The NMR data presented in Table 2 and Table 3 were derived from spectra acquired on a Bruker Neo spectrometer with a 9.4 T magnetic field, equipped with a 5 mm 15N,77Se, 31P {19F,1H} nitrogen cryoprobe. Chemical shifts are referenced to internal tetramethylsilane or trichlorofluoromethane. The spectra were acquired at 298 K.
Neo spectrometer
Manufactured by Bruker
Sourced in Germany
The Bruker Neo spectrometer is a compact and versatile nuclear magnetic resonance (NMR) spectrometer designed for various analytical applications. It provides reliable and accurate measurements of chemical structures and compositions. The Neo spectrometer offers high-performance NMR capabilities in a space-saving design.
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11 protocols using neo spectrometer
1
NMR Spectroscopy of Compounds
2
NMR Characterization of cMyc and 199-NT RNA
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RNA samples were prepared from the 5′UTR of 0 hp cMyc-NT, 10 hp cMyc-NT, 0 hp 199-NT, and 10 hp 199-NT DNA. The DNA templates were PCR-amplified by T7 forward primer and short-length primer 1 (see Supplementary Table 2 ). RNA synthesis and purification protocol was described in RNA Preparation. The length of 0 hp and 10 hp cMyc-NT RNA was 94 bases, and the length of 0 hp and 10 hp 199-NT RNA was 109 bases. For NMR, the samples contained 90–130 μM RNA in 20 mM potassium phosphate buffer pH 7.0, and 5% D2O. The cMyc-NT samples contained 70 mM KCl, and the 199-NT samples contained 150 mM KCl. The final sample volume was adjusted to 130 μL and loaded into a 3 mm Wilmad tube (Sigma Aldrich). 1D 1H spectra were obtained on an 800 MHz (1H) Bruker NEO spectrometer, equipped with a triple-resonance cryogenic probe. A double-echo watergated sequence zggpw5 from the Bruker library was used for high-quality water suppression and was optimized for maximum excitation in the 10–16 ppm region. Experimental parameters were as follows: 60 °C temperature, 80 ms acquisition time and 512 scans per FID; interscan delay 1.5 s; interpulse delay in the zggpw5 sequence 30 ms; total time per spectrum 14 min.
3
NMR Spectroscopy Protocol for Structural Analysis
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NMR spectra were recorded at 298 K using a Bruker Neo spectrometer at 700 MHz or 800 MHz, equipped with a standard triple resonance gradient probe or cryoprobe, respectively. Bruker TopSpin version 4.0 (Bruker BioSpin) was used to collect data. NMR data were processed with NMR Pipe/Draw51 (link) and analyzed with Sparky 3 (T.D. Goddard and D.G. Kneller, University of California).
4
NMR Structural Characterization of H2B-H2A.Z Interactions
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NMR spectra were recorded on a 600 MHz Bruker Neo spectrometer equipped with a QCI-F cryoprobe at 308 K. NMR samples were prepared in 20 mM MES buffer (pH 6.0) containing 200 mM NaCl. Initial 15N-H2B-H2A.Z sample concentrations for the titrations ranged between 95 and 170 μM; titrations with each of the three peptides were conducted until four molar equivalents had been added. 1H-15N TROSY spectra were recorded with 16 scans, 128 complex increments in the indirect 15N dimension and spectral widths of 16 and 30 ppm for the 1H and 15N dimensions, respectively. Spectra were processed using TopSpin ver. 4.2.0 (Bruker) and analyzed using NMRFAM-Sparky ver. 1.47065 (link).
5
NMR Analysis of ClTx-NRP1 Interaction
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15N-labelled ClTx was dissolved in 50 mM sodium citrate (pH 5.5), 150 mM NaCl and 5% D2O, to a final concentration of 55 μM. The 1H–15N HSQC spectrum of ClTx was acquired at 298 K using Bruker Neo spectrometer (900 MHz instrument as above). Titration experiments were performed by gradual addition of stock solution (396 μM) of NRP1-b1 into 15N-labelled ClTx solution, to final NRP1-b1 concentrations of 21 μM, 34 μM, 45 μM, 57 μM, 95 μM and 125 μM.
To map the interaction interface of ClTx and NRP1-b1, competition titrations were performed using a previously characterised NRP1-b1 antagonist – EG00229. To the final titration point of 15N-labelled ClTx (55 μM) and NRP1-b1 (125 μM), concentrated solution (50 mM) of EG00229 (dissolved in dimethyl sulfoxide) was added to the final concentration of 83 μM. In the subsequent titration, concentration of EG00229 was increased to 413 μM.
At each titration point, a 1H–15N HSQC spectrum was acquired at 298 K under identical experimental conditions (using 32 scans). All spectra were processed using Topspin 4.0 (Bruker, Massachusetts, USA) and Rowland NMR toolkit (University of Connecticut, USA). Peak assignments of 15N-labelled ClTx were performed using CCPNMR version 3.0.
To map the interaction interface of ClTx and NRP1-b1, competition titrations were performed using a previously characterised NRP1-b1 antagonist – EG00229. To the final titration point of 15N-labelled ClTx (55 μM) and NRP1-b1 (125 μM), concentrated solution (50 mM) of EG00229 (dissolved in dimethyl sulfoxide) was added to the final concentration of 83 μM. In the subsequent titration, concentration of EG00229 was increased to 413 μM.
At each titration point, a 1H–15N HSQC spectrum was acquired at 298 K under identical experimental conditions (using 32 scans). All spectra were processed using Topspin 4.0 (Bruker, Massachusetts, USA) and Rowland NMR toolkit (University of Connecticut, USA). Peak assignments of 15N-labelled ClTx were performed using CCPNMR version 3.0.
6
NMR Analysis of Cas9 HNH Domain
7
Solid-State NMR Protocol for 13C Analysis
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Experiments were performed using a Bruker Neo spectrometer operating at a 1H Larmor frequency of 600.0 MHz, corresponding to a 13C Larmor frequency of 150.9 MHz. A 3.2 mm HXY probe at 12.5 kHz MAS in double resonance mode was used. The 1H 90° pulse duration was 2.5 μs. CP was achieved using a ramp26 (link) on 1H, (90–100%) for 1H–13C. SPINAL-6427 (link)1H heteronuclear decoupling at 100 kHz, was applied during the acquisition of the 13C FID with a pulse duration of 5.8 μs. The nutation frequencies for 1H and 13C during CP were 75 kHz and 20 kHz, respectively, with a pulse duration of 2 ms. The phase cycling employed was as follows: 1H 90° pulse (90° 270°), CP contact pulse (2{0°} 2{180°} 2{90°} 2{270°}), receiver (0° 180° 180° 0° 90° 270° 270° 90°). A recycle delay of 7 s was used.
8
NMR Characterization of SARS-CoV-2 Nucleocapsid Protein
9
NMR Characterization of Isolated Substances
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Isolated substances were measured on a Bruker Advance II NMR-spectrometer (Bruker, Rheinstetten, Germany) at 700 MHz proton frequency and 25 °C in chloroform-d1 with an internal standard of TMS or on a Bruker Neo spectrometer at 400 MHz proton frequency. Data sets comprised 1H, 13C and 2D experiments COSY, HSQC and HMBC.
10
Solid-State NMR Characterization Protocol
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1H solid-state
NMR spectra were acquired on a Bruker Avance II+ spectrometer operating
at a 1H Larmor frequency of 600 MHz using a 1.3 mm Bruker
HXY probe or on a Bruker NEO spectrometer operating at a 1H Larmor frequency of 850 MHz using a 4 mm Bruker HXY probe in double-resonance
mode. A π/2 pulse of 2.5 μs and a recycle delay of 3 s
was used. 32 (600 MHz) or 4 (850 MHz) transients were co-added. The 1H spectra were referenced using the CH3 resonance
ofl -alanine to 1.1 ppm, relative to adamantane at 1.85 ppm.97 (link)
NMR spectra were acquired on a Bruker Avance II+ spectrometer operating
at a 1H Larmor frequency of 600 MHz using a 1.3 mm Bruker
HXY probe or on a Bruker NEO spectrometer operating at a 1H Larmor frequency of 850 MHz using a 4 mm Bruker HXY probe in double-resonance
mode. A π/2 pulse of 2.5 μs and a recycle delay of 3 s
was used. 32 (600 MHz) or 4 (850 MHz) transients were co-added. The 1H spectra were referenced using the CH3 resonance
of
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