FTIR spectra were recorded on an infrared spectrophotometer (JASCO 6200, JASCO International Co., Easton, MD, USA), equipped with SPECTRA MANAGER v2 software (JASCO, International Co., Easton, MD, USA) and with an attenuated total reflectance (ATR) accessory. FTIR measurements were performed from 400 to 4000 cm−1 with a 0.25 cm−1 resolution.
Spectra manager v2
Manufactured by Jasco
Sourced in United States, Japan
Spectra Manager v2 is a software application designed for the analysis and management of spectroscopic data. It provides a comprehensive suite of tools for the visualization, processing, and interpretation of spectroscopic measurements. The software is compatible with a wide range of spectroscopic instrumentation and supports multiple data formats.
Automatically generated - may contain errors
Lab products found in correlation
Allegra x 15r centrifuge, by Beckman Coulter (2 mentions)
J 1500 spectrometer, by Jasco (1 mentions)
J 1500 circular dichroism spectrometer, by Jasco (1 mentions)
V 560 spectrophotometer, by Jasco (1 mentions)
J 815 circular dichroism spectropolarimeter, by Jasco (1 mentions)
J 815 cd spectropolarimeter, by Jasco (1 mentions)
J 810, by Jasco (1 mentions)
V 630, by Jasco (1 mentions)
V 660, by Jasco (1 mentions)
V 660 spectrophotometer, by Jasco (1 mentions)
Miracle atr, by PIKE Technologies (1 mentions)
J 810 cd spectrometer, by Jasco (1 mentions)
15 protocols using spectra manager v2
1
FTIR Spectroscopy of Diverse Samples
2
Protein Conformational Analysis by CD
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Experiments were carried on a Jasco J-1500 spectrometer equipped with a Peltier-cooled, six-position cuvette holder (0.3–10 μΜ protein; 20°C; buffer U or as indicated; data pitch, 1 nm; slit, 1 nm; signal averaging time, 1 s; 0.1 mm [Hellma] or 10 mm [Jasco] quartz cuvettes). Urea-purified proteins were incubated with 10 mM DTT (30 min; ice), dialyzed in buffer U supplemented with 5 liters 8M urea (15 h; 4°C). Natively purified proteins were dialyzed in 5 liters buffer U (15 h; 4°C). Samples were centrifuged (20,000 g; 20 min; 4°C) before determining protein concentration. Spectra were recorded (190–260 nm) in buffer U supplemented with 1 mM EDTA, 0.2 M urea, and DTT as indicated at 5 min, 1 h, or 24 h after the chaotrope dilution (n = 5). Data analysis was performed using the Spectra Manager v.2 software (Jasco).
3
Circular Dichroism Spectroscopy Protocol
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CD spectra were collected on a Jasco J-1500 Circular Dichroism Spectrometer. The system was purged with oxygen-free nitrogen for 10 minutes before lamp ignition and the lamp allowed to stabilise for at least 10 minutes before acquisition. A nitrogen purge flow of at least 5 L/min was employed during data collection. Temperature was regulated by a Peltier thermostat monitored at the cell holder at 20 °C.
CD spectra were collected from 400 nm down to 190 nm which was the limit of solvent absorption allowing a HT maximum of 600 V; scan speed was 50 nm/min, bandwidth 1 nm and 5 scans were averaged. Samples were measured in 1 mm path length quartz cuvettes at the specified concentration. Blank spectra were collected in the same cuvette as the sample using the same solvent, and subtracted from the sample spectra. Data analysis was performed with Jasco Spectra Manager v2 software. UV absorption spectra of the samples were collected on a Jasco V560 spectrophotometer in the same cuvettes over the range 400 to 210 nm.
CD spectra were collected from 400 nm down to 190 nm which was the limit of solvent absorption allowing a HT maximum of 600 V; scan speed was 50 nm/min, bandwidth 1 nm and 5 scans were averaged. Samples were measured in 1 mm path length quartz cuvettes at the specified concentration. Blank spectra were collected in the same cuvette as the sample using the same solvent, and subtracted from the sample spectra. Data analysis was performed with Jasco Spectra Manager v2 software. UV absorption spectra of the samples were collected on a Jasco V560 spectrophotometer in the same cuvettes over the range 400 to 210 nm.
4
FTIR Spectral Analysis of Samples
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The Fourier-transform infrared radiation (FTIR) spectral readings were noted at environment temperature by employing attenuated total reflection mode (ATR-FTIR) in a JASCO 6200 FT-IR (Tokyo, Japan) spectrometer with SPECTRA MANAGER V2 software (JASCO, Tokyo, Japan). The test sample was examined without advance conduct at ambient temperature with fifty scans and a 4 cm resolution [38 (link)].
5
Thermal Denaturation and Circular Dichroism Analysis
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Thermal denaturation and CD studies were performed using a Jasco J-815 Circular Dichroism (CD) Spectropolarimeter equipped with a temperature controller. For duplex formation, equimolar amounts of complementary sequences were combined, dried down and resuspended in 300 μl pH 7 sodium phosphate buffer (90.0 mM NaCl, 10.0 mM Na2HPO4, 1.00 mM EDTA). Samples were heated at 90°C for 2 min and then allowed to slowly cool to room temperature. To determine melting temperature (Tm), UV absorbance was measured at 260 nm and temperature was increased from 10 to 95°C at a rate of 0.5°C per minute. Tm data was analysed using Meltwin v3.5 software and represents the average of three independent runs. Circular dichroism spectra were recorded at 25°C, scanning from 200 to 350 nm with a screening rate of 20.0 nm/min and a 0.20 nm data pitch. All scans were performed in triplicate and averaged using Jasco's Spectra Manager v2 software.
6
Thermodynamic Analysis of Nucleic Acid Duplexes
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For duplex formation, equimolar amounts of the respective sense and antisense strands were combined, dried down and resuspended in 400 μL sodium phosphate buffer (90 mM NaCl, 10 mM Na2HPO4, 1 mM EDTA; pH 7.0). Samples were heated for 2 minutes at 90 °C and allowed to slowly equilibrate to room temperature. Thermal denaturation and CD studies were performed using a Jasco J-815 CD Spectropolarimeter equipped with a temperature controller. To determine the melting temperature (Tm) of each duplex, the change in absorbance at 260 nm was measured against a temperature gradient from 15 to 95 °C, at 0.5 °C min−1. Data were analysed using Meltwin v3.5 software. CD spectra were recorded at 25 °C, scanning from 200 to 40 nm with a screening rate of 20.0 nm min−1 and a 0.20 nm data pitch. Scans were performed in triplicate and averaged using Jasco's Spectra Manager v2 software.
7
Circular Dichroism Analysis of Recombinant Proteins
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Secondary structure content was analysed on a Jasco J-715 spectropolarimeter at 4 °C using 0.1 mg ml−1 of recombinant purified proteins in a 0.1-cm quartz cuvette. The measurements were performed in 10 mM HEPES 7.5, 100 mM NaCl, 10% glycerol and 5 mM DTT. Data were obtained and processed using the Spectra Manager v2.06 software from Jasco. The measured curves were buffer corrected and secondary structure assignments were done using the CONTIN fitting method and SMP56 as the reference protein set. Melting curves were measured continuously from 10 to 90 °C, with additional full spectra taken in 10 °C steps. Data analysis was performed in Spectra Manager v2.06.
8
CD Spectroscopy of Purified Proteins
9
Far-UV Circular Dichroism Spectroscopy
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The FUV-CD measurements were performed on JASCO (Tokyo, Japan) J-810 and J-1500 spectropolarimeters. The temperature of the cells was controlled by a Peltier-type heating system. JASCO Spectra Manager v2.0 was used to collect and process data. Samples were measured in 1.0 mm path-length quartz cuvettes at 25 °C. Each spectrum was the average of three scans collected as follows: spectral scanning speed of 50 nm/min; the bandwidth of 1 nm; 0.2 nm step resolution over the wavelength range of 185–260 nm (far-UV). All spectra were corrected by subtracting the solvent spectrum and by smoothing with a convolution width of seven, using the Savitzky-Golay method. The raw ellipticity (mdeg) data were converted into mean residue molar ellipticity units ([θ]MR/ deg cm2 dmol−1).
10
Far-UV CD Spectroscopy of SitA Protein
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Far-UV CD spectra were recorded from 190 to 260 nm at 25°C using a Jasco-810 spectropolarimeter (Jasco). The cuvette chamber temperature was regulated using a PCB-1500 Peltier temperature system controller (Perkin-Elmer). SitA samples with or without 1 mM MnCl2 were prepared at 0.2 mg.ml−1 (~6 μM) in 5 mM KH2NaPO4 buffer, pH 7.2. A quartz cuvette with an optical path length of 1 mm was used. Spectra were acquired at 1 nm bandwidth, 0.5 s response time, 0.2 nm step size and 10 nm.min−1 scan speed. Each spectrum was calculated as the average of five accumulations. The spectra were corrected by subtracting the buffer baseline followed by application of a smoothing function in Spectra Manager v2.0 (Jasco).
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