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16 protocols using 1 cm quartz cuvette

1

Dityrosine Fluorescence and Absorbance Assay

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Dityrosine has a fluorescence maximum at 410 nm, using an excitation wavelength of 310 nm. Dityrosine emission was monitored between 300 and 500 nm using a 1 cm quartz cuvette (Hellma) and a Hitachi F-2500 fluorescence spectrophotometer.
UV absorbance was also used to monitor dityrosine production of the covalent dimer by monitoring the absorbance spectrum at 315 nm with an extinction coefficient of 5,000 M−1 cm−171 (link),72 (link), using a 1 cm quartz cuvette (Hellma). Difference spectra, with non-oxidized Aβ subtracted from each spectrum are presented.
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2

Amyloid-beta Preparation and Quantification

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Aβ was prepared by dissolution in 10% (v/v) 60mM NaOH, 45% (v/v) Milli-Q water, and 45% (v/v) 22.2 mM sodium phosphate, pH 7.5, to yield a nominal Aβ concentration of 1 mg/mL in 10 mM sodium phosphate, pH 7.5. The Aβ solution then was sonicated for 1 min in a bath sonicator (Branson Model 1510, Danbury, CT, USA) and filtered through a prewashed 30,000 molecular weight cut-off Microcon centrifugal filter device (Milli-pore, Billerica, MA, USA) for 15 min at 16,000 × g. The eluate containing Aβ was quantified using UV absorbance (ε280 = 1280 cm−1 M−1), using a 1 cm quartz cuvette (Hellma, Plainview, NY, USA) and a Beckman DU-640 spectrophotometer (Beckman Instruments, Fullerton, CA, USA), prepared with 10 mM sodium phosphate, pH 7.5. All measurements were performed at 22°C.
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3

Peptide-Cu(II) Binding Analysis

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A total volume of 1 mL of 100 μM peptide sample was prepared in a 1 cm quartz cuvette (Hellma, Müllheim, Germany) and titrated with 5 mM CuCl solution in the glove box. Between each titration step the cuvette was sealed with a vacuum grease-coated cap and circular dichroism (CD) and absorption spectra were measured outside the glove box.
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4

Preparation of Uniform LMW Aβ Peptide

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Stock solutions of Aβ were prepared by reconstituting the lyophilized peptide in a 1:4.5:4.5 (v/v/v) mixture of 60 mM NaOH, Milli-Q water, and 22.2 mM sodium phosphate (pH 7.5) to yield a nominal Aβ concentration of 1 mg/mL in 10 mM sodium phosphate (pH 7.5). The peptide solution then was sonicated for 1 min in a bath sonicator (model 1510, Branson, Danbury, CT) and filtered through a 30 kDa molecular weight cutoff Microcon centrifugal filter device (Millipore, Billerica, MA) for 15 min at room temperature (RT, 22 °C) at 16000g. The filtrate was collected, and the Aβ concentration was determined by UV absorbance (ε280 = 1280 cm−1 M−1) using a 1 cm quartz cuvette (Hellma, Plainview, NY) and a Beckman DU-640 spectrophotometer (Beckman Instruments, Fullerton, CA). All measurements were performed at RT. This protocol results in uniform and reproducible material termed low-molecular weight (LMW) Aβ.14 (link)
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5

Soluble Aβ42 Peptide Preparation

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Aβ42 and [F10, Y42]Aβ42 were synthesized using solid phase peptide synthesis and Fmoc chemistry on an Applied Biosystems model 433A peptide synthesizer (Foster City, CA, USA), as described previously [3 (link)]. Peptide lyophilizates (200 μ g of approximately 80% peptide by weight) were dissolved in 25 μ L of 60 mM sodium hydroxide (Fisher, Waltham, MA, USA) in water to increase solubility and decrease de novo peptide aggregation [29 (link)]. Immediately thereafter, 112.5 μ L of water and 112.5 μL of 22.2 mM sodium phosphate, pH 7.4, were added, and the solution was sonicated in an ultrasonic water bath (model 1510, Branson Ultrasonics Corp., Danbury, CT, USA) for 1 min at 22°C. The pH of the solution at this stage of peptide preparation is ≈11, which facilitates peptide manipulation by increasing solubility and preventing spontaneous self-association [29 (link)]. Protein concentration was determined at 22°C by UV absorbance (ε274=1280 cm−1M−1) using a 1 cm quartz cuvette (Hellma, Plainview, NY, USA) and a Beckman DU-640 spectrophotometer (Beckman Instruments, Fullerton, CA, USA). Peptide concentration was adjusted to 80 μ M using 10 mM sodium phosphate, pH 7.4. This yielded a final pH of 7.4.
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6

Spectroscopic Characterization of Proteins

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Absorption and fluorescence spectra were recorded in cuvettes with 1 cm optical path (Hellma, Müllheim, Germany). Absorption was collected at 25 °C on a JASCO V550 spectrophotometer (JASCO Europe, Cremella (LC), Italy) using 1 nm band-pass and 0.25 s integration time. Fluorescence intensity spectra were recorded at 25 °C by a Fluoromax-4 fluorometer (Jobin-Yvon, Milan, Italy) with 1–2 nm excitation/emission bandpass and 0.2–0.5 s integration time. In a typical spectroscopic experiment, 1–5 µL of mother protein solution was dissolved in 1.2 mL of buffer at desired pH and placed in a 1-cm quartz cuvette of 1.5 mL volume (Hellma, Milan, Italy) to obtain maximum absorbance values 0.1–0.2 in the visible range of spectrum. High pH buffer (pH 8) was 20 mM diethanolamine (DEA). Low pH buffer (pH 5.2) was 4 mM citrate-20 mM phosphate buffer. In both cases, pH was adjusted to the desired value by small aliquots of sulfuric acid or NaOH 1 N.
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7

Steady-State Absorption and Fluorescence

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The steady-state absorption spectrum was obtained using a two-beam absorption spectrometer (Perkin Elmer, Lambda 19) and a 1 cm quartz cuvette (Hellma Analytics). The steady-state fluorescence spectrum was recorded using a Kerr gate set-up with parallel polarizers, i.e. in the open state. The sample solution was guided through a flow cell (Hellma, suprasil, pathlength 1 mm). The same flow system was used for time resolved measurements. The fluorescence spectrum was corrected for the offset and spectral sensitivity of the instrument.
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8

Thermal Stability of DNA Duplexes

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To anneal the DNA duplexes (Tables 1 and 2), solutions of complementary single-stranded oligonucleotides in a buffer consisting of 10 mM Tris-HCl (pH 7.8), 150 mM KCl, and 10 mM MgCl2 were heated at 90°C for 5 min and then were slowly cooled down to the room temperature. Thermal stability of the duplexes (0.4–0.5 μM) was determined from the dependence of the solution’s optical density on temperature. The measurements were performed in triplicate on a U-2800A spectrophotometer (Hitachi, Japan) equipped with an SPR-10 temperature regulator, in 1 cm quartz cuvettes (Hellma, Germany) at 260 nm. DNA duplexes were incubated at 15°C for 10 min and then heated to 65°C during 100 min. Melting temperatures of the DNA duplexes were calculated as a maximum of f'(T) = ΔA260/(ΔT); the standard error did not exceed 1°C.
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9

Spectroscopic Monitoring of GSH-Cu(II) Interactions

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The spectra were recorded every 10 min over a period of 24 h on a Cary 60 spectrophotometer at room temperature (22–24 °C) in the spectral range 250–850 nm in 1 cm quartz cuvettes (Hellma). A 500 mM potassium phosphate buffer stock at pH 7.4 was prepared by mixing potassium dihydrogen phosphate 99% (KH2PO4) with potassium hydrogen phosphate 98% (K2HPO4) in Milli-Q water. Stock solutions were further diluted to the desired 100 mM concentration for the following experiments. 200 mM reduced GSH stock solutions were prepared immediately before the experiment and appropriate portions for the 7:1, 5:1, 3:1, and 1:1 (GSH:Cu) ratios were added to the cuvette containing 1 mM Cu(NO3)2 to obtain final GSH concentration of 0.35–2.45 mM and Cu(II) 0.35 mM. Experiments with such different ratios gave qualitatively the same general results, differing only by the Cu(I) reoxidation time, which was correlated with the excess of GSH not bound to Cu(I). The Cu(I) reoxidation to the Cu(II) complex of GSSG was enabled by oxidative exhaustion of GSH by ambient oxygen, as verified by ESI-MS.
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10

Time-Resolved CD Spectroscopy of J-Aggregates

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To measure CD spectra at different times (typically at 4 h, 3 days and 6 days after collection), 2.5 mL of the J-aggregate solutions were gently transferred to 1 cm quartz cuvettes (Hellma) by a micropipette just before the measurements. After each measurement, the solutions were then transferred back to the original glass vial and stored in dark. This procedure was aimed at preventing an overlong contact of the solutions with the quartz cuvette, which may result in the deposition of the aggregated material onto the cuvette walls and, consequently, in possible CD artefacts35 ,36 . CD spectra were recorded on static solutions on a Jasco J-815 spectropolarimeter. UV-Vis absorption spectra were recorded on an Agilent Cary 60 spectrophotometer.
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