sample in 100 mM phosphate buffer
(pH 6.5) supplemented with 50 mM KCl and 10% 2H2O. The 100 mM phosphate buffer was used to avoid unwanted effects
caused by pH changes induced by the presence of the tested compounds
at high concentrations. 2D 1H–15N HSQC
measurements were performed with 100 μM FOXO-DBDs and a given
concentration of the compound. All spectra were processed in TopSpin
software (v3.6) and evaluated in Sparky software (v3.1).43 (link) CSP values obtained from 2D 1H–15N HSQC experiments were calculated using the following formula44 (link)
spectra were acquired
on both Bruker Avance III HD 850 MHz and Bruker Avance III 600 MHz
(Bruker, Billerica, Massachusetts) spectrometers equipped with a 13C/1H/15N cryoprobe. All HSQC experiments
were measured at 298 K in Shigemi NMR tubes (Shigemi Co., Ltd., Tokyo,
Japan) containing 350 μL of sample in 100 mM phosphate buffer
(pH 6.5) supplemented with 50 mM KCl and 10% 2H2O. The 100 mM phosphate buffer was used to avoid unwanted effects
caused by pH changes induced by the presence of the tested compounds
at high concentrations. 2D 1H–15N HSQC
measurements were performed with 100 μM FOXO-DBDs and a given
concentration of the compound. All spectra were processed in TopSpin
software (v3.6) and evaluated in Sparky software (v3.1).43 (link) CSP values obtained from 2D 1H–15N HSQC experiments were calculated using the following formula44 (link)
8
STD NMR Study of FOXO3-DBD Interaction
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
STD experiment was performed at
298 K on a Bruker Avance III HD 850 MHz spectrometer (Bruker, Billerica,
Massachusetts) equipped with a 13C/1H/15N cryoprobe. The 550 μL sample contained 15 μM FOXO3-DBD
and 1 mM5cj in 20 mM phosphate buffer (pH 6.5) supplemented
by 50 mM KCl and 10% 2H2O. 1H STD
NMR was performed using a standard “stddiffesgp” pulse
sequence with excitation sculpting and pulse-field gradients for water
suppression. On-resonance irradiation was done at −0.54 ppm
and off-resonance irradiation at 30 ppm, using a 50 ms shaped Eburp2.1000
pulse of power 40 dB for a saturation time of 3 s. The difference
spectra were obtained by subtracting the on-resonance spectrum from
the off-resonance spectrum. The spectra were analyzed using TopSpin
software (v3.6).
298 K on a Bruker Avance III HD 850 MHz spectrometer (Bruker, Billerica,
Massachusetts) equipped with a 13C/1H/15N cryoprobe. The 550 μL sample contained 15 μM FOXO3-DBD
and 1 mM
by 50 mM KCl and 10% 2H2O. 1H STD
NMR was performed using a standard “stddiffesgp” pulse
sequence with excitation sculpting and pulse-field gradients for water
suppression. On-resonance irradiation was done at −0.54 ppm
and off-resonance irradiation at 30 ppm, using a 50 ms shaped Eburp2.1000
pulse of power 40 dB for a saturation time of 3 s. The difference
spectra were obtained by subtracting the on-resonance spectrum from
the off-resonance spectrum. The spectra were analyzed using TopSpin
software (v3.6).
9
NMR Metabolite Profiling of Lyophilized Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The lyophilized samples were dissolved with 18.3 μL of PBS (1.5 M K2HPO4/NaH2PO4, pH 7.4) and 531.7 μL of D2O, containing 1 mM sodium 3-(trimethylsilyl)-propionate-2,2,3,3-d4 (TSP), vortexed and centrifuged (4 °C, 12,000 rpm, 5 min) to remove precipitates. Finally, the collected supernatant (about 500 μL per sample) was transferred to 5 mm NMR tube. 1D 1H-NMR spectra were recorded on a Bruker AVANCE III HD 850 MHz (Bruker Bio Spin, Germany) at 25 °C using a TCI cryoprobe. The pulse sequence NOESYGPPR1D [(RD)-90°-t1-90°-τm-90°-ACQ] with water suppression was used to record the NMR spectra. The relaxation delay time (RD) was 2 s, and the mixing time (τm) was 10 ms. The spectral width was 20 ppm, and a total of 32 transients were collected into 64 K data points with an acquisition time (ACQ) of 1.88 s. The free induction delay (FID) signal was processed by a window function with a line broadening of 0.3 Hz, followed by Fourier transformation to obtain 1D 1H spectra. Both two-dimensional (2D) 1H-13C heteronuclear single quantum coherence (HSQC) and 2D 1H-1H total correlation spectroscopy (TOCSY) spectra were recorded to assist in resonance assignments of metabolites.
10
NMR Spectroscopy of Biomolecular Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
NMR spectra were
collected at 298 K
on a Bruker AVANCE III HD 850 MHz solution-state spectrometer equipped
with a cryogenically cooled TCI probe. 2D 1H–1H TOCSY spectra were collected (Bruker pulse program “dipsi2ggpphpr”)
with 256 complex t1 and 2048 complex t2 points
for a measurement time of 4 h. The spectral widths along the indirect
and direct dimensions were 10,202.0 and 10,204.1 Hz, and the number
of scans per t1 increment was 14. 2D 13C–1H HSQC spectra (Bruker pulse program “hsqcetgpsisp2.2”)
were collected with 512 complex t1 and 2048 complex t2 points for a measurement time of 16 h. The spectral widths
along the indirect and direct dimensions were 34,206.2 and 9375.0
Hz, and the number of scans per t1 increment was 32. The
transmitter frequency offset values were 75 ppm in the 13C dimension and 4.7 ppm in the 1H dimension for all experiments.
NMR data was zero-filled four-fold in both dimensions, apodized using
a cosine-squared window function, Fourier transformed, and phase corrected
using NMRPipe.28 (link)
collected at 298 K
on a Bruker AVANCE III HD 850 MHz solution-state spectrometer equipped
with a cryogenically cooled TCI probe. 2D 1H–1H TOCSY spectra were collected (Bruker pulse program “dipsi2ggpphpr”)
with 256 complex t1 and 2048 complex t2 points
for a measurement time of 4 h. The spectral widths along the indirect
and direct dimensions were 10,202.0 and 10,204.1 Hz, and the number
of scans per t1 increment was 14. 2D 13C–1H HSQC spectra (Bruker pulse program “hsqcetgpsisp2.2”)
were collected with 512 complex t1 and 2048 complex t2 points for a measurement time of 16 h. The spectral widths
along the indirect and direct dimensions were 34,206.2 and 9375.0
Hz, and the number of scans per t1 increment was 32. The
transmitter frequency offset values were 75 ppm in the 13C dimension and 4.7 ppm in the 1H dimension for all experiments.
NMR data was zero-filled four-fold in both dimensions, apodized using
a cosine-squared window function, Fourier transformed, and phase corrected
using NMRPipe.28 (link)
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!