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6 protocols using organic solvents

1

Ultralipid Separation and Quantification

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MS-grade H2O, organic solvents, and formic acid (FA) were purchased from Biosolve Chimie SARL (Dieuze, France). ULN and ULN-d6 were provided by BioMed Valley Discoveries (Kansas City, MO, USA). The purity of the two compounds were 99% and 98.26%, respectively. The structure of ULN is provided in Figure 1A.
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2

Quantitative Analysis of DNA Adducts

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MS-grade water, organic solvents, and formic
acid (FA) were purchased from Biosolve Chimie SARL (Dieuze, France).
2dGO, O6-m2dGO, 2′-deoxy-N-ethyl-guanosine (2dNetGO), d3-O6-methyl-2′-deoxyguanosine
(d3-O6-m2dGO), N7-mG, O6-mG, and N2-methyl-2′-deoxyguanosine
(N2-m2dGO) were purchased from Toronto Research Chemicals (North York,
Canada) (Supporting Information, Figure S1). Nucleoside Digestion Mix NEB #M0649 was purchased from New England
Biolabs (New England Biolabs, Ipswich, MA, USA). Cell culture medium,
Dulbecco’s Modified Eagle’s Medium (DMEM), and fetal
calf serum (FCS) were purchased from PAN-Biotech (Aidenbach, Germany).
Glutamine and penicillin/streptomycin were purchased from Sigma-Aldrich
(Taufkirchen, Germany). Crystal violet was purchased from Applichem
(Darmstadt, Germany). The bromodeoxyuridine (BrdU) assay kit was purchased
from Merck (Darmstadt, Germany). The DNA extraction kit was purchased
from Qiagen (Hilden, Germany).
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3

Characterization of Organic Compounds

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Materials: Chemicals were purchased from Sigma‐Aldrich Chemical Co. (St. Louis, MO), TCI Europe N.V., Thermo Fisher Scientific (Geel, Belgium) or Fluorochem Co. (UK). Organic solvents were purchased from Biosolve (Valkenswaard, The Netherlands). Oligonucleotides were purchased from Eurofins Scientific (Ebersberg, Germany). Proteins were analysed by SDS‐PAGE on precast gels (NuPAGETM 12 % Bis‐Tris protein gels). High performance liquid chromatography (HPLC) was performed with a Shimadzu LC‐10AT HPLC and a Shimadzu SPD‐M20A diode array detector. GC‐MS was conducted with a Shimadzu GC‐MS‐QP2010 SE. NMR spectra were recorded on a Bruker 500 MHz machine at the Drug Design laboratory of the University of Groningen. Chemical shifts (δ) are reported in parts per million (ppm). Spectrophotometric measurements were performed on a V‐650 or V‐660 spectrophotometer from Jasco (IJsselstein, The Netherlands). Spectrophotometric measurements in 96‐well format were performed on a SPECTROstar Omega plate reader (BMG LABTECH, Isogen Life Science, de Meern, The Netherlands) in 96‐well microtiter plates (UV‐star μclear, Greiner Bio‐one). DNA was purified using a PCR purification kit (QIAquick®, QIAGEN).
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4

Characterization of SLX Compounds

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MS-grade water, organic solvents, and formic acid (FA) were purchased from Biosolve Chimie SARL (Dieuze, France), and 2,5-dihydroxybenzoic acid (2,5-DHB), alpha-cyano-4-hydroxycinnamic acid (CHCA), trifluoroacetic acid (TFA), bovine serum albumin (BSA), and red phosphorus were obtained from Sigma-Aldrich (Darmstadt, Germany). SLX (Figure 1A) and [2H5]-SLX (Figure 1B) were provided by Karyopharm Therapeutics Inc. (Newton, MA, USA). The certificate of analysis of [2H5]-SLX reported a chemical purity of >97% from liquid chromatography (LC)-MS analyses. LC-MS analyses also reported the incomplete incorporation of 2H at C2 (10% of H based on MS ratio). 1H-NMR analyses reported the incomplete incorporation of 2H at C2 (8% of H based on integration) and 12% of 2H incorporated at C3.
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5

Quantification of Urine Leukocyte Esterase

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MS-grade H2O, organic solvents, and formic acid (FA) were purchased from Biosolve Chimie SARL (Dieuze, France). Solutions of ULN and its deuterated IS, ULN-d6, were provided by BioMed Valley Discoveries (Kansas City, MO, USA) with purities of 99% and 98.26%, respectively [16 (link)].
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6

Mass Spectrometry Reagents and Standards

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MS-grade water, organic solvents, and formic acid (FA) were purchased from Biosolve Chimie SARL (Dieuze, France). Alpha-cyano-4-hydroxy-cinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), trifluoroacetic acid (TFA), 3-hydroxypicolinic acid (3-HPA), graphene, red phosphorus, and guanine were purchased from Sigma-Aldrich (Darmstadt, Germany). 2dGO, O6-m2dGO and N7-mG were purchased from Toronto Research Chemicals (North York, ON, Canada). 2,3,4,5-tetrakis(3′,4′-dihydroxylphenyl)thiophene (DHPT) was synthesized as described in the following paragraph.
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