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15 protocols using prominence chromatograph

1

Peptide Synthesis and Purification

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Peptides were identified with numbers from 1 to 7 in order to facilitate the description of results. Peptide 1 was synthesized using PS3TM synthesizer (Protein Technologies, Inc) by chemical solid phase synthesis using the Fmoc strategy. Cleavage of peptides was carried out manually as described by Chan & White (2000)[61 ], and purification was performed by high performance liquid chromatography, with using a Shimadzu Prominence chromatograph. The other peptides were synthesized by the company Genescript with more than 90% purity. All peptides were diluted in DMSO (dimethyl sulfoxide) at a concentration of 1 μg/μL and stored at -70°C.
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2

Reverse-phase HPLC Globin Chain Analysis

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HPLC analyses were performed with a Prominence chromatograph (Shimadzu, Somerset, NJ, USA) and its LC Solution software. Globin chains from pooled erythroid colonies were separated by reverse-phase HPLC using a 4.6-mm Aeris 3.6-μM Widepore C4 Column (Phenomenex, Torrance, CA, USA). Samples were eluted with a gradient mixture of solution A (water with 0.1% trifluoroacetic acid) and solution B (acetonitrile with 0.08% trifluoroacetic acid). The absorbance was measured at 220 nm.
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3

Enzymatic Geranylation of tRNA Anticodon Stem-Loop

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The 17-mer S2U-RNA (assigned as Sh) of the 5′-UCAGACUS2UUUAAUCUGA-3′ sequence, isosequential to the anticodon-stem-loop (ASL) of human tRNALys3UUU (1 OD, 40 μg) was incubated with the purified enzyme SelU-His6 (10 μg) in the presence of 5-fold molar excess of ammonium geranyl pyrophosphate (Sigma-Aldrich). The reaction was performed in the buffer composed of 10 mM Tris-HCl pH 8.0, 0.2 mM dithiothreitol and 2% glycerol without or with addition of MgSO4 salt (up to 100 mM), in total reaction volume 50 μl, at 25°C. A reaction with the thermally inactivated enzyme served as the negative control. After 24 h incubation the mixture was analyzed by RP-HPLC (a Prominence chromatograph, Shimadzu, Japan) using a Kinetex 5μ C-18 column (100Å; 250 × 4.60 mm, Phenomenex) eluted with a mixture of two buffers (A: 0.1 M CH3COONH4; B: 0.1 M CH3COONH4/40% ACN) according to the following gradient: 0% B for 20 min.; 0→100 % B over 30 min.; then isocratically 100% B for 10 min. The fractions collected at Rt = 39 min were desalted using a standard SepPak C-18 (Waters) procedure and the identity of the geranylated product was confirmed by MALDI-TOF MS (m/z 5477, MW 5483, Supplementary Figure S4).
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4

Synthesis of Fluorinated Phosphoramidates

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All solvents were used as received from commercial suppliers. All of the other reagents used in the synthesis were purchased from Sigma‒Aldrich except the reagent for the phosphoramidation reaction ((S)-isopropyl 2-(((S)-(perfluorophenoxy) (phenoxy) phosphoryl) amino) propanoate), purchased from ALCHIMIA LIMITED. All reactions were carried out under an argon atmosphere. Reactions were monitored with analytical TLC on silica gel 60-F254 precoated aluminum plates and visualized under UV (254 nm). Purification was performed by column chromatography on silica gel (35–70 μM) or by crystallization. NMR data were recorded on a Bruker Fourier 80, or Bruker 500 MHz spectrometer in the deuterated solvents indicated, and the spectra were calibrated on TMS. Chemical shifts (δ) are quoted in ppm, and J values are quoted in Hz. In reporting spectral data, the following abbreviations were used: s (singlet), d (doublet), t (triplet), q (quartet), dd (doublet of doublets), dddd (doublet of double doublets) and m (multiplet). Mass spectrometry analysis was performed on a Shimadzu LCMS-8045. HPLC was carried out on a Shimadzu Prominence chromatograph equipped with a DAD detector (Xterra RP18, 250 × 4.6 mm 5 mm – part n°:186000496 column). Solvents were used as HPLC grade. Structural details are highlighted in the Supplementary Chemical information.
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5

Erythroid Burst Hemoglobin Analysis by HPLC

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Cells from erythroid bursts were lysed by adding 100 μL of H2O and centrifuging at 20,000 × g. The nuclei were retained for qPCR and the assessment of vector modification, whereas hemoglobin from individual erythroid colony supernatants was separated by ion exchange high-pressure liquid chromatography (HPLC) on a PolyCAT A column (PolyLC). Elution was achieved with a linear gradient of buffer A (40 mM Tris, 3 mM KCN; pH adjusted to 6.5 with acetic acid) and buffer B (40 mM Tris, 3 mM KCN, 200 mM NaCl; pH adjusted to 6.5 with acetic acid) of different ionic strengths at a flow rate of 0.4 mL/min at 40°C. The detection wavelength was 418 nm. HPLC analyses were performed with a Prominence chromatograph (Shimadzu) and LC Solution software.
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6

Quantifying Therapeutic Globin Chains

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Percentage of the therapeutic globin βA-T87Q chain in human and mouse samples was determined by high-performance liquid chromatography with a Prominence chromatograph (Shimadzu). Cells lysates were injected onto a C4 column EC 250/4 Nucleosil 300-5 (Macherey-Nagel) and elution was achieved with a gradient of Milli-Q water (Millipore), acetonitril (Carlo Erba), trifluoroacetic (Fluka) acid and heptafluorobutyric acid (Fluka). The detection wavelength was 220 nm. Data acquisition was performed with the LC Solution software (Shimadzu).
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7

Quantification of Fructose, Glucose, and Sucrose in Samples

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Fructose, glucose and sucrose content were determined by means of High Performance Liquid Chromatography (HPLC) [35 ]. Samples for chromatographic analyses were 3-fold diluted with ultrapure deionized water and filtered through a 0.2 μm nylon membrane filter. Analyses were performed using a Shimadzu Prominence chromatograph (Shimadzu Corp., Tokyo, Japan) equipped with a Luna NH2 column (250 mm × 4.6 mm) (Phenomenex, Torrance, CA, USA). Samples were loaded onto a 10 µL injection loop and eluted at 40 °C with 80:20 acetonitrile:water (ACN:H2O) mobile phase at a flow rate of 1.2 mL/min. The detection of compounds was performed using Shimadzu RID-20A refractive index detection, at a temperature of 30 °C. Integration and quantification were performed using the LabSolutions software (Shimadzu Corp., Kyoto, Japan).
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8

HPLC Analysis of Propolis Extracts

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The obtained propolis extracts were filtered with Iso-Disc™ Filters PTFE-25-2, diameter 25 mm, pore size 0.20 μm (Supelco Analytical™, Bellefonte, PA, USA) and subjected to HPLC. A Shimadzu Prominence chromatograph equipped with an auto sampler SIL-20AC HT, photodiode array detector SPD-M20A, and LC solution 1.21 SP1 chromatography software (Shimadzu, Kyoto, Japan) were used. Separations were achieved using a 100 × 4.60 mm, C18 reversed-phase column, 2.6-μm particles with solid core and porous outer layer (Kinetex™, Phenomenex®, Torrance, CA, USA). Binary gradient of deionized water (WCA R03 DP ECO, COBRABiD Aqua, Warsaw, Poland) adjusted to pH 2 with phosphoric acid (Merck) and filtered with 47-mm nylon membrane filter 0.20 μm (Phenex™, Phenomenex®, Torrance, CA, USA) as mobile phase A and MeCN (acetonitrile for HPLC ≥ 99.9%, Merck) as phase B was used as follows: 0 min–12.5% B; 25.0 min–40% B; 34.0 min–60% B; 37.0 min–95% B; 37.1 min–12.5% B; 40 min–stop. The flow rate was set to 2.0 mL/min, oven temperature 45 °C, injection volume 1 μL. Peak identification was carried out by comparison of retention time as well UV spectra with standards. The content of the determined compounds was calculated in mg per 100 mL of propolis extract.
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9

Carbohydrate and Ethanol Analysis in Ciders and Juices

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Concentration of carbohydrates (sucrose, glucose and fructose) in ciders, apple and pear juices and ethanol content of ciders was assessed by the means of high performance liquid chromatography (HPLC). Samples of cider and juice were 3-fold diluted with de-ionized water and filtered through 0.2 µm nylon membrane filter. Analyses were performed using Shimadzu Prominence chromatograph (Shimadzu Corp., Tokyo, Japan) equipped with Rezex ROA-Organic Acid H+ column (300 × 7.8 mm) (Phenomenex, Torrance, USA). The samples were loaded into 20 µL injection loop and eluted at 50 °C with 0.005 M H2SO4 as a mobile phase at a flow rate of 0.4 mL min−1. The compounds were detected using Shimadzu RID-10A refractive index detector; detection temperature was maintained at 50 °C. Integration and quantification of chromatograms were performed using Chromax 10 software (Pol-Lab, Warsaw, Poland). Degree of attenuation was calculated using the formula below:


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10

Analytical Methods for Natural Product Characterization

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Silica gel (230–400
mesh, Merck) and Sephadex LH-20 (Aldrich) were applied in column chromatography
(CC), and Silica gel 60 PF254 (Merck) was applied in thin layer chromatography
(TLC). 1H (500 and 600 MHz) and 13C (125 and
150 MHz) NMR spectra were documented on a Varian INOVA 500 spectrometer
with CD3OD (Sigma-Aldrich) as the solvent and tetramethylsilane
(TMS) as the internal standard. ESI-HRMS spectra were obtained with
electrospray ionization in the positive ion mode on a Bruker Daltonics
MicroTOF QII spectrometer. The equipment for high-performance liquid
chromatography was a ultra performance liquid chromatography (UPLC)
Prominence chromatograph (Shimadzu, Japan) supplied with LC-20AT gradient
pumps and a ultraviolet (UV)–visible photodiode array detector
(190–800 nm). MALDI-TOF/MS was performed on a Bruker MicroFlex
spectrometer at a 20 kV accelerating voltage in the positive mode
(500 laser shots). The signals were collected in a range between 2,000
and 20,000 m/z with the AutoXecute
tool (Bruker Daltonics).56 (link)
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