5 mm txi cryoprobe

Manufactured by Bruker

Sourced in United States

The 5 mm TXI cryoprobe is a type of nuclear magnetic resonance (NMR) probe designed for use in Bruker NMR spectrometers. It features a triple-resonance (TXI) configuration, allowing for the detection of multiple nuclei simultaneously. The probe is cryogenically cooled to enhance signal-to-noise ratio and improve sensitivity during NMR experiments.

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CryoProbe (153 citations) TXI cryoprobe (18 citations) 5 mm cryoprobe (9 citations) CryoProbe: 5 mm TXI probe of Z-Gradient (2 citations)

10 protocols using 5 mm txi cryoprobe

Characterization of Metabolites from Streptomyces albus

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S. albus ATGSal2P2::Tn14 was grown at 30 °C for 3 days in 6 × 500-mL flasks containing 50 mL of TSB, and pre-culture was used to inoculate 100 × 500-mL flasks containing 50 mL of NL19 media. Cultures were incubated at 30 °C for 5 days. Metabolites were extracted as described above. The extracts from biomass and the supernatant were combined and fractionated by size-exclusion chromatography on an LH 20 Sephadex column (Sigma-Aldrich, USA) using methanol as the solvent. The fractions were collected every 15 minutes., evaporated and dissolved in 0.5 mL of MeOH. Samples were further separated by preparative HPLC (Dionex UltiMate 3000, Thermo Fisher Scientific, USA) using a NUCLEODUR® C18 HTec column (250 × 10 mm, 5 µm) (Macherey-Nagel, Germany) with a linear gradient of solvent B (acetonitrile with 0.1% of formic acid) against solvent A (water with 0.1% of formic acid) at a flow rate of 4.5 mL/min at 45 °C. Compounds were separated using a gradient starting from 30% and increasing to 70% of B over 30 min. UV spectra were recorded with a DAD detector at 280 nm. Individual peaks were collected and analyzed by LC-MS as described above.
NMR spectra were acquired on a Bruker Ascend 700 MHz NMR spectrometer equipped with a 5 mm TXI cryoprobe (Bruker, USA). Deuterated CDCL₃ was used as a solvent and HSQC, HMBC and ¹H-¹H COSY spectra were recorded using standard pulse programs (Table 5S).

Ahmed Y., Rebets Y., Tokovenko B., Brötz E, & Luzhetskyy A. (2017). Identification of butenolide regulatory system controlling secondary metabolism in Streptomyces albus J1074. Scientific Reports, 7, 9784.

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NMR Spectroscopy of HIV-1 L63P Mutant

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All spectra were obtained at 293 K. All 600 MHz measurements were made on a Bruker Avance spectrometer with a 5 mm TXI cryoprobe (AMRIS Facility, University of Florida). All 700 MHz data were collected on a Bruker Avance system with a 5 mm TCI 700S4 h-C/N-D-05Z Cryoprobe (NHMFL facility, Department of Chemistry and Biochemistry, Florida State University,). NMRPipe [20 (link)] and Sparky (Goddard and Kneller, Sparky 3, UCSF, San Francisco) were used for processing and analysis of all NMR data. Given that the L63P construct contains only one mutation compared to subtype B, assignments were made based upon previously published results [21 ].
Relaxation measurements were performed on ¹⁵N L63P at 600 MHz and 700 MHz as described previously [12 ]. Experimental errors for NOE values were evaluated by error propagation using resonance intensity errors. Consistency of measurements performed at different magnetic field strengths was confirmed as proposed by Morin et al. [22 (link)]. Model-free analysis was performed using relaxGUI (http://www.nmr-relax.com/) [23 (link)–25 (link)].

Carter J.D., Gonzales E.G., Huang X., Smith A.N., deVera I.M., D’Amore P.W., Rocca J.R., Goodenow M., Dunn B.M, & Fanucci G.E. (2014). Effects of PRE and POST Therapy Drug-Pressure Selected Mutations on HIV-1 Protease Conformational Sampling. FEBS letters, 588(17), 3123-3128.

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NMR Analysis of a-factor Peptides

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For NMR analysis, the a-factor precursor peptide (8a) was dissolved in DMSO-d₆ to a concentration of 700 μM. The a-factor peptide (9a) was dissolved in DMSO-d₆ to a concentration of 2.4 mM. NMR data was acquired on a Bruker Avance 700-MHz spectrometer with a 5-mm TXI cryoprobe, and processed using TopSpin software. 1D ¹H spectra were acquired with 64 scans using 1 s recycle delay, 30° pulse, 3.1 s acquisition time with a sweep width of 15 ppm. Data was Fourier transformed with 0.3 Hz line broadening applied and manually phase-corrected. ¹H-¹H-TOCSY spectra were acquired using 32 scans/increment, spectral widths of 15 ppm and a 60-ms mixing time. 6300 × 256 points were collected in the directly and indirectly detected dimensions, respectively. Data was zero-filled and Fourier-transformed with a shifted sine-bell squared function. 2× linear prediction was applied in the indirect dimension.

Diaz-Rodriguez V., Ganusova E., Rappe T.M., Becker J.M, & Distefano M.D. (2015). Synthesis of Peptides Containing C-Terminal Esters Using Trityl Side-Chain Anchoring: Applications to the Synthesis of C-Terminal Ester Analogs of the S. cerevisiae Mating Pheromone a-Factor. The Journal of organic chemistry, 80(22), 11266-11274.

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NMR Analysis of Metabolite Profiles

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NMR spectra were acquired at 298 K using a Bruker AVANCE 800 MHz system equipped with a 5 mm TXI cryoprobe. To remove the effect of macromolecules on spectral broadening and to suppress the resonance from water, a Carr–Purcell–Meiboom–Gill pulse sequence with presaturation was applied as a T₂ filter. For each sample, 512 transients were collected into 64 K data points using a spectral width of 12,820 Hz, an acquisition time of 2.56 s, a relaxation delay of 3 s, and a pulse width of 11.30 μs. Using TopSpin 2.1 (Bruker Biospin, Coventry, UK), all NMR spectra were manually phased, baseline corrected, and shift referenced to TSP at 0 ppm. These pre-processed spectra were then imported into Chenomx NMR Suite 7.1 (Chenomx Inc., Edmonton, AB, Canada) for spectral binning. Binning was performed from 0.04 to 10 ppm with a bin size of 0.04 ppm but with the water (4.68–4.88 ppm) and methanol (3.32–3.36 ppm) regions excluded. Binning data were normalized based on the total binned area in each file.

Wong L.R., Wong P, & Ho P.C. (2020). Metabolic Profiling of Female Tg2576 Mouse Brains Provides Novel Evidence Supporting Intranasal Low-Dose Pioglitazone for Long-Term Treatment at an Early Stage of Alzheimer’s Disease. Biomedicines, 8(12), 589.

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Characterization of Chemical Compounds

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1D and 2D NMR spectra were recorded on a Bruker Avance III 700 spectrometer with a 5 mm TXI cryoprobe (¹H 700 MHz, ¹³C 175 MHz) and a Bruker Avance III 500 (¹H 500 MHz, ¹³C 125 MHz) spectrometer; optical rotations were measured on a Perkin-Elmer 241 polarimeter, IR spectra were measured with a Nicolet Spectrum 100 FTIR spectrometer (Perkin-Elmer, Waltham, MA, USA). All HPLC-MS analyses were performed on Agilent 1260 Infinity Systems with a diode array detector and C₁₈ Acquity UPLC BEH column (2.1 × 50 mm, 1.7 μm) from Waters with the gradient described by Helaly et al. [22 (link)] combined with ion trap MS (amazon speed, Bruker, Bremen, Germany), and HR-ESIMS spectra on a time-of-flight (TOF) MS (Maxis, Bruker). Chemicals and solvents were obtained from AppliChem GmbH (Darmstadt, Germany), Avantor Performance Materials (Deventor, The Netherlands), Carl Roth GmbH & Co. KG (Karlsruhe, Germany), and Merck KGaA (Darmstadt, Germany) in analytical and HPLC grade.

Helaly S.E., Kuephadungphan W., Phongpaichit S., Luangsa-ard J.J., Rukachaisirikul V, & Stadler M. (2017). Five Unprecedented Secondary Metabolites from the Spider Parasitic Fungus Akanthomyces novoguineensis. Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry, 22(6), 991.

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NMR Structural Elucidation of Compound 2

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One-dimensional and two-dimensional NMR data used for the elucidation of the structure of 2 are acquired on a Bruker Ascend 700 spectrometer equipped with a 5 mm TXI cryoprobe (¹H at 700 MHz, ¹³C at 175 MHz). All observed chemical shift values (δ) are given in ppm and coupling constant values (J) in Hz. Standard pulse programs are used for HMBC, HSQC and gCOSY experiments. HMBC experiments are optimized for ^2,3J_C-H = 6 Hz. The spectra are recorded in methanol-d₄, and chemical shifts of the solvent signals at δ^H 3.31 ppm and δ^C 49.2 ppm are used as reference signals for spectra calibration. Respective measurements for 1 are carried out in DMSO-d₆ with reference signals at δ^H 2.50 ppm and δ^C 39.5 ppm for calibration; temperature is set to 313 K for resolution improvement. To increase sensitivity, all measurements are conducted in a 5 mm Shigemi tube (Shigemi Inc., Allison Park, PA, USA). The NMR signals are grouped in tables and correspond to the numbering in the schemes corresponding to every table. All structure formulae devised by NMR will be made publicly available under their corresponding name in NPatlas [37 ,38 (link)].

Hug J.J., Frank N.A., Walt C., Šenica P., Panter F, & Müller R. (2021). Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C–N Biaryl Crosslinking in RiPP Biosynthesis. Molecules, 26(24), 7483.

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NMR Experiments of AFABP Protein Characterization

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The two- and three-dimensional NMR experiments [14] were performed at 20 °C on a Bruker Avance I spectrometer operating at 500 MHz and equipped with a 5-mm TXI cryoprobe (Bruker Biospin, Billerica, MA). The AFABP sample (400 μM, assuming all proteins are monomers) was prepared in a solution that contained 10% (v/v) D₂O, 10 mM potassium phosphate, 150 mM potassium chloride and 0.2 g/L sodium azide, adjusted to pH 7.4. The 2D ¹H–¹⁵N heteronuclear single quantum correlation (HSQC) spectra were acquired with respective spectral widths of 14 ppm and 32 ppm in the ¹H and ¹⁵N dimensions, requiring 8–128 scans (0.7–11 h) in separate experiments at a range of protein concentrations. For 2D nuclear Overhauser and total correlation spectroscopy (¹H–¹⁵N NOESY-HSQC and ¹H–¹⁵N TOCSY-HSQC) experiments, the typical mixing and spin-lock times were 150 ms and 70 ms, respectively. The triple-resonance experiments (HNCO, HN(CA)CO, HNCACB and CBCA(CO)NH) were conducted using typical acquisition and processing parameters described previously [15] (link), [16] (link). The resulting data were processed using NMRPipe software [17] (link) and analyzed by NMRViewJ software [18] (link).

Wang Q., Rizk S., Bernard C., Lai M.P., Kam D., Storch J, & Stark R.E. (2017). Protocols and pitfalls in obtaining fatty acid-binding proteins for biophysical studies of ligand-protein and protein-protein interactions. Biochemistry and Biophysics Reports, 10, 318-324.

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NMR Characterization of MycG Protein

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All NMR spectra were acquired at 298 K on a Bruker Avance spectrometer (Brandeis University Landsman Research Facility) equipped with a 5 mm TXI cryoprobe and operating at 800.13, 201.20, and 81.086 MHz for ¹H, ¹³C, and ¹⁵N respectively. Standard TROSY-based pulse sequences were used to acquire 2D-¹H,¹⁵N-HSQC, 2D–HNCO, 3D-HNCA, 3D-HN(CO)CA, 3D-HNCACB and ¹⁵N-edited 3D-NOESY data sets with triply labeled (U-¹³C, ¹⁵N, ²H) MycG samples. 2D-HSQC (U-¹⁵N, or U-¹⁵N,²H-MycG) and 2D-HNCO (U-¹⁵N, ¹³C-Pro-MycG) experiments were obtained with 2048 (¹H) × 128 (¹⁵N) complex points and 16 scans per t₁ increment. Triple resonance experiments were run with 2048 (¹H) × 96 (¹³C) × 64 (¹⁵N) complex points and 16 scans per t₁ increment, with the exception of the HNCACB which was run with 32 scans per t₁ increment. Sweep widths were 14367 Hz (¹H) and 2919 Hz (¹⁵N) for all experiments, while ¹³C spectral widths were 6438 Hz [HNCA and HN(CO)CA] and 15090 Hz for the HNCACB. The 3D, ¹H, ¹⁵N NOESY-TROSY was acquired with 2048 × 40 × 128 complex points using 12818 Hz (¹H), 2919 Hz (¹⁵N) and 12818 Hz (¹H) spectral widths respectively, using a 100 ms mixing time and a recycle delay of 1.5 seconds. All data sets were processed using Bruker Topspin 3.2 and analyzed using CCPN 2.3.1 or Sparky.

Tietz D.R., Podust L.M., Sherman D.H, & Pochapsky T.C. (2017). Solution conformations and dynamics of substrate-bound cytochrome P450 MycG. Biochemistry, 56(21), 2701-2714.

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Spectroscopic Characterization of Alliporin

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Melting points were determined on the Koffler block (Boetius) without correction. Optical rotations were measured using polarimeter Autopol IV (Rudolph Research Analytical, Flanders, NJ, USA). NMR spectra were measured on a Bruker AVANCE III HD 600 of Bruker Gmbh, Germany (¹H at 600.13 MHz and ¹³C at 150.9 MHz) using a 5 mm TXI cryoprobe (Bruker Gmbh, Germany), in d₅-pyridine at 25 °C. Chemical shifts were referenced to the solvent signal (δ_H(3,5) = 7.20, δ_C(4) = 135.5). The additional set of NMR spectra was measured for alliporin (3) in d₄-methanol and chemical shift referenced to the solvent signal (δ_H = 3.31, δ_C = 49.0). Mass spectra, including HR-MS, were recorded on LTQ Orbitrap XL (Thermo Fisher Scientific, Bremen, Germany) spectrometer.

Harmatha J., Buděšínský M., Zídek Z, & Kmoníčková E. (2021). Spirostanol Saponins from Flowers of Allium Porrum and Related Compounds Indicating Cytotoxic Activity and Affecting Nitric Oxide Production Inhibitory Effect in Peritoneal Macrophages. Molecules, 26(21), 6533.

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Spectroscopic Characterization of Fungal Metabolites

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Optical rotations were determined with a model 241 MC polarimeter (Perkin-Elmer). IR spectra were measured with a Spectrum 100 FTIR spectrometer (Perkin-Elmer); UV spectra were recorded with a UV-2450 UV-Vis spectrophotometer (Shimadzu). NMR spectra were recorded with an Ascend 700 spectrometer (Bruker Biospin) equipped with a 5-mm TXI cryoprobe ( 1 H 700 MHz, 13 C 175 MHz). ESI-MS spectra were obtained with an Amazon ion trap mass spectrometer (Bruker Daltonik); HRESIMS spectra were obtained with a Maxis time-of-flight mass spec- Isolation of fungal strains, dual culture tests, bioactivity-guided fractionation
The techniques are described in previous publications [6, 7] .

Surup F., Medjedović A., Schroers H.J, & Stadler M. (2015). Production of Obionin A and Derivatives by the Sooty Blotch Fungus Microcyclospora malicola. Planta medica, 81(15).

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