Hcn cryogenic probe

Manufactured by Bruker

The HCN cryogenic probe is a specialized laboratory equipment designed for Nuclear Magnetic Resonance (NMR) spectroscopy. It is capable of operating at cryogenic temperatures, enabling enhanced sensitivity and resolution in NMR experiments involving a range of nuclei, including hydrogen (H), carbon (C), and nitrogen (N).

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Lab products found in correlation

Nmr spectrometer, by Bruker (4 mentions) 600 mhz spectrometer, by Bruker (1 mentions)

Close spelling variants of this product

Cryogenic probe (39 citations) Triple-resonance HCN cryogenic probe (2 citations)

7 protocols using hcn cryogenic probe

NMR Spectroscopy of Aromatic Molecules

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NMR experiments were performed on a 600 MHz Bruker NMR spectrometer equipped with an HCN cryogenic probe. Data were processed and analyzed using NMRpipe (42 (link)). The NMR buffer used was: 15 mM sodium phosphate pH 7.5 and 50 mM KCl. 2D CD SOFAST-HMQC aromatic data were obtained and analyzed as previously described (43 (link)).

Travis B., Shaw P.L., Liu B., Ravindra K., Iliff H., Al-Hashimi H.M, & Schumacher M.A. (2018). The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA. Nucleic Acids Research, 47(4), 2130-2142.

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NMR spectroscopy analysis protocol

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All NMR experiments were collected on a 600 MHz or a 700 MHz Bruker NMR spectrometer equipped with an HCN cryogenic probe. Data were processed and analyzed using NMRpipe^{33 (link) 1995} and SPARKY^{34 San Francisco}, respectively. Complete assignment experiments were obtained using 2D [¹³C, ¹H] Heteronuclear Single Quantum Coherence (HSQC), 2D [¹H, ¹H] WATERGATE Nuclear Overhauser Effect Spectroscopy (NOESY, mixing time of 150 ms) experiments.

Kladwang W., Topkar V.V., Liu B., Rangan R., Hodges T.L., Keane S.C., al-Hashimi H, & Das R. (2020). Anomalous reverse transcription through chemical modifications in polyadenosine stretches. Biochemistry, 59(23), 2154-2170.

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NMR Characterization of Biomolecular Interactions

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All NMR experiments were collected on a 600 MHz or a 700 MHz Bruker NMR spectrometer equipped with an HCN cryogenic probe. Data were processed and analyzed using NMRpipe 60 1995 and SPARKY 61 San Francisco , respectively. Complete assignment experiments were obtained using 2D [ 13 C, 1 H] Heteronuclear Single Quantum Coherence (HSQC), 2D [ 1 H, 1 H] WATERGATE Nuclear Overhauser Effect Spectroscopy (NOESY, mixing time of 150 ms) experiments.

Kladwang W., Topkar V.V., Liu B., Hodges T.L., Keane S.C., Al‐Hashimi H.M., & Das R. (2020). Anomalous reverse transcription through chemical modifications in polyadenosine stretches.

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NMR Analysis of Modified TAR RNA

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All NMR experiments were performed on a 600 MHz Bruker NMR spectrometer equipped with an HCN cryogenic probe. Data were processed using NMRpipe (77) and analyzed using SPARKY (T.D.
Goddard and D.G. Kneller, SPARKY 3, University of California, San Francisco). Resonances in Nmmodified TAR were assigned based on prior assignments of unmodified TAR (33) and confirmed using 2D HSQC, HMQC, and 1 H-1 H NOESY experiments (150 ms mixing time).

Assi H.A., Shi H., Liu B., Clay M.C., Erharter K., Kreutz C., Holley C.L., & Al‐Hashimi H.M. (2020). 2’-O-methylation alters the RNA secondary structural ensemble.

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Analyzing RNA Structural Changes by NMR

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The impact of the mutations on RNA structure was initially assessed by recording 1D [¹H] and 2D [¹³C-¹H] SOFAST-HMQC NMR experiments (Sathyamoorthy et al., 2014 (link)) using unlabeled RNA samples. All NMR experiments were carried out at 298 K on a 600 MHz Bruker spectrometer equipped with HCN cryogenic probes. Data were processed using NMRpipe (Delaglio et al., 1995 (link)) and analyzed using SPARKY (Goddard and Kneller, SPARKY 3).

Ganser L.R., Chu C.C., Bogerd H.P., Kelly M.L., Cullen B.R, & Al-Hashimi H.M. (2020). Probing RNA conformational equilibria within the functional cellular context. Cell reports, 30(8), 2472-2480.e4.

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NMR Characterization of Biomolecular Interactions

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NMR data were collected on Bruker 500, 600 and 800 MHz spectrometers equipped with HCN cryogenic probes. 1D ¹H experiments were conducted at multiple temperatures using excitation sculpting for water suppression. 2D ¹H–¹H nuclear Overhauser effect spectroscopy (NOESY) spectra were collected in H₂O NMR buffer (20 mM potassium phosphate pH 6.5, 50 mM sodium chloride) at 5 °C. NOESY spectra with mixing times of 10 ms and 100 ms were recorded to measure exchange rates with EXSYCALC (Mestrenova). All NMR data were processed using Bruker Topspin (3.1) or NMRPipe and visualized with Topspin and Sparky.

Menendez C., Bauer Z., Huber H., Gad’on N., Stetter K.O, & Fuchs G. (1999). Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CoA Carboxylase in Autotrophic Crenarchaeota and Indication for Operation of a 3-Hydroxypropionate Cycle in Autotrophic Carbon Fixation. Journal of Bacteriology, 181(4), 1088-1098.

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NMR Characterization of RNA-Small Molecule Interactions

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All NMR experiments were performed at 25°C on a Bruker 600 MHz spectrometer equipped with triple resonance HCN cryogenic probes. ¹³C/¹⁵N labeled RNA was exchanged into NMR buffer (15 mM NaH₂PO₄/Na₂HPO₄, 25 mM NaCl, 0.1 mM EDTA, 10% (v/v) D₂O at pH 6.4). For spectra in the presence of magnesium, Mg²⁺ was added directly to the sample to a final concentration of 3 mM. NMR spectra were processed with NMRPipe (Delaglio et al. 1995 (link)) and visualized with SPARKY (Goddard and Kneller 2006 ). All molecules were soluble in water except DPQ, which was dissolved in DMSO. NMR spectra for free and small molecule bound RNAs were recorded in 2% DMSO for the DPQ panels in Figure 2, and Supplemental Figures S1 and S2. NMR samples were prepared by mixing the RNA (50 µM) with small molecules (DPQ and pentamidine) at a 1:4 molar ratio. A molar ratio of 1:60 was used for yohimbine to observe the CSPs shown in Figure 2 and Supplemental Figures S1 and S2 consistent with its lower affinity to its target RNA (Tibodeau et al. 2006 (link)). This titration is shown in Supplemental Figure S3.

Kelly M.L., Chu C.C., Shi H., Ganser L.R., Bogerd H.P., Huynh K., Hou Y., Cullen B.R, & Al-Hashimi H.M. (2021). Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays. RNA, 27(1), 12-26.

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