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9 protocols using j 720w spectropolarimeter

1

Circular Dichroism Spectroscopy of Recombinant DOG1

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Circular dichroism (CD) spectra of the purified recombinant DOG1 were recorded on a J-720W spectropolarimeter (Jasco) in the far-UV range from 185 to 260 nm using a 0.2-mm thermostatted cell at 25 °C, using the following parameters: resolution, 0.2 nm; bandwidth, 1.0 nm; sensitivity, 50 mdeg; response, 1 s; speed, 100 nm/min; accumulation, 8. Solutions used to record CD spectra contained apo-DOG1 or heme-bound DOG1 dissolved in 10 mM sodium phosphate buffer pH 7.5, with 5 mM DTT at protein concentration of 20 μM.
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2

Characterizing CDP Thermal Stability and Proteolysis

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In order to determine resistance to high temperatures, CDPs were incubated at 0.5 mM in PBS at 75° C or 100° C for 1 h, pelleted, and the supernatant analyzed by RPC. To determine resistance to proteolytic digestion, CDPs were mixed with 50 U of porcine pepsin (Sigma-Aldrich P7012) in Simulated Gastric Fluid43 (link) at pH 1.05, or 50 U of porcine trypsin (Sigma-Aldrich 6567) in PBS, incubated for 30 m at 37° C, and analyzed by RPC. Oxidized and reduced forms (adding 10 mM DTT) were compared. CD spectra were measured with a Jasco J-720W spectropolarimeter using a 1.0 mm path length cell, with CDPs diluted into 20 mM phosphate buffer, pH 7.4, at a concentration of 15–25 µM.
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3

Spectroscopic Analysis of Compounds

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Optical rotations were measured on a JASCO P-2200 polarimeter in a 0.5-dm cell. UV spectra were obtained with a Shimadzu BioSpec-mini spectrophotometer. The ECD spectra were measured on a JASCO J-720W spectropolarimeter in a 10-mm cell. The IR spectra were measured on a JASCO FT/IR-4100 Fourier transform infrared spectrometer using a KBr disk. The NMR spectra were measured on a JEOL ECA-500 spectrometer with deuterated solvent used as the internal reference. The 1H NMR spectra were measured at 500 MHz, and the 13C NMR spectra were measured at 125 MHz. HRESIMS was conducted using a Q-Exactive Hybrid Quadrupole Orbitrap mass spectrometer. Diaion HP-20 (Mitsubishi Chemical Corporation, Tokyo, Japan), Silica gel (Chromatorex PEI MB 100–40/75, Fuji Silysia Chemical Ltd., Aichi, Japan), and ODS (Cosmosil 75C18-PREP, Nacalai Tesque, Inc., Kyoto, Japan) were used for column chromatography. For preparative HPLC, a Waters 515 HPLC pump, equipped with an ERC RefractoMax520 differential refractometer detector and a Shimadzu SPD-10A UV-vis detector were used. For reversed-phase HPLC separations, a RP-C18 silica gel column (YMC-Actus Triart C18, 5 μm, 150×20 mm) was used, at a flow rate of 8.0 mL/min.
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4

Spectroscopic Analysis of Chemical Compounds

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Optical rotations were measured using a JASCO DIP-1000 polarimeter. UV spectra were recorded on a JASCO V730-BIO Spectrophotometer. CD spectra were measured using a JASCO J-720 W spectropolarimeter. IR spectra were recorded on a JASCO FT/IR-4200 spectrometer. All NMR data were recorded on a JEOL JNM-ECX400 spectrometer for 1H (400 MHz) and 13C (100 MHz). 1H NMR chemical shifts (referenced to residual CHCl3 observed at δH 7.26) were assigned using a combination of data from COSY and HMQC experiments. Similarly, 13C NMR chemical shifts (referenced to CDCl3 observed at δC 77.16) were assigned based on HMBC and HMQC experiments. HRESIMS spectra were obtained on an LCT premier XE time-of-flight (TOF) mass spectrometer (LCT premier XE; Waters). Reverse-phase HPLC was performed (500 × 10 mm I.D. ODS AQ-325; YMC Co., Ltd., Kyoto, Japan), eluted at a flow rate of 1.5 mL/min with 45% (v/v) aqueous methanol, and detected at wavelength 220 nm.
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5

CD Analysis of DNA Thermal Stability

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CD spectra of CT DNA upon heating were measured in the presence of each polyamine in 1 mM Tris‐HCl buffer (pH 7.5) on a J‐720W spectropolarimeter (JASCO, Tokyo, Japan). The DNA concentration was 30 μM in nucleotide units for all of the CD measurements. The cell path length was 1 cm. Data were collected every 1 nm between 220 and 340 nm at a scan rate of 100 nm/min, and were accumulated 3 times.
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6

Characterizing CDP Thermal Stability and Proteolysis

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In order to determine resistance to high temperatures, CDPs were incubated at 0.5 mM in PBS at 75° C or 100° C for 1 h, pelleted, and the supernatant analyzed by RPC. To determine resistance to proteolytic digestion, CDPs were mixed with 50 U of porcine pepsin (Sigma-Aldrich P7012) in Simulated Gastric Fluid43 (link) at pH 1.05, or 50 U of porcine trypsin (Sigma-Aldrich 6567) in PBS, incubated for 30 m at 37° C, and analyzed by RPC. Oxidized and reduced forms (adding 10 mM DTT) were compared. CD spectra were measured with a Jasco J-720W spectropolarimeter using a 1.0 mm path length cell, with CDPs diluted into 20 mM phosphate buffer, pH 7.4, at a concentration of 15–25 µM.
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7

Synthesis and Characterization of Chiral Phosphonic Acid

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R- or S-(1-phenylethylamino)methylphosphonic acid (pempH2) was prepared according to methods reported in the literature38 (link). All other starting materials were of reagent grade and were used as received from commercial sources without further purification. Elemental analyses for C, H and N were carried out on a PE 240C analyser. IR spectra were recorded with a Bruker Tensor 27 spectrometer using KBr discs. The pH value was measured by a Sartorius PB-10 pH metre. Thermal analyses were performed under nitrogen in the temperature range of 25–800 °C at a heating rate of 5 °C min−1 on a METTLER TOLEDO TGA/DSC 1 instrument. PXRD data were collected using a Bruker D8 advance diffractometer. SEM measurements were performed on SHIMADZU SSX-550. The UV–Vis spectra were recorded on Perkin Elmer Lambda 950 UV–Vis/NIR Spectrometer. The circular dichroism spectra were recorded on a JASCO J-720 W spectropolarimeter at room temperature. The simultaneous CD and LD measurements were conducted for R-1 and S-1 using the multi-probe function in the J-1500 CD spectrometer. Each sample was diluted by KCl with a ratio of 1/50 and pressed into a pellet.
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8

Structural Characterization of CDPs

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All proteins were analyzed by SDS-PAGE (NuPAGE 4–12% Bis-Tris, Thermo Fisher) and Coomassie staining; full gels can be found in Fig. S12. CDPs were run both non-reduced and reduced with 10 mM DTT. Proteolysis and reduction resistance testing was performed on the same RP-HPLC instrumentation as used for purification, after treatment of ~10 μg CDP with either 50 U of porcine pepsin (Sigma-Aldrich P7012) in 100 μL simulated gastric fluid [54 (link)] or 50 U of porcine trypsin (Sigma-Aldrich 6567) in 100 μL PBS followed by incubation for 30 min at 37°C. Similarly, glutathione or DTT reduction involved treatment of the CDPs with 10 mM glutathione or DTT in PBS for > 5 min prior to RP-HPLC analysis. CD spectra of TfRB1G3 were measured with a Jasco J-720W spectropolarimeter (1 mm path length) in 20 mM phosphate buffer, pH 7.4, with or without 10 mM DTT at a concentration of 15–25 μM. Data are expressed in terms of relative ellipticity [θ] change at 210 nm, reported in mdeg.
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9

Myoglobin Structural Analysis Protocol

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Myoglobin (horse heart: M1882; ≥ 90%) , SDS (71725; ≥ 99%) , and NaCho (C6445; ≥ 99.0%) were purchased from Sigma-Aldrich Co., U. S.
Sodium phosphate buffer (pH, 7.0; ionic strength, 0.014 [14] [15] [16] ) was exclusively used to prepare each solution. Absorbance and CD were measured using Hitachi U-3310 spectrophotometer and JASCO J-720W spectropolarimeter, respectively, at 25℃. The concentration of Myoglobin was determined spectrophotometrically using ε 409 =1.71×10 5 M -1 cm -1 13) and adjusted to 10 µM. A 1.0 mm-path length cell was used in the CD measurement.
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