Txi probe

Manufactured by Bruker

Sourced in Germany

The TXI probe is a multi-nuclear probe designed for Bruker NMR spectrometers. It enables the acquisition of high-resolution NMR data for a variety of nuclei, including 1H, 13C, 15N, and 31P. The probe features a robust design and advanced electronics to provide reliable performance and optimal sensitivity.

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5-mm TXI probe (13 citations) 5-mm 1H TXI probe (7 citations) Triple resonance TXI probe (4 citations) 5 mm TXI triple resonance probe (3 citations) CryoProbe: 5 mm TXI probe of Z-Gradient (2 citations) TXI cryogenic probe (2 citations) TXI probe head (2 citations) Z‐axis gradient and triple resonance TXI probe (2 citations) 5 mm inverse probe TXI (1H/13C/15N) (2 citations)

8 protocols using txi probe

NMR Spectroscopy Protocol for Biomolecular Structure

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¹H NMR measurements were performed on a Bruker AVANCE III 600 MHz spectrometer equipped with a Bruker TXI probe. Nuclear Overhauser effect spectroscopy (NOESY) experiments were performed with a mixing time

(t_{mix})

of 200 ms unless noted otherwise. Measurements were performed in both 95% H₂O/5% D₂O and fully deuterated pH* 6.8 400 mM SPB solutions. 2048 and 1900 complex points were acquired in detection

(t_{2})

and evolution

(t_{1})

delays, respectively, over spectral widths of 24 ppm for 95% H₂O samples and 12 ppm for fully deuterated solutions. Solutions contained ~1 mM 3-(Trimethylsilyl)propionic-2,2,3,3-d₄ acid (TMSP, Sigma-Aldrich) as a frequency reference.
Total correlation spectroscopy (TOCSY) temperature series measurements were measured with DIPSI II isotropic mixing and

t_{mix} = 20 ms

. The sample was equilibrated for 5 min and auto gradient and lock shimmed with TopShim at each temperature prior to acquiring spectra. 2048 and 512 complex points were acquired in

t_{2}

and

t_{1}

, respectively, over spectral widths of 12 ppm.

Ashwood B., Jones M.S., Lee Y., Sachleben J.R., Ferguson A.L, & Tokmakoff A. (2023). Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics. bioRxiv.

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NMR Characterization of mCCL2 Proteins

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All of the NMR experiments were recorded
on a Bruker 500 MHz spectrometer
equipped with a TXI probe at 298 K. For all NMR-based experiments
(except for 2D translational diffusion spectroscopy), ¹⁵N-labeled mCCL2-WT and mCCL2-P8A protein samples were prepared in
50 mM sodium phosphate and 50 mM sodium chloride buffer (pH 6.0) in
10% D₂O. For 2D-DOSY, unlabeled protein samples were prepared
and dissolved in 100% D₂O solvent. DOSY experiments were
recorded on a Bruker 800 MHz spectrometer as described elsewhere.^{89 (link),90 (link)} For mCCL2-P8A, ¹H–¹⁵N HSQC spectra
were recorded in the concentration range of 50–500 μM.

Joshi N., Kumar D, & Poluri K.M. (2020). Elucidating the Molecular Interactions of Chemokine CCL2 Orthologs with Flavonoid Baicalin. ACS Omega, 5(35), 22637-22651.

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NMR Spectroscopy of Biomolecules in Deuterated Buffer

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NMR spectra were acquired on a Bruker AVANCE III 500 MHz spectrometer equipped with a Bruker TXI probe. Temperature series were performed in 2.5 °C steps and the sample was equilibrated for 5 min and auto gradient and lock shimmed with TopShim at each temperature. prior to acquiring spectra. Samples were prepared in fully deuterated 400 mM SPB for all measurements and contained ~1 mM 3-(Trimethylsilyl)propionic-2,2,3,3-d₄ acid (Sigma-Aldrich) as a frequency reference.
Total correlation spectroscopy (TOCSY) measurements were measured with DIPSI II isotropic mixing and a mixing time of 60 ms. 2048 and 256 complex points were acquired in t2 and t1, respectively, over sweep widths of 24 ppm.
Diffusion-ordered spectroscopy (DOSY) was performed on a Bruker AVANCE IIIHD 600 MHz spectrometer. Measurements were performed using 2D stimulated echo pulse sequence with bipolar gradients and WATERGATE solvent suppression (Bruker TopSpin, stebpgp1s19). Spectra were acquired from 0 to 95% of the maximum gradient field strength in 5 % intervals where the maximum field strength was 5.35 T/cm. The magnetic field gradient was calibrated with a 3D printed phantom with known spacing between the water samples.

Ashwood B., Jones M.S., Radakovic A., Khanna S., Lee Y., Sachleben J.R., Szostak J.W., Ferguson A.L, & Tokmakoff A. (2023). Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs. bioRxiv.

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NMR Characterization of Acyl-ACP Protein

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NMR samples for ¹H¹⁵N comprised 0.3 to 0.5 mM acyl-ACP and ∼1 mM for triple resonance experiments, 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 10% D₂O, and 0.5% Sodium Azide. Two- and three-dimensional NMR experiments, namely ¹H¹⁵N HSQC, HNCACB, CBCAcoNH, CCcoNH, HNcoCA, and HNCA, were acquired on a Bruker Avance III 700 MHz NMR spectrometer, equipped with a TXI probe, installed at the National Institute of Immunology, New Delhi, India. Experiments were performed at 298 K throughout. NMR data were processed on a workstation running Red Hat Enterprize Linux 5.0, using NMRPipe/NMRDraw (49 (link)). The data were multiplied by a phase-shifted sinebell apodization function in all dimensions and analyzed using Sparky (50 ).
¹H¹⁵N HSQC spectra were acquired using 1024 data points (t2) dimension and 512 data points (t1) dimension. CBCAcoNH, HNCACB, CCcoNH experiments were collected with 1024 (t3) × 128 (t1) × 32 (t2) complex data points. Data were linear predicted in the forward direction for up to half the number of experimental points in the indirect dimension. ¹⁵N¹³C spectra were referenced indirectly using sodium 2, 2-dimethyl-2-silapentane-5-sulfonate (DSS) as a chemical shift standard (51 (link)).

G.a.r.i.m.a., Prem R., Yadav U, & Sundd M. (2021). A GX2GX3G motif facilitates acyl chain sequestration by Saccharomyces cerevisiae acyl carrier protein. The Journal of Biological Chemistry, 297(6), 101394.

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NMR-Based Metabolite Profiling Protocol

Cited 1 time

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All ¹H ¹D NMR experiments were performed at 310 K on a Bruker Avance III 500 MHz spectrophotometer equipped with a TXI probe (Bruker Daltonics, Bremen, Germany). A 1D CPMG pulse sequencer (Carr-Purcell-Meiboom-Gill) with cpmgpr1d parameters, 73,728 points in F1, 12,019.230 Hz spectral width, 2048 pass, with a cyclic delay of 4 secs, was used for the measurement, with water suppression using presaturation. We used the reference chemical database Madison-Qingdao Metabolomics Consortium Database to analyze the obtained metabolites^{103 (link)} and all determined metabolites were compared with reference compounds. We acquired, processed, and evaluated the results using Bruker Topspin 3.1, and MestReNova 10.0 software (Mestrelab Research, Santiago de Compostela, Spain). We related the concentration of metabolites to the TSP standard. We performed measurements in triplicate for each monitored condition.

Špaková I., Rabajdová M., Mičková H., Graier W.F, & Mareková M. (2021). Effect of hypoxia factors gene silencing on ROS production and metabolic status of A375 malignant melanoma cells. Scientific Reports, 11, 10325.

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NMR Spectra Acquisition and Processing

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NMR spectra were acquired on 14.1 T Agilent (600 MHz ¹H Larmor frequency) or 16.5 T Bruker (700 MHz) spectrometers equipped with a ¹H/¹³C/¹⁵N triple resonance single-axis gradient cryoprobe (600 MHz spectrometer) or a room temperature TXI probe (700 MHz Bruker spectrometer). All NMR measurements were carried out at 25 °C. NMR datasets were processed and visualized using NMRPipe (67 (link)) and NMRFAM-Sparky (68 (link)) software packages respectively.

Narayanan V., Bobbili K.B., Sivaji N., Jayaprakash N.G., Suguna K., Surolia A, & Sekhar A. (2022). Structure and carbohydrate recognition by the non-mitogenic lectin horcolin. Biochemistry, 61(6), 464-478.

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NMR analysis of trans-B[a]P-dG:AB duplex

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Through-space nuclear Overhauser effects and through-bond correlated 2D spectra were recorded and analyzed in order to assign the B[a]P and nucleic acid protons in the trans-B[a]P-dG:AB abasic 11-mer duplex. To visualize the imino protons, 2D nuclear Overhauser effect spectroscopy (NOESY) data for the modified duplex in 10% H₂O buffer (100 mM NaCl, 10 mM phosphate, pH 6.8) at 10 ⁰C were recorded; a mixing time of 200 ms employing a jump-return pulse sequence for solvent suppression on a Bruker 500 Mhz NMR spectrometer equipped with a TXI probe was utilized. The corresponding NOESY spectra in D₂O buffer at 10°C were recorded at a mixing time of 300 ms. Through-bond correlation spectroscopy (COSY) and total correlation spectroscopy (TOCSY) at a 300 ms mixing time were recorded using a Bruker 800 MHz NMR instrument equipped with a cryoprobe at the New York Structural Biology Center (NYSBC). Peak assignments were obtained using the SPARKY program [27 ].

Liu Z., Ding S., Kropachev K., Lei J., Amin S., Broyde S, & Geacintov N.E. (2015). Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. PLoS ONE, 10(9), e0137124.

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Proton NMR Spectroscopy of Metabolites

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The instrumental conditions were as described by Sundekilde, Poulsen, Larsen, and Bertram (2013b), using Proton ( 1 H) NMR spectroscopy at 298 K (25°C) on a Bruker Avance III 600 spectrometer equipped with a TXI-probe (Bruker Biospin, Rheinstetten, Germany). Briefly, operating conditions were: 1 H frequency 600.13 MHz, 5 s relaxation delay, 0.1 s mixing time, 64 scans, 32 K data point and 12.15 ppm spectral width. Acquisition time was 2.25 s and standard 1D spectra were acquired using a NOESY sequence 90° pulse with water suppression by presaturation during relaxation delay and mixing time (Bruker pulse: noesypr1d). The Free Induction Decay (FID) data were multiplied by 0.3-Hz line-broadening function before Fourier transformation. Topspin 3.0 (Bruker BioSpin) was used for phase and baseline correction of 1 H NMR spectra. Spectra were referenced using a TSP signal. NMR signals were identified in accordance with the literature (Sundekilde, Larsen, & Bertram, 2013a), the Human Metabolome Database (www.HMDB.ca) and the Chenomx NMR suite (Chenomx Inc., Alberta, Canada).

Panthi R.R., Sundekilde U.K., Kelly A.L., Hennessy D., Kilcawley K.N., Mannion D.T., Fenelon M.A, & Sheehan J.J. (2019). Influence of herd diet on the metabolome of Maasdam cheeses. Food research international (Ottawa, Ont.), 123.

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