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4 protocols using 4 nitrobenzyl alcohol

1

Single-Molecule Imaging of Multidrug Resistance Protein

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Single-molecule experiments were performed at room temperature (23 ± 1°C) on an objective-type total-internal-reflection fluorescence microscope (Olympus IX83 cellTIRF). Microfluidic imaging chambers were passivated with a mixture of PEG and biotin-PEG (Laysan Bio), and incubated with 0.8 µM streptavidin (Invitrogen) followed by 2 nM fluorescently labeled, His-tagged bMRP1 that had been preincubated with biotinylated anti-His6 antibodies (Invitrogen) for 1 hr on ice in a buffer containing 50 mM Tris-HCl pH 8.0, 150 mM KCl, 2 mM MgCl2, 0.06% digitonin, 0.5 mg/mL BSA, 10 mM phosphocreatine (Sigma), and 0.1 mg/mL creatine kinase (Sigma). A triplet-state quenching cocktail (Dave et al., 2009 (link)) of 1 mM cyclooctatetraene (Sigma), 1 mM 4-nitrobenzyl alcohol (Sigma), and 1 mM Trolox (Sigma), as well as an oxygen scavenging system (Aitken et al., 2008 (link)) containing 10 nM protocatechuate-3,4-dioxygenase (Sigma) and 2.5 mM protocatechuic acid (Sigma) were supplemented to the imaging buffer. ATP and/or LTC4 were included in the imaging buffer at concentrations specified in the text. Fluorescence signals were split with a W-View Gemini-2C (Hamamatsu), directed to two CMOS cameras (Flash 4.0 v3, Hamamatsu), and acquired by MetaMorph software (Molecular Devices) at a frame rate specified in the text.
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2

Visualizing DNA-ORC-Cdc6 Interactions

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Optical traps tethering a single bare DNA or nucleosomal DNA were moved to a separate channel containing 2 nM Cy3- or LD650-ORC and 5 nM Cdc6 in an imaging buffer containing 25 mM Tris-OAc pH 7.5, 5% glycerol, 40 µg/ml BSA, 3 mM DTT, 2 mM TCEP, 0.1 mM EDTA, 10 mM Mg(OAc)2, 50 mM potassium glutamate, and 2.5 mM ATP. The imaging buffer was supplemented with an ATP-regeneration system [60 mg/ml creatine phosphokinase (Sigma) and 20 mM phosphocreatine (Sigma)], a triplet-state quenching cocktail [1 mM cyclooctatetraene (Sigma), 1 mM 4-nitrobenzyl alcohol (Sigma) and 1 mM Trolox (Sigma)], as well as an oxygen scavenging system [10 nM protocatechuate-3,4-dioxygenase (Sigma) and 2.5 mM protocatechuic acid (Sigma)]. Kymographs were typically recorded for 4–10 min.
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3

BPDE-DNA Adduct Formation Protocol

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Benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide (+/-) (anti) (anti BPDE) was from National Cancer Institute Chemical Carcinogen Reference Standard Repository. Triethylammonium bicarbonate (TEAB, 1.0 M, pH 8.4-8.6) and 4-nitrobenzyl alcohol were from Sigma-Aldrich. Custom made single stranded DNA oligomers and the 32-base pair oligonucleotide were from Sigma-Aldrich. HPLC grade solvents, methanol, tetrahydrofuran and water were from Fischer Scientific. Restriction enzyme, NIaIII was from New England Biolabs.
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4

DNA Adduct Identification Protocol

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Benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide (±) (anti) (anti BPDE) was from National Cancer Institute Chemical Carcinogen Reference Standard Repository. Triethylammonium bicarbonate (TEAB, 1.0 M, pH 8.4–8.6) and 4-nitrobenzyl alcohol were from Sigma-Aldrich. Custom made single stranded DNA oligomers and the 32-base pair oligonucleotide were from Sigma-Aldrich. HPLC grade solvents, methanol, tetrahydrofuran and water were from Fischer Scientific. Restriction enzyme, NlaIII was from New England Biolabs.
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