The largest database of trusted experimental protocols

29 protocols using cary 3500 uv vis spectrophotometer

1

Thermal Denaturation of HP1-UUCG RNA

Check if the same lab product or an alternative is used in the 5 most similar protocols
Thermal denaturation of HP1-UUCG was monitored on a CARY3500 UV/vis spectrophotometer (Agilent) equipped with an eight-position sample holder and a Peltier temperature control accessory. The experiments were performed at 1 µM final concentration in 50 mM sodium phosphate buffer, at pH 5.2, 6.4 and 7.5 at 20°C, in 100 µL micro quartz cuvettes. The RNA was refolded as described above and the magnesium was next added in order to have a monomeric form of HP1 as we previously determined. For each pH, magnesium was added at concentrations ranging from 0.1 to 6 mM. A cuvette that contained the buffer with no magnesium was used as a reference. Samples were overlaid with 200 µL of mineral oil to prevent evaporation at high temperature. An initial 15 min equilibrium time at 25°C was included prior to the temperature ramping. Denaturation of the samples was achieved by increasing the temperature at 1°C/min from 25 to 95°C and followed at 260 nm. The melting temperature (Tm) was determined as the maximum of the first derivative of the UV melting curves. Each experiment was repeated independently two or three times.
+ Open protocol
+ Expand
2

Thermal Stability Analysis of Nucleic Acids

Check if the same lab product or an alternative is used in the 5 most similar protocols
Melting experiments were performed on Cary 3500 UV-Vis spectrophotometer (Agilent Technologies, Santa Clara, CA, USA). A temperature range from 5 to 95 °C was scanned while monitoring absorbances at 260 nm and 295 nm with 0.5 °C min−1 melting/annealing rate. Sample solutions contained 100 mM KCl and 20 mM K-phosphate buffer (pH 6.5). Measurements were made in 1 cm path-length cells.
+ Open protocol
+ Expand
3

Thermal Stability of dsRNA Analyzed by UV-Vis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Absorbance spectra (225 nm to 340 nm) were collected with a scan speed of 3,000 nm/min and a data interval of 1 nm on a Cary 3500 UV-Vis spectrophotometer (Agilent) at two temperatures, one above (95 °C) and one below (20 °C) the Tm of all dsRNAs under study. Samples contained ∼25 μg of RNA in a solution of 25 mM 3-(N-morpholno)propanesulfonic acid (pH 7.4) containing 10 mM NaCl, 7 mM MgCl2, and 0.1 mM ethylenediaminetetraacetic acid. Individual spectra were normalized and difference spectra obtained by subtracting the low-temperature spectrum from the high-temperature spectrum (SI Appendix, Fig. S3A). Final plots were cut at 240 nm due to variability at shorter wavelengths (225 nm to 240 nm; SI Appendix, Fig. S3B) despite minimal variability between dsRNA preparations (SI Appendix, Fig. S3C). Three independent experiments were plotted with SEM using GraphPad Prism 9.
+ Open protocol
+ Expand
4

Partition Coefficient Determination of CAPE

Check if the same lab product or an alternative is used in the 5 most similar protocols
Organic solvents (1-octanol)/aqueous (100 mM phosphate buffer at pH 7.4) phase partition for CAPE and its analogues were conducted using the shake-flask method [38 (link)], with the concentration in each phase determined by a Cary 3500 UV–Vis spectrophotometer (Agilent, Santa Clara, CA, USA).
+ Open protocol
+ Expand
5

Rapamycin-Induced Protein Aggregation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Protein aliquots were thawed
and solubilized at 50 °C and then diluted to 6 μM in buffer
to adjust to a final salt concentration of 150 mM in 20 mM, Tris-HCl,
pH 8.5. SYNZIP-tagged constructs were similarly adjusted to 10 μM
in 150 mM NaCl, 20 mM HEPES, pH 6.8. The protein mixture, 60 μL
in volume, was added to quartz microcuvettes (10 mm path length) (Starna
Cells, Inc. Atascadero, CA). Cuvettes were inserted into a Cary 3500
UV–vis spectrophotometer controlled by an Agilent multizone
Peltier temperature controller (Agilent Technologies; Santa Clara,
CA). To test kinetics of rapamycin-induced dimerization and phase
separation of FRB and FKBP-tagged RGG constructs, rapamycin (Sigma-Aldrich;
St. Louis, MO) was spiked into the protein mixtures to a final concentration
of 10 μM and absorbance at 600 nm was measured over time. For
mapping the temperature-dependent phase separation, protein mixtures
were applied to quartz cuvettes preincubated at 50 °C. Cuvettes
were then inserted into the preheated spectrophotometer, set to 50
°C, and samples were cooled to 5 °C at a rate of 1 °C/min
while measuring the absorbance at 600 nm.
+ Open protocol
+ Expand
6

Dextran Turbidity Measurement Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
The turbidity of dextran samples with various material properties and solution conditions was obtained by measuring solution absorbance at 400 nm wavelength as a function of temperature. All samples were characterized in a glass cuvette for turbidity assay using a Cary 3500 UV–Vis spectrophotometer (Agilent Technologies, Santa Clara, CA) equipped with a temperature-controlled cell holder. The solution temperature was increased from 10 to 60 °C at a constant 1 or 2 °C/min interval heating scanning rate until a plateau was achieved in absorbance value. A baseline absorbance curve of PBS solution was collected as a reference before each sample run. The transition temperature was determined considering the start of the rise in the absorbance value of the UV–Vis spectra.
+ Open protocol
+ Expand
7

UV Spectroscopic Analysis of Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols
An Agilent Cary 3500 UV-Vis spectrophotometer (Melbourne, Australia) was used to obtain UV absorbance spectra. Samples were prepared in water at room temperature. A 1 cm quartz cuvette was used to collect data from 190–400 nm, with water as the reference. To determine the extinction coefficients, a concentrated stock solution of each complex (1 mM) was initially prepared in water and aliquoted (2–5 µL) into a cuvette containing water (3000 µL). Experiments were repeated in triplicate and the average extinction coefficients were calculated.
+ Open protocol
+ Expand
8

Spectrophotometric Determination of Photoprotective Capacity

Check if the same lab product or an alternative is used in the 5 most similar protocols
The photoprotective capacity of SR hydroethanolic extract and its fractions was determined spectrophotometrically according to the method described by Oliveira et al. [70 (link)]. As a universal measure of photoprotective activity, the sun protection factor (SPF) was calculated. Solutions of examined samples at concentrations of 0.05, 0.1 and 0.2 mg/mL were prepared in phosphate buffer (pH 7.0). Absorption of each solution was measured in triplicate at 290–320 nm, with 5 nm increments, using Agilent Cary 3500 UV-Vis Spectrophotometer. Phosphate buffer was used as a blank. SPF was calculated using the following formula: SPF=CF×290320EE(λ)I(λ)Abs(λ)
where CF is the correction factor (equal to 10); EE (λ) is the erythemal effect spectrum; I (λ) is the solar intensity spectrum, and Abs (λ) is the absorbance of the solution at a wavelength (λ). The values of EE × I are constants, and were determined by Sayre et al. [71 (link)].
+ Open protocol
+ Expand
9

UV Melting of DNA Oligonucleotides

Check if the same lab product or an alternative is used in the 5 most similar protocols
UV melting experiments were carried out on Agilent Cary 3500 UV-Vis spectrophotometer with the Cary Win UV Thermal program in 1.0 cm path length quartz cuvettes. The samples were prepared from the same stock solution as NMR samples and diluted to 5 μM DNA concentration by 20 mM KPi buffer of pH 7.2. The samples were heated and cooled in a temperature range from 10 to 90°C at a rate of 0.5°C·min−1. The absorbance was monitored at 260 nm in 0.5°C steps. The heating and cooling were repeated twice and only the second round was used for the analysis. The temperatures of mid-transition (T1/2) were determined from a zero-crossing of the second derivative of heating/cooling curves, which were smoothened using a Savitzky-Golay 20-point quadratic function. The error in determination of T1/2 is estimated to be ±1°C based on the repeated measurements. The data processing was done in Origin 2018.
+ Open protocol
+ Expand
10

Synthesis and Loading Determination of Fmoc-PAMBA-OH Resin

Check if the same lab product or an alternative is used in the 5 most similar protocols
An amount of 1 g of 2-chlorotrityl chloride resin (approx. 1.6 mmol chloride) was pre-swelled for 30 min in 10 mL of dry dichloromethane (DCM) in a syringe reactor (Multisyntech, Witten, Germany). Then DCM was removed by vacuum filtration. The resin was agitated for 60 min with a solution containing 3 mL of N,N-dimethylformamide (DMF), 4 mL of dry DCM, 0.6 mmol of 4-(Fmoc-aminomethyl)benzoic acid (Fmoc-PAMBA-OH) and 1.8 mmol N,N-diisopropylethylamine (DIPEA). Afterwards, the solution was discarded by vacuum filtration and a capping solution containing 4 mL DCM, 3 mL methanol and 500 μ L DIPEA was added. After agitation for 30 min, the solution was removed and the resin was washed three times with DMF and DCM. The resin was dried under high vacuum and three samples were taken for loading determination. The samples were agitated with 1 mL of 20% piperidine in DMF at RT for 1 h. 50 μ L of the supernatant of each sample was diluted with 1.95 mL DMF and the absorbance at 301 nm was measured with a Cary 3500 UV-Vis spectrophotometer (Agilent Technologies, U.S.). As blank solution, 50 μ L of 20% piperidine in DMF diluted with 1.95 mL DMF was used. The resin loading was determined based on the following formula: resin load[mmol/g]=(A301nm×1000)/(resin mass[mg]×7800[L×mol-1×cm-1]×0.025)
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!