Electrochemical Interrogation of Kinetically-Controlled Dendritic DNA/PNA Assembly for Immobilization-Free and Enzyme-Free Nucleic Acids Sensing

Abstract

We present an immobilization-free and enzyme-free electrochemical nucleic acid sensing strategy, which uses kinetically controlled dendritic assembly of DNA and peptide nucleic acid (PNA). In the presence of a target sequence, ferrocene-labeled PNA probes (Fc-PNAs) and specially designed DNA strands are autonomously assembled into dendritic nanostructures through a cascade of toehold-mediated strand displacement reactions. The consumption of freely diffusible Fc-PNAs (neutrally charged), due to incorporation to DNA/PNA dendrimer, results in a significant electrochemical signal reduction of Fc on a negatively charged electrode from which the hyperbranched and negatively charged dendrimer of DNA/PNA would be electrostatically repelled. The cascade-like assembly process and large electrostatic affinity difference between Fc-PNAs and DNA/PNA dendrimer toward the sensing electrode offer a detection limit down to 100 fM and an inherently high specificity for detecting single nucleotide polymorphisms. The target-triggered mechanism was examined by PAGE analysis, and morphologies of the assembled dendrimers were verified by AFM imaging.