Vnmrj

Manufactured by Agilent Technologies

Sourced in United States

VNMRJ is a nuclear magnetic resonance (NMR) software package developed by Agilent Technologies. It is designed to control and acquire data from NMR spectrometers. The software provides a user interface for setting up and running NMR experiments, as well as analyzing the resulting data.

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33 protocols using vnmrj

NMR-based Metabolomic Analysis of Cell Extracts

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All acquired FIDs were Fourier transformed, phase corrected and aligned to the chemical shift of DSS-d₆ at 0 ppm using Varian software VNMRJ version 2.2C (Agilent Technologies). The ¹H NMR spectra of cell extracts were then baseline-corrected using the Processor module of the Chenomx NMR suite version 7.1 (Chenomx Inc.). Assignments of NMR signals were based on total correlation spectroscopy (2D ¹H-¹H TOCSY; Figure S9), spiking experiments, and comparison to previous reports. The identification of metabolites and determination of concentration were performed using the Profiler module of Chenomx NMR suite version 7.1. The data were then normalized to the total protein concentration, as determined by the Bradford assay. The resulting ¹H NMR data were imported into SIMCA-P version 12.0 (Umetrics) for chemometric analyses. All imported data sets were mean-centered and scaled to unit-variance, which gives base weight to the data sets. Subsequently, supervised regression analysis was conducted using PLS-DA to examine the differences among groups. The fit of the model to the data was described by R² and Q² values (where R² describes the goodness of fit and Q² indicates predictability). A VIP column plot was generated to identify the metabolites responsible for the differences among groups.

Lee J., Kee H.J., Min S., Park K.C., Park S., Hwang T.H., Ryu D.H., Hwang G.S, & Cheong J.H. (2016). Integrated omics-analysis reveals Wnt-mediated NAD+ metabolic reprogramming in cancer stem-like cells. Oncotarget, 7(30), 48562-48576.

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NMR Analysis of DNA Oligonucleotides

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¹H NMR spectra were collected on Agilent Technologies DD2 600 MHz NMR spectrometer at 298 and 273 K using a cold probe. DNA oligonucleotides were dissolved in H₂O/D₂O (9:1) solution containing KCl 100 mM and lithium cacodylate 10 mM, pH 5.0. Oligonucleotide concentrations were between 0.2 and 0.4 mM per strand. Double pulsed field gradient spin echo (DPFGSE) pulse sequence was used to suppress the water signal. Spectra were processed with program VNMRJ (Agilent Technologies).

Ruggiero E., Lago S., Šket P., Nadai M., Frasson I., Plavec J, & Richter S.N. (2019). A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription. Nucleic Acids Research, 47(21), 11057-11068.

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Quantifying Dynamic Changes in Relaxation Rate

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Under experimental conditions, ie, using a dual-echo gradient echo sequence (the “mgems” sequence in the Agilent VnmrJ library), and assuming that the flip angle is known across the brain of the rodent, an estimate of the time trace of ΔR₁ can be calculated from the following equation:

S (t) = \frac{M_{0} Sin (θ) (1 - e^{- TR * R_{1} (t)}) e^{- TE * R_{2}^{*} (t)}}{1 - Cos (θ) e^{- TR * R_{1} (t)}}

where S(t) is the signal intensity at time t, M₀ is the equilibrium magnetization of the protons, θ is the flip angle, TR is the repetition time between pulses, TE is the echo time (the time between the center of the excitation pulse and the readout gradient), and R*₂(t) is the transverse relaxation rate. Equation 2 can be solved for R₁(t):

R_{1} (t) = \frac{1}{TR} \ln [\frac{1 - (\frac{S (t) Cos (θ)}{M_{0} e^{- \frac{TE}{T 2 *}} Sin (θ)})}{1 - (\frac{S (t)}{M_{0} e^{- \frac{TE}{T 2 *}} Sin (θ)})}]

Shankar A., Borin T.F., Iskander A., Varma N.R., Achyut B.R., Jain M., Mikkelsen T., Guo A.M., Chwang W.B., Ewing J.R., Bagher-Ebadian H, & Arbab A.S. (2016). Combination of vatalanib and a 20-HETE synthesis inhibitor results in decreased tumor growth in an animal model of human glioma. OncoTargets and therapy, 9, 1205-1219.

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In Vivo Magnetic Resonance Imaging of Arterial Nanoparticles

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All MR images were acquired on a 9.4 T 31 cm MRI scanner (Agilent Technologies) with software designed for pre-clinical MR imaging research (Vnmrj, Agilent Technologies). A custom three-loop volume coil was used. Both 3D multi-band SWIFT (MB-SWIFT) and 3D gradient echo (GRE) images were acquired (25 (link)). MR imaging was performed at 4 h and 24 h after loading and then unloading msIONPs from the lumen of an artery. The detailed methods are given in the Supplementary Materials and closely follow previous protocols (25 (link)).

Manuchehrabadi N., Gao Z., Zhang J., Ring H.L., Shao Q., Liu F., McDermott M., Fok A., Rabin Y., Brockbank K.G., Garwood M., Haynes C.L, & Bischof J.C. (2017). Improved Tissue Cryopreservation using Inductive Heating of Magnetic Nanoparticles. Science translational medicine, 9(379), eaah4586.

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1H-NMR Spectroscopy of Samples

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¹H-NMR spectra were acquired on 600 MHz Agilent NMR spectrometer (Agilnet Technologies). For the analysis, 20 mg of sample and 20 μl of D₂O with 2 mM TSP-d4 was added to NMR nano tube. For each sample, 128 transients were scanned. The spectra were Fourier transformed using Vnmrj (version 4.2 Agilent Technologies, Palo Alto, CA, USA) and all spectra were assigned and processed using Chenomx NMR Suite 7.1 professional and the Chenomx 600 MHz library database.

Lee S., Hallis S.P., Jung K.A., Ryu D, & Kwak M.K. (2019). Impairment of HIF-1α-mediated metabolic adaption by NRF2-silencing in breast cancer cells. Redox Biology, 24, 101210.

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NMR Characterization of RNA Structure

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Spectra were recorded with the RNA either in a 100% ²H₂O or 5% ²H₂O, 95% H₂O. 1D ¹H and 2D NOESY, DQF-COSY and TOCSY NMR spectra were recorded with the natural abundance sample. 2D ¹³C and ¹⁵N HSQC and HCN spectra were recorded with the isotopically enriched sample. 3D NOESY-HSQC and HCCH-TOCSY spectra were also acquired, but gave poor S/N ratio due to low RNA concentration. Cross-peak intensities were therefore evaluated from 2D NOESY spectra.
All spectra were acquired on an Agilent VNMRS 600 MHz spectrometer equipped with a cryogenic probe. DPFGSE water suppression scheme was used for suppression of the water signal. All experiments were performed at temperatures of 0, 25 or 37 °C. NMR spectra were processed and analysed using VNMRJ (Agilent), NMRpipe and Sparky software (UCSF).

Podbevšek P., Fasolo F., Bon C., Cimatti L., Reißer S., Carninci P., Bussi G., Zucchelli S., Plavec J, & Gustincich S. (2018). Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Scientific Reports, 8, 3189.

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DOSY Spectroscopy for Water Diffusion

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As described in our previous work [44 (link)], Diffusion-ordered NMR Spectroscopy (DOSY) measurements are carried out on a Varian Agilent NMR spectrometer (Agilent Technologies, Santa Clara, CA, USA) operating at 600 MHz. Gradient strengths (Gz) are varied from 500 to 32,500 G/cm. The gradient pulse duration (δ) is kept constant to 2 ms while the diffusion delay (Δ) is increased from 7 to 1000 ms. After Fourier transformation and baseline correction, DOSY spectra are processed and analysed using Varian software VNMRJ (Agilent Technologies, Santa Clara, CA, USA) in order to obtain the values of water self-diffusion coefficient, which is then plotted as a function of Δ.

Ponsiglione A.M., Russo M, & Torino E. (2020). Glycosaminoglycans and Contrast Agents: The Role of Hyaluronic Acid as MRI Contrast Enhancer. Biomolecules, 10(12), 1612.

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MRI Detection of Gadolinium Contrast

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MRI experiments were done using a 4.7 T small animal MRI (Agilent Technologies Inc., Santa Clara, CA, USA) and acquired using VnmrJ (Agilent Technologies). After scout scans, isotropic 3D T1-weighted scans were used to detect gadolinium using the following parameters: TR = 9.3 ms; TE = 4.7 ms; flip angle = 20°; field of view = 40 × 20 × 20 mm; resolution = 256 × 128 × 128; averages = 4; voxel size≈156 µm³. These resulted in a time scan of approximately 11 min. Animals were anesthetized using isoflurane administered through a nose-cone, and 10 µl of gadolinium was injected into the cisterna magna at a rate of 2 µl/min. Respiratory rates were monitored to ensure normal physiology. A baseline scan was acquired prior to gadolinium injection, and image processing was done using FIJI software.

Hsu M., Rayasam A., Kijak J.A., Choi Y.H., Harding J.S., Marcus S.A., Karpus W.J., Sandor M, & Fabry Z. (2019). Neuroinflammation-induced lymphangiogenesis near the cribriform plate contributes to drainage of CNS-derived antigens and immune cells. Nature Communications, 10, 229.

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NMR Spectroscopy of Recombinant BilRI Protein

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NMR spectra were collected at 298 K using either Varian INOVA 600 MHz or INOVA 800 MHz NMR spectrometers (Agilent, Santa Clara, CA, USA), both equipped with cryogenically cooled ¹H, ¹³C, ¹⁵N triple-resonance probeheads with z-gradient coils. For ¹H NMR spectra, measured at 600 MHz, the recombinant BilRI was diluted in 95%/5% H₂O/D₂O, 50 mM NaCl, pH 7 buffer in a Shigemi microcell (250 μL). The final BilRI concentration was 4.6 mM. The ¹H spectrum was sampled with 20,438 complex points using 64 transients per free induction decay (FID), resulting in an acquisition time of 500 ms in the ¹H dimension. The two-dimensional ¹H-¹⁵N HSQC spectrum of BilRI at pH 5 was measured at the 800 MHz ¹H frequency using 128 and 852 complex points in ¹⁵N and ¹H dimensions, corresponding to acquisition times of 49 ms and 85.2 ms, respectively. A total of 256 transients per FID were used to assure sufficient signal accumulation. The total experimental time was 18 h. Spectra were processed with VnmrJ (Agilent, Santa Clara, CA, USA) and analyzed with Sparky (T. D. Goddard and D. G. Kneller, University of California, San Francisco, CA, USA) software packages.

Ahlstrand T., Tuominen H., Beklen A., Torittu A., Oscarsson J., Sormunen R., Pöllänen M.T., Permi P, & Ihalin R. (2016). A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-8. Virulence, 8(2), 115-134.

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NMR Spectroscopy of Syntaxin-1A Protein

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All NMR spectra except for syntaxin-1A (191-253) 214C were acquired at 25°C on Agilent DD2 spectrometers operating at 600 or 800 MHz and equipped with cold probes. Spectra of syntaxin-1A (191-253) 214C were collected at 20°C. All 1D ¹H NMR spectra listed in Table 1 were acquired on the same Agilent DD2 600 MHz spectrometer. The ¹H-¹³C HMQC spectra of Fig. 1 were collected with 100% D₂O as the solvent. All other 1Ds, ¹H-¹⁵N HSQC, ¹H-¹⁵N TROSY-HSQC and ¹H-¹³C HMQC spectra were acquired on samples with 10% D₂O as the solvent. The buffer used for all the NMR experiments was 20 mM HEPES pH 7.4, 125 mM KCl with protease inhibitor cocktail A added. Some experiments were performed in the presence of 1 mM Ca²⁺ or 1 mM EGTA as indicated in the figures. All 1D ¹H NMR spectra were processed and analyzed with Agilent VNMRJ. Two-dimensional spectra were processed with NMRPipe (Delaglio et al., 1995 (link)) and analyzed with NMRView (Johnson and Blevins, 1994 (link)).

Voleti R., Bali S., Guerrero J., Smothers J., Springhower C., Acosta G.A., Brewer K., Albericio F, & Rizo J. (2021). Evaluation of the tert-butyl group as a probe for NMR studies of macromolecular complexes. Journal of biomolecular NMR, 75(8-9), 347-363.

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