Amperometric Bioplatforms To Detect Regional DNA Methylation with Single-Base Sensitivity

• Published in: Analytical chemistry (Washington) 2020-04, Vol.92 (7), p.5604-5612
• Main Authors: Povedano, Eloy, Ruiz-Valdepeñas Montiel, Víctor, Gamella, Maria, Pedrero, María, Barderas, Rodrigo, Peláez-García, Alberto, Mendiola, Marta, Hardisson, David, Feliú, Jaime, Yáñez-Sedeño, Paloma, Campuzano, Susana, Pingarrón, José M
• Format: Article
• Language: English
• Subjects: 5-Methylcytosine - analogs & derivatives; 5-Methylcytosine - metabolism; Amperometry; Amplification; Analytical chemistry; Antibodies; Biosensors; Cancer; Cell Line, Tumor; Chemistry; Colorectal cancer; Colorectal carcinoma; Complementary DNA; Deoxyribonucleic acid; DNA; DNA Methylation; Electrical measurement; Electrochemical analysis; Electrochemistry; Electrochemistry - methods; Electrodes; Genomes; Horseradish peroxidase; Humans; Hybridization; Hydrogen peroxide; Hydroquinone; Limit of Detection; Microspheres; Nanoparticles; Nucleotide sequence; Nucleotides; Peroxidase; Sensitivity; Streptavidin; Tumor suppressor genes
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.0c00628

This work reports the first bioplatform able to determine electrochemically 5-hydroxymethylcytosine (5-hmC) methylation events at localized sites and single-base sensitivity. The described bioplatform relies on a specific antibody (anti-5-hmC), further conjugated with commercial bioreagents loaded with multiple horseradish peroxidase (HRP) molecules, recognizing the epimark in a target DNA, captured through hybridization onto streptavidin–magnetic microbeads (Strep–MBs) modified with a complementary DNA capture probe. The electrochemical detection is performed by amperometry (−0.20 V vs Ag pseudoreference electrode) at disposable screen-printed carbon electrodes (SPCEs) in the presence of H2O2/hydroquinone (HQ) upon magnetic capture of the modified MBs onto the SPCE. The use of the commercial bioreagents ProtA–polyHRP80 and Histostar, very scarcely explored so far in electrochemical biosensors, provides high sensitivities for a synthetic target DNA sequence with a unique 5-hmC in the promoter region of MGMT tumor suppressor gene. Amplification factors of 43.6 and 55.2 were achieved using ProtA–polyHRP80 or Histostar, respectively, compared to the conventional secondary antibody labeling. This amplification was crucial to detect methylation events at single-nucleotide resolution achieving limits of detection (LODs) of 23.0 and 13.2 pM, respectively, without any target DNA amplification. The ProtA–polyHRP80-based bioplatform, selected as a compromise between sensitivity and cost per determination, exhibited full discrimination toward the target 5-hmC against the closely related 5-mC. In addition, the bioplatform detected 5-hmC at the regional level (MGMT promoter region) in just 10 ng of genomic DNA (gDNA, ∼2700 genomes) extracted from cancer cells and tissues from colorectal cancer (CRC) patients within 60 min.