Acrylamide bis acrylamide 19 1

Oligonucleotides were purchased from Integrated
DNA Technologies (IDT, Coralville, IA), Eurofins Genomics (Louisville,
KY), and Sigma-Aldrich (St. Louis, MO). Some Oligonucleotides purchased
from IDT contained a 1,1′-diethyl-2,2′-dicarbocyanine
(Cy5) fluorophore on the 5′-end and were HPLC purified before
use. Uracil DNA glycosylase (UDG), human apurinic/apyrimidinic endonuclease
(APE1), and endonuclease IV (Endo IV) were purchased from New England
Biolabs (Ipswich, MA). [γ-³²P]-ATP (6000 C_i/mmol) was purchased from PerkinElmer, C-18 Sep-Pak cartridges were
purchased from Waters (Milford, MA), BS Poly prep columns were obtained
from BioRad (Hercules, CA), and acrylamide/bis-acrylamide 19:1 (40%
solution, electrophoresis grade) was purchased from Fisher Scientific
(Waltham, MA). Glutathione, NaBH₃CN, and buffers were purchased
from Sigma-Aldrich (St. Louis, MO,). Quantification of radioactivity
or fluorescence in polyacrylamide gels was carried out using a Personal
Molecular Imager (BioRad) with Quantity One software (v.4.6.5). The
pH of buffers was adjusted to the reported values at 24 °C. DMBAA
(dimethylbutylammonium acetate) solutions used in the ESI-MS experiments
was prepared as follows: a stock solution of N,N-dimethylbutylamine (7.125 M) was diluted to 100 mM with
water and adjusted to pH 7.1 with glacial acetic acid.

Tris(hydroxymethyl)-aminomethane (tris), boric acid, acetic acid, KCl, EDTA, acrylamide/bisacrylamide (19:1), ammonium persulfate (prepared as a 10% solution in sterile water and stored at 4°C) and tetramethylethylenediamine (TEMED) were purchased from Fisher Scientific. Magnesium chloride hexahydrate, 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (trolox) and 30% ammonia water were purchased from Arcos Organics. Sodium chloride, ethidium bromide, streptavidin, protocatechuic acid (PCA), MES monohydrate, sodium hydroxide and hydrogen peroxide were purchased from VWR. Bovine serum albumin (BSA) was purchased from New England Biolabs (NEB). Protocatechuate 3,4-dioxygenase (PCD) was purchased from MP Biomedicals, and suspended in a pH 8.0 PCD buffer (100 mM Tris-HCl, 50 mM KCl, 1 mM EDTA, 50% glycerol) at 0.2 μM, sterile filtered and stored at −20°C. Biotin-modified BSA was purchased from Peirce, dissolved in sterile H₂O at 1 mg/ml, sterile filtered and stored at −20°C. Catalase from bovine liver and glucose oxidase from Asperigillus niger were purchased from Sigma Aldrich. For nanopore experiments, hexadecane, pentane, potassium chloride and Tris were purchased from Sigma-Aldrich. 1,2 diphytanoyl-sn-glycero-3-phosphocholine (DPhyPC) lipid was purchased from Avanti polar lipids. Alpha toxin from Staphylococcus Aureus was purchased from List Biological.