Tci cryogenic probe

Manufactured by Bruker

Sourced in Germany, United States

The TCI cryogenic probe is a high-performance NMR probe designed for cryogenic operation. It features a cooled radio frequency (RF) coil and preamplifier, allowing for enhanced sensitivity and signal-to-noise ratio during NMR experiments. The probe is optimized for use in cryogenic NMR systems.

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Close spelling variants of this product

Cryogenic probe (39 citations) 5-mm TCI cryogenic probe (6 citations) 5 mm TCI cryogenic probe head (6 citations) 1H/13C/15N TCI cryogenic probe (3 citations) TCI 1.7mm z-PFG cryogenic probe (3 citations) 1H/13C/15N TCI cryogenic probe head (3 citations) TCI z-axis gradient cryogenic probe (3 citations) Bruker TCI ( 1 H/ 13 C/ 15 N) cryogenic probe (3 citations) 1.7mm TCI cryogenic probe (2 citations) 5-mm TCI cryogenic probe and Z-axis gradient (2 citations)

20 protocols using tci cryogenic probe

NMR Spectroscopy of 3m-Pin1 Protein

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All 3m-Pin1 spectra were recorded on a Bruker Avance I spectrometer at 16.4 T (700.13 MHz ¹H frequency) equipped with a TCI cryogenic probe (Bruker Biospin, Inc.). Sample concentrations ranged from 80 to 100 μm. The 3m-pin1 backbone assignments were confirmed using established three-dimensional HNCACB (49 (link)), HNCOCACB (50 (link)), and 2D ¹H-¹⁵N HSQC (51 (link)) experiments at a nominal temperature of 295 K and comparisons with the WT-Pin1 assignments. NMR data processing used TopSpin 3.5 (Bruker Biospin) and resonance assignments made with Sparky 3 (52 ) and CARA (53 ). Amide ¹H-¹⁵N CSPs were calculated using Equation 1,

{Δ δ}_{NH} = \sqrt{{(Δ δ_{H})}^{2} + {(0.154 {Δ δ}_{N})}^{2}}

where Δδ_H and Δδ_N are ¹H and ¹⁵N chemical shift differences, respectively.

Zhang M., Frederick T.E., VanPelt J., Case D.A, & Peng J.W. (2021). Coupled intra- and interdomain dynamics support domain cross-talk in Pin1. The Journal of Biological Chemistry, 295(49), 16585-16603.

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NMR Analysis of HRAS-JAM20 Interaction

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For solution NMR experiments, proteins were produced as described above. The ¹⁵N-labeled HRAS(WT)⋅GDP and unlabeled JAM20(Y83S) were added in a 1:1 ratio with a final concentration of 107 μM. For ¹⁵N-labeled HRAS(WT)⋅GDP only, 107 μM protein was used. Both spectra were collected with samples in a buffer made up of TBS (pH 7.5), 20 mM MgCl₂, 1 mM DTT, and 5% D₂O. All NMR spectra were collected at 298 K on a Bruker 600 MHz (14.1 T) spectrometer, which was equipped with a triple-resonance TCI cryogenic probe. The 2D ¹H/¹⁵N-HSQC experiments were recorded with a spectral width of 9,615.4 Hz (¹H) and 2,189.7 Hz (¹⁵N). The acquisition (¹H) and evolution times (¹⁵N) were set to 62.3 ms and 22.8 ms, respectively. The 2D ¹H/¹⁵N-HSQC spectra were processed in NMRPipe (54 (link)) and analyzed by using NMRFAM-SPARKY (55 (link)). Assignments were based on a deposited assignment of HRAS(WT)⋅GDP (Biological Magnetic Resonance Bank [BMRB] ID: 18479) (56 (link)). CSPs were quantified with the equation below:

Δ δ = \sqrt{{(0.154 Δ δ_{N})}^{2} + Δ δ_{H}^{2}} .

Δ δ_{N}

and

Δ δ_{H}

are the ¹⁵N and ¹H chemical-shift changes, respectively, between HRAS in the absence and presence of JAM20.

Wallon L., Khan I., Teng K.W., Koide A., Zuberi M., Li J., Ketavarapu G., Traaseth N.J., O’Bryan J.P, & Koide S. (2022). Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket. Proceedings of the National Academy of Sciences of the United States of America, 119(43), e2204481119.

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Cisplatin-B-GNPs Binding Study by DOSY NMR

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The confirmation of binding of cisplatin drug with B-GNPs was also studied, for the very first time, through 2D DOSY ¹HNMR. For the analysis, all the spectra were gathered on a Bruker 800-MHz NMR spectrometer outfitted with a triple-resonance TCI cryogenic probe. For 2D DOSY ¹HNMR, stimulated echo bipolar gradient pulse experiments were utilized with a pulse hindrance of 5 ms following every gradient, a pulse field gradient length of 2.2 ms and with 15 s relaxation decay^{45 (link)}. Chemical shift (δ, ppm) and diffusion coefficient (m² s⁻¹) was plotted against log concentration (molar).

Iram S., Zahera M., Wahid I., Baker A., Raish M., Khan A., Ali N., Ahmad S, & Khan M.S. (2019). Cisplatin bioconjugated enzymatic GNPs amplify the effect of cisplatin with acquiescence. Scientific Reports, 9, 13826.

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NMR Spectroscopy of Lyophilized Samples

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1D ¹H NMR data were collected on a Bruker Avance II (600 MHz), equipped with a triple resonance, TCI cryogenic probe, and z-axis pulsed field gradients. Spectra were collected at 60 °C, with 128 scans and a free induction decay size of 84,336 points. Standard Bruker pulse sequences were used to collect the 1D data (p3919gp and zggpw5). Data were processed in Topspin (Bruker version 3.5) by truncating the free induction decay to 8192 points using a squared cosine bell window function and zero filling to 65,536 points.
Lyophilized samples were solubilized in deuterated water to a concentration of 500 mg/ml. Native samples were diluted by adding 300 μl of D₂O to 200 μl of sample. All NMR samples contained DSS-d₆ for chemical shift calibration and peak intensity comparisons.
Spectra were deconvoluted using the MNova program (through NMRbox) line fitting algorithm with a Lorentzian-Gaussian shape type and either 100 or 500 iterations to identify the SRG region peak sets.

Wear M.P., Jacobs E., Wang S., McConnell S.A., Bowen A., Strother C., Cordero R.J., Crawford C.J, & Casadevall A. (2022). Cryptococcus neoformans capsule regrowth experiments reveal dynamics of enlargement and architecture. The Journal of Biological Chemistry, 298(4), 101769.

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PKBα Structural NMR Analysis

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The phosphorylated PKBα was dissolved in 50 mM potassium phosphate buffer (pH 7.0) containing 100 mM KCl, 0.1 mM EDTA and 1 mM TCEP in 93% H₂O/7% ²H₂O. The final protein concentration was 50 μM. A ¹H NMR spectrum was acquired at 25°C using an AVANCE III 600 NMR spectrometer equipped with a TCI cryogenic probe (Bruker). ¹H 1D NMR was performed with water suppression by WATERGATE and water flip back techniques. The time domain data were processed using NMRPipe39 (link).

Maesaki R., Satoh R., Taoka M., Kanaba T., Asano T., Fujita C., Fujiwara T., Ito Y., Isobe T., Hakoshima T., Maenaka K, & Mishima M. (2014). Efficient and cost effective production of active-form human PKB using silkworm larvae. Scientific Reports, 4, 6016.

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NMR Characterization of Antp Homeodomain

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The NMR experiments were conducted at 25°C using a Bruker Avance III spectrometer equipped with a TCI cryogenic probe operated at the ¹H frequency of 800 MHz. Resonances of the Arg side chains of the Antp homeodomain under the same conditions were assigned in our previous work (Nguyen et al. 2017 (link)). The HNN experiment (Löhr and Rüterjans 1998 ) was conducted using 1-ms rSNOB pulses (Kupče et al. 1995 (link)) for ¹⁵N 180° pulses at ¹H-¹⁵N INEPT schemes to selectively observe signals from Arg side chains. The spin-echo ²J_NN modulation constant-time HISQC experiment was conducted as described in the figure caption. The ¹⁵N CPMG experiment for Arg side chains was conducted as previously described (Esadze et al. 2016 (link)). During the CPMG scheme, ¹H continuous wave (CW) was applied in the manner of the CW-CPMG method (Hansen et al. 2008 (link)). The NMR spectra were processed by the NMR-Pipe program (Delaglio et al. 1995 (link)) and analyzed by the NMR-View program (Johnson and Blevins 1994 (link)). Numerical calculations and nonlinear least-squares fittings were conducted with MATLAB software (MathWorks, Inc.).

Nguyen D, & Iwahara J. (2018). Impact of two-bond 15N-15N scalar couplings on 15N transverse relaxation measurements for arginine side chains of proteins. Journal of biomolecular NMR, 71(1), 45-51.

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NMR Experiments on Bruker Spectrometer

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All NMR experiments were carried out on Bruker Avance 600 MHz or 800 MHz spectrometer equipped with 5 mm triple-resonance TCI cryogenic probe. The samples were measured at 10 °C unless otherwise specified.

Wang Y., Han G., Jiang X., Yuwen T, & Xue Y. (2021). Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states. Nature Communications, 12, 1595.

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Water-Saturated 2D HSQC Analysis of Ribosome Complex

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2D HSQC experiments modified with water saturation during the relaxation delay were performed on riboA71-adenine complex at 5°C, 10°C, 15°C and 20°C on a Bruker Avance 600 MHz spectrometer equipped with a 5 mm triple-resonance TCI cryogenic probe. A series of spectra was collected under a weak B1 field of 50 Hz with different saturation times for the water presaturation. All spectra were processed and analyzed using NMRPipe (Delaglio et al., 1995 (link)) and autofit script to extract intensities.

Zhao S., Li X., Wen Z., Zou M., Yu G., Liu X., Mao J., Zhang L., Xue Y., Fu R, & Wang S. (2022). Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy. iScience, 25(11), 105322.

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NMR Characterization of WT Z7 Peptide

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Experiments for NMR assignments were done at a temperature of 25 °C on a Bruker Avance 600 MHz instrument equipped with a TCI cryogenic probe that was part of the Francis Bitter Magnet Lab of MIT. A sample containing 2.4 mM of the WT Z7 peptide (determined by A₂₈₀) and 4.4 mM ZnSO₄ in 90% H₂O/10%D₂O at pH 6.2, was used to collect 2D TOCSY (70 ms mix time), NOESY (200 ms mix time), DQF-COSY, and natural abundance ¹⁵N-sofast-HMQC spectra. The sample was lyophilized and resuspended in an equivalent volume of 99.96% D₂O to identify exchange-protected amide protons using 1D ¹H-NMR spectra. A 2D TOCSY experiment on the D₂O sample was collected to assign aromatic spin systems, and a ¹H-¹³C HSQC spectrum was used for ¹³C assignments. NOESY (50 ms mix time) and E.COSY spectra for the D₂O sample were used for stereospecific methylene proton assignments (Case et al. 1994 (link)). The extent of assigned resonances was ¹H (93%), backbone ¹⁵N (92%) and ¹³C (67%, excluding C’). The ¹⁵N assignments should be considered tentative, however, since the ¹⁵N-sofast-HMQC experiment had poor sensitivity at natural isotope abundance (0.36% for ¹⁵N). ¹H chemical shifts were referenced to internal DSS (2,2-dimethyl-2-silapentane-5-sulfonate), while ¹³C and ¹⁵N shifts were referenced indirectly as described in the literature (Wishart et al. 1995 (link)).

Rua A.J, & Alexandrescu A.T. (2024). Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure. bioRxiv.

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Backbone NMR Assignments of FN1 Protein

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¹H–¹⁵N HSQC, HNCA, HNCO, HN(CA)CO, HN(CO)CA, HNCACB, and CBCACONH spectra for FN1 backbone assignments were recorded at 25 °C on a Bruker 600 MHz DRX spectrometer equipped with a 5 mm inverse cryogenic probe. NMR spectra for HSQC titrations were recorded on a Bruker 900 MHz AVANCE spectrometer equipped with a 5 mm TCI cryogenic probe. Samples for all the NMR experiments were in a buffer containing 300 mM NaCl and 20 mM KH₂PO₄ (pH 6.6), supplemented with 10% D₂O. Backbone dihedral angles and the secondary structure of FN1 were predicted using Talos+.^{41 (link)} All NMR data were processed using NMRPipe^{42 (link)} and analyzed using UCSF Sparky. HSQC titrations were recorded in a 5 mm NMR tube at 1:0 (8 scans), 1:5 (32 scans), and 1:10 (64 scans) ratios of FN1 to 6xHis-SUMO-PBR and its mutant (R82A/R93A).

Bhide G.P., Prehna G., Ramirez B.E, & Colley K.J. (2017). The Polybasic Region of the Polysialyltransferase ST8Sia-IV Binds Directly to the Neural Cell Adhesion Molecule, NCAM. Biochemistry, 56(10), 1504-1517.

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