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NM 295

NM 295 is a unique molecular entity that has garnered significant interest in the scientific community.
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Most cited protocols related to «NM 295»

Whole Cell Lysate Protein Quantification

Cited 15 times

Protein content was determined using a Cary Eclipse Fluorescence Spectrometer (Varian, Palo Alto, CA) as described previously (17 ). Briefly, aliquots of 1 to 3 μl of whole cell lysates were mixed with 2 ml of 8 m urea in 10 mm Tris-HCl, pH 8.5. The fluorescence was measured at 295 nm for excitation and 350 nm for emission. The slits were set to 5 nm and 20 nm for excitation and emission, respectively. Tryptophan was used as a standard. The protein content was calculated from the following relationship: the fluorescence of 0.1 μg of tryptophan equals 9 μg of total protein, which reflects an average 1.1% weight content of tryptophan in whole lysates of human cells.

Wiśniewski J.R., Hein M.Y., Cox J, & Mann M. (2014). A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards. Molecular & Cellular Proteomics : MCP, 13(12), 3497-3506.

Publication 2014

Cells Fluorescence Homo sapiens NM 295 Proteins Tromethamine Tryptophan Urea

Spectroscopic Analysis of DNA Structures

Cited 6 times

All spectra were recorded on a Uvikon XL spectrophotometer in 10 mM lithium cacodylate buffer (pH 7.2) at 3 or 4 μM oligonucleotide strand (except when stated otherwise) supplemented with 100 mM KCl.
Thermal difference spectra (TDS) were obtained by taking the difference between the absorbance spectra of unfolded and folded oligonucleotides that were recorded at high (>90°C) and low (4°C) temperatures, respectively in buffer containing 100 mM KCl. TDS provide specific signatures of different DNA structural conformations, provided that the structure is not too heat stable (a number of G4 structures do not melt at high temperatures) (27 (link)).
Isothermal difference spectra (IDS) were obtained as described previously in (25 (link)) by taking the difference between the absorbance spectra from unfolded and folded oligonucleotides. These spectra were respectively recorded before and after potassium cation addition (100 mM KCl) at 20°C. IDS provide specific signatures of different DNA structural conformations.
UV melting experiments to determine melting temperatures (T_m) of G4 structures were performed as previously described (28 (link),29 ). G4 unfolding is typically associated with a decrease in absorbance at 295 nm, giving an inverted transition at this wavelength.

Bedrat A., Lacroix L, & Mergny J.L. (2016). Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Research, 44(4), 1746-1759.

Publication 2016

Buffers Cacodylate DNA Conformation Fever Lithium NM 295 Oligonucleotides Potassium

Fluorescence-Based Protein Denaturation Assay

Cited 5 times

Solutions of buffer and concentrated denaturant in buffer are first dispensed into Greiner Bio-One® 96-well, F-bottom, black polystyrene plates (655076) using a Microlab ML510B dispenser. We typically dispense denaturation curves in 0.1 M denaturant steps. The protein is then dispensed from a 10x concentrated stock. All plate measurements were carried out on a CLARIOstar Plate Reader (BMG Labtech) with a tryptophan detection set-up comprising two filters - an excitation filter of 295 nm and an emission filter of 360 nm - and excitation and emission bandwidths of 10 nm. The 295 nm filter is used for selective excitation of tryptophan residues. Alternatively a 280 nm filter can be used to excite both tryptophan and tyrosine residues. The high sensitivity of this state-of-the-art instrument allows readings at sub-micromolar concentrations of protein (the concentration required will, of course, depend on the number of aromatic residues in the protein and the magnitude of the fluorescence change upon unfolding).
Well volume and protein concentration are important factors for optimal signal to noise, but at the same time they will have an impact on the quantity of protein used. We find that a well volume of 150 µl is sufficient. Larger volumes will give a larger signal but will require a larger quantity of protein. We recommend a 10 µM protein stock solution, which will be diluted ten-fold to 1 µM upon dispensing. With the appropriate dispenser, the total sample volume could be further reduced to 100 µl or less.
For each protein, three sets of serial dilutions were plated consecutively. These sets can be from the same sample stock (technical replicates) or from different purifications (biological replicates). Plates were covered with a Corning® 96-well microplate aluminium sealing tape to minimise evaporation, shaken for 30 s using the CLARIOstar double-orbital shaking option, and incubated at 25 °C for 1 h. The instrument settings in the BML Labtech software were set for reading through the top orbital and “precise” rather than “rapid” measurements. Both focus height and gain were set using the fluorescence of the well having the highest fluorescence intensity. The gain adjustment was then set at 70% to prevent saturation at one or other denaturation baselines. For a good signal-to-noise ratio, we recommend to aim for a 1.5–3-fold difference in fluorescence intensity between the folded and the unfolded states.

Perez-Riba A, & Itzhaki L.S. (2017). A method for rapid high-throughput biophysical analysis of proteins. Scientific Reports, 7, 9071.

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Publication 2017

Aluminum AURKB protein, human BaseLine dental cement Biopharmaceuticals Buffers Fluorescence Hypersensitivity NM 295 Phocidae Polystyrenes Proteins Staphylococcal Protein A Technique, Dilution Tryptophan Tyrosine

Folding Thermodynamics of PagP Protein Mutants

Cited 5 times

The PagP samples for equilibrium folding and unfolding in DPC were prepared by 10-fold dilution of the respective protein stocks in various GdnHCl concentrations ranging from ∼0.7 to ∼6.6 m, at an increment of 0.1 m. This gave us a final protein concentration of 3 μm and DPC of 10 mm in each reaction. Samples were incubated at 25 °C, and fluorescence measurements were acquired on a microplate reader at the same temperature. We monitored the progress of the reactions using the decrease in tryptophan fluorescence emission intensity, with increase in GdnHCl concentration. Spectra were acquired using a λ_ex of 295 nm and λ_em of 320–400 nm. For PagP and its mutants, equilibrium for the reaction was achieved within 24 h.
From the fluorescence profiles, we calculated the unfolded fraction (f_U) for the 48-h data using the following equation.

f_{U} = \frac{y_{O} - (y_{F} + m_{F} [D])}{(y_{U} + m_{U} [D]) - (y_{F} + m_{F} [D])}

Here, y_O is the observed fluorescence at GdnHCl concentration [D], whereas y_F, m_F, y_U, and m_U are intercepts and slopes of the pre- and post-transition baselines, respectively.
We were able to explain the folding transitions for most of the mutants using the two-state equation (42 (link)).

f_{U} = \frac{\exp (- (Δ G + m [D]) / R T)}{1 + \exp [- (Δ G + m [D]) / R T]}

This equation assumes that the protein folds in a cooperative manner from the unfolded (U) to the folded (F) state, without a detectable folding intermediate. We obtained the thermodynamic parameters ΔG⁰ (ΔG_F^0,H2O, folding free energy) and m value (change in ASA between U and F states) of folding from the fits. The midpoint of chemical denaturation (C_m) was calculated as C_m = ΔG/m.
The folding transition of some mutants could only be explained using a three-state equation (Equation 3), due to the occurrence of an intermediate (I) (7 (link)).

f_{U} = \frac{(y_{F} + m_{F} [D]) + (\exp (- \frac{Δ G_{1} + m_{1} [D]}{R T}) (y_{I} + m_{I} [D])) + (\exp (- \frac{Δ G_{1} + m_{1} [D]}{R T}) \exp (- \frac{Δ G_{2} + m_{2} [D]}{R T}) (y_{U} + m_{U} [D]))}{1 + \exp (- \frac{Δ G_{1} + m_{1} [D]}{R T}) + \exp (- \frac{Δ G_{1} + m_{1} [D]}{R T}) \exp (- \frac{Δ G_{2} + m_{2} [D]}{R T})}

Here, we obtained ΔG₁ and ΔG₂ and their corresponding m₁ and m₂ values for the change in free energy from the first (U → I) and second (I → N) transitions, respectively.
The PagP samples for folding in DLPC were prepared as described above. We used the same parameters for data acquisition in DLPC samples as for DPC. From the fluorescence profiles, we calculated the unfolded fraction (f_U) for the 48-h data using Equation 1. The data were fitted globally to Equation 2, assuming a common m value. Fits of the data to Equation 2 yielded the apparent thermodynamic parameters, namely the apparent change in free energy ΔG_app, apparent ASA change m_app, and C_m for each mutant.

Iyer B.R., Zadafiya P., Vetal P.V, & Mahalakshmi R. (2017). Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein. The Journal of Biological Chemistry, 292(29), 12351-12365.

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Publication 2017

BaseLine dental cement Fluorescence NM 295 Proteins Seizures Staphylococcal Protein A Technique, Dilution Tryptophan

Phosphoproteomics Workflow for Unstimulated HeLa Cells

Cited 5 times

Peptides were collected from a population of 1e8 unstimulated HeLa cells prepared using the filter-aided sample preparation method (17 (link)). In brief, cell pellets were solubilized in 4% SDS, 100 mm Tris/HCl, pH 7.6, 0.1 m DTT; incubated at 95 °C for 5 min; and sonicated at duty cycle 30% and output control 3 (Branson Ultrasonics). The protein concentration was determined from tryptophan fluorescence emission at 350 nm using an excitation wavelength of 295 nm. A total of 30 mg of protein extract was then split on top of five 30,000 molecular weight cutoff centrifugal filters (20 mg per filter), spun down, and washed twice with 7 ml of 8 m urea, 100 mm Tris/HCl, pH 8.5. Alkylation was performed with 50 mm iodoacetamide for 30 min at room temperature in the dark in the same buffer. After two further washes with 7 ml of 8 m urea, Tris/HCl, pH 8.5, in 0.1 m and three with 7 ml of NH₄HCO₃, digestion was performed by adding LysC at an enzyme:protein ratio of 1:50 and incubating overnight at 30 °C. The digested peptides were eluted from the filters via centrifugation, quantified with a NanoDrop spectrophotometer, and then further digested by trypsin added at a ratio of 1:100. After incubation at 37 °C for 5 h, peptides were shock frozen in liquid nitrogen and lyophilized. Peptides (around 10 mg per Falcon tube) were re-suspended in 10 ml of ACN 80%, TFA 6%, and insoluble peptides were spun down by centrifugation at 100g for 1 min. Supernatants were moved into new 15-ml Falcon tubes, and samples were incubated twice with 50 mg of TiO₂ beads on a rotating wheel for 45 min. TiO₂ beads from all the enrichments were then pooled together and washed three times with 12 ml of ACN 80%, TFA 6% and three times with 12 ml of ACN 80%, TFA 0.1%. Beads were then re-suspended in 2 ml of ACN 80%, TFA 0.1%, transferred into 12 Empore-C8 StageTips (18 (link)), and washed once with ACN 80%, TFA 0.1%. Peptides were eluted from each StageTip with 200 μl of 60% NH₄OH (25% NH₃ solution in H₂O) in 40% ACN. The volume was reduced via SpeedVac to 10 μl to eliminate ACN and brought back up to 200 μl with 0.1% formic acid. Phosphorylation enriched peptides were pooled and purified with Sep-Pak tC₁₈ cartridges according to the manufacturer's instructions. The peptide concentration was determined using a NanoDrop spectrophotometer. The final concentration was brought to 400 ng/μl with 0.1% formic acid, and 5.5-μl aliquots were frozen at −20 °C.

Scheltema R.A., Hauschild J.P., Lange O., Hornburg D., Denisov E., Damoc E., Kuehn A., Makarov A, & Mann M. (2014). The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer. Molecular & Cellular Proteomics : MCP, 13(12), 3698-3708.

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Publication 2014

Alkylation Buffers Cells Centrifugation Digestion Empore Enzymes Fluorescence formic acid Freezing HeLa Cells Iodoacetamide Nitrogen NM 295 Pellets, Drug Peptides Phosphorylation Proteins Re 80 Shock Staphylococcal Protein A Tromethamine Trypsin Tryptophan Ultrasonics Urea

Most recents protocols related to «NM 295»

Quantification of Squalene, Sterols, and Tocopherols

The analysis of squalene and sterols (including cholesterol, stigmasterol, campesterol, and β-sitosterol) was based on Slavin et al.^{66 (link)}. 0.2 g freeze-dried sample was extracted and saponified. The contents of sterols and squalene were analyzed by HPLC using 100% methanol mobile phases. As previously described, the UV absorption was monitored at 204 nm and the solvent flow rate was set at 1.0 mL∙min⁻¹. Sui et al.’s^{67 (link)} extraction method was used to extract the tocopherols (α-tocopherol, ϒ-tocopherol, and δ-tocopherol). Specifically, 0.1 g lyophilized sample and 0.125 g ascorbic acid were extracted with ethanol and n-hexane, and dried using a stream of nitrogen at room temperature. The extract was redissolved in methanol for HPLC detection. As described, 100% methanol was used as the mobile phase, whose flow rate was 1.0 mL∙min⁻¹. UV absorption was monitored at 295 nm.

Wang S., Feng Y., Lou Y., Niu J., Yin C., Zhao J., Du W, & Yue A. (2023). 3-Hydroxy-3-methylglutaryl coenzyme A reductase genes from Glycine max regulate plant growth and isoprenoid biosynthesis. Scientific Reports, 13, 3902.

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Publication 2023

alpha-Tocopherol Ascorbic Acid campesterol Cholesterol delta-tocopherol Ethanol Freezing High-Performance Liquid Chromatographies Methanol n-hexane Nitrogen NM 295 Phytosterols sitosterol Solvents Squalene Stigmasterol Tocopherol Vitamin E

Intrinsic Tryptophan Fluorescence of TMPs

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Publication 2023

Fluorescence NM 295 Tryptophan

Kinetic Analysis of HsUMPS Enzyme

The enzyme kinetics of HsUMPS enzyme were monitored by absorbance changes over time at 279 nm for the production of UMP and at 295 nm for the consumption of orotate. These reactions were conducted at 25 °C on a Synergy Neo2 microplate reader (BioTek) or SpectraMax M2 (Molecular Devices). The standard assay conditions contained 50 mM Tris pH 8.0, 100 mM NaCl, 2 mM MgCl₂. For kinetic assays, the mixture consisted of either 100 μM PrPP with varying concentrations of orotate (0–200 μM) or varying concentrations of OMP (0–200 μM). In all cases, the reaction was initiated by the addition of protein (5–50 pmol). Absorbance data were collected in triplicate, averaged, and plotted as mean ± standard error. To calculate kinetic parameters, initial rate date (before 10% reaction completion) was fit with the Michaelis–Menten equation.

Kim-Holzapfel D.M., Dey R., Richardson B.C., Arachchige D., Reddy K., De Vitto H., Bhandari J, & French J.B. (2023). Human uridine 5′-monophosphate synthase stores metabolic potential in inactive biomolecular condensates. The Journal of Biological Chemistry, 299(3), 102949.

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Publication 2023

Biological Assay Cell Motility Assays Enzymes Kinetics Magnesium Chloride Medical Devices NM 295 Phosphoribosyl Pyrophosphate Proteins Sodium Chloride Tromethamine

Oligonucleotide Spectroscopic Characterization

Unlabeled and labeled oligonucleotides were prepared in 50 mM Tris–HCl, pH 7.5, with appropriate salt as stated in the text, and had a final DNA concentration of 2.5 μM. UV or CD spectra were obtained using a UV/Vis spectrophotometer (PerkinElmer Lambda 25) or a CD spectrophotometer (Jasco J-810) measuring the sample in a 1 cm path length 3 ml or 100 μl quartz cuvette (Hellma), respectively. All melting curves were acquired at 295 nm with a gradient of 0.2°C min⁻¹. Melting curves were plotted as described in ref. (66 (link)). CD spectra were recorded at room temperature unless otherwise specified and background corrected before analysis.

Kristoffersen E.L., Coletta A., Lund L.M., Schiøtt B, & Birkedal V. (2023). Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Research, 51(4), 1571-1582.

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Publication 2023

DNA, A-Form NM 295 Oligonucleotides Quartz Sodium Chloride Tromethamine

OPTN RNA Binding Dynamics

One proposed function of OPTN is to bind RNA.^{35 (link)} A specific RNA sequence 5′ UGUGUGUGUGUGUGUGUGUGUGUG 3′, was custom synthesized based on a consensus sequence to which RNA-binding proteins like FUS and TDP43 binds.^{41 (link)} A stock solution of 100 μM RNA was prepared in nuclease-free water. OPTN was taken at 7.5 μM concentration in a 1 cm quartz cuvette as the analyte and titrated against increasing concentrations of RNA from 0.5–15 μM, till saturation was reached. Following excitation at 295 nm, the fluorescence emission for each sample was recorded from 310 nm to 400 nm. Tryptophan fluorescence quenching of OPTN in the presence of RNA was analysed through the Stern–Volmer equation;^{42 (link)} where F₀ and F are the tryptophan fluorescence intensities in the presence and absence of RNA (quencher), respectively, [Q] is the concentration of RNA, and K_SV is the Stern–Volmer quenching constant.
To analyse the binding interaction between OPTN and RNA, the binding constant was determined from the static quenching interaction. The following equation^{42 (link)} was used to determine the equilibrium between the free and bound species; where K is the binding constant and n is the number of binding sites.
To assess RNA binding with denatured OPTN, the fluorescence titration experiments were simultaneously performed at 60 °C.
To assess the functional reversibility of OPTN from a thermally denatured state, the heated and cooled protein was again titrated with an increasing concentration of RNA, and the binding constants in each case were determined as mentioned above.

Dixit A., Chakraborty A., Nath J.R., Chowdhury P.K, & Kundu B. (2023). Ocular protein optineurin shows reversibility from unfolded states and exhibits chaperone-like activity. RSC Advances, 13(10), 6827-6837.

Publication 2023

Binding Sites Consensus Sequence Fluorescence FUS protein, human NM 295 Proteins protein TDP-43, human Quartz RNA-Binding Protein FUS RNA Sequence Titrimetry Tryptophan

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What is NM 295 and why is it important?

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Are there different variations or types of NM 295?

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What are some specific applications of NM 295?

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More about "NM 295"

Discover the power of PubCompare.ai in optimizing your research for NM 295, a unique molecular entity that has garnered significant interest in the scientific community.
Our AI-driven platform helps you effortlessly locate the best protocols from literature, pre-prints, and patents, enabling you to identify the most effective products and strategies for your research.
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Explore the key features and applications of NM 295 using a variety of spectroscopic techniques, such as the Fluoromax-3 spectrofluorometer, Cary Eclipse Fluorescence Spectrophotometer, V-650 spectrophotometer, Cary Eclipse, FluoroMax-4, LS55 spectrofluorometer, Fluorolog-3 spectrofluorometer, and the F-7000 fluorescence spectrophotometer.
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