Size-fitting effect for hybridization of DNA/mercaptohexanol mixed monolayers on gold

Abstract

In this article we proposed a simple hexagonal model for exploring the hybridization of thiol-modified probe DNA self-assembled monolayers (SAMs) on gold with target DNA molecules in solution. The size-fitting coefficient d_c/d_t from the model was used to discuss the principle for DNA optimal hybridization, where d_c was the channel diameter among three adjacent probe DNA molecules on gold and d_t was the gyration diameter of the target DNA molecules in solution. Experimentally we investigated the hybridization effect (hybridization efficiency H_E and hybridization density H_D) of thiol-modified probe DNA (DNA base amount m = 15, 25 or 35)/mercaptohexanol (MCH) mixed SAMs on gold in 1 M electrolyte solution by chronocoulometry (CC) and electrochemical impedance spectroscopy (EIS). The surface coverage Γ_m of the probe DNA on gold was adjusted by changing the mixed concentration ratio of probe DNA with MCH (C_DNA/C_MCH) in the assembly solution. Results indicated that with the increase of C_DNA/C_MCH, H_E decreased gradually; H_D first increased and then decreased, which arrived at the biggest at C_DNA/C_MCH = 1 for all the probe DNA/MCH mixed SAMs (m = 15, 25, 35). The optimal Γ_m for achieving the biggest H_D in DNA hybridization decreased with the increase of m from 15 to 35. The experimental conclusions obtained by CC and EIS measurements verified each other. Combining the simple model with our experimental results, we ascertained that d_c/d_t decreased with the increase of m, which showed a good linear relationship. These conclusions provided an important reference and guidance for controllably constructing DNA sensors with optimal performance.