Characterization of boron doped diamond electrodes with engineered sp2 carbon content and their application to structure-dependent DNA hybridization

Abstract

Boron doped diamond electrodes brought a new potential in bioanalytical chemistry including studies of structure and interactions of nucleic acids. Herein, deposition conditions were optimized to produce a set of polycrystalline BDD electrodes with comparable boron concentration in solid phase of (1.8 − 2.1) · 10²¹ cm⁻³ akin to metallic-type conductivity but with increasing sp² carbon content. Increase of [CH₄]/[H₂] from 0.25 % to 2.0 % during deposition led to an obvious decrease in grain size from ca. 300 nm (BDD_0.25) to < 100 nm (BDD_2.0). Adsorption of oligodeoxynucleotides and their structural changes in the presence of K⁺ and Li⁺ ions were evaluated through enzyme-linked DNA hybridization assay in which oxidizable 1-naphthol was released from its phosphoester by streptavidin–alkaline phosphatase conjugate upon successful hybridization of the target oligodeoxynucleotide with a biotinylated complementary probe. With increasing sp² carbon content, the hybridization assay showed improved discrimination between a target forming guanine quadruplex (stabilized by K⁺ ions), yielding by 40 % – 60 % lower hybridization signal with the complementary probe, compared to the same but unstructured target oligodeoxynucleotide in the presence of Li⁺ ions that don’t stabilize the quadruplex structure. Such behaviour was observed also for commercial BDD electrode with surface roughness < 10 nm.