Encapsulation and Release of Recognition Probes Based on a Rigid Three-Dimensional DNA “Nanosafe-box” for Construction of a Electrochemical Biosensor

Abstract

Herein a rigid three-dimensional (3D) DNA “nanosafe-box” (DNB) for encapsulation and release of a recognition probe (N3) is designed to construct an electrochemical biosensor with the use of electroactive two-dimensional metal–organic framework (2D MOF) nanosheets as signal tags for ultrasensitive detection of mercury ion (Hg2+). Initially, N3 is locked in the 3D cavity of DNB by blocker DNA. After addition of target Hg2+, exonuclease III (Exo-III) digestion is initiated to the liberate DNA “key” (K); thereby, the free K triggers a strand displacement reaction for exposing the prelocked N3 to successfully ligate dibenzocyclooctyne (DBCO)-tagged anchor via metal-catalyst-free click chemistry, in which amounts of 2D MOF nanosheets containing Co­(II) as electron mediator are introduced accompanied by significant electrochemical response. Compared with traditional linear or stem-loop DNA nanostructure, the well-designed 3D DNB possesses remarkably enhanced mechanical rigidity and structural stability, resulting in improved accessibility of probes and increased loading amounts of signal tags. More importantly, by this way of encapsulation and release of recognition probes, the background signal is decreased dramatically, leading to increased sensitivity of the proposed biosensor. Consequently, this electrochemical biosensor exhibits outstanding analytical performance for Hg2+ detection with a low detection limit of 33 fM and dynamic linear range of 0.1 pM to 10 nM. This strategy offers an ingenious method for detection of metal ions and biomarkers, possessing potential applications in environmental tests and clinical diagnosis.

Tetrahedral DNA framework assisted rotational paper-based analytical device for differential detection of SARS-CoV-2 and influenza A H1N1 virus

“…With the rapid development of DNA nanotechnology, various exquisite DNA nanostructures with good biocompatibility, simple synthesis and high stability have been widely used in biosensing analysis [ [22] , [23] , [24] , [25] ]. Of note, tetrahedral DNA framework (TDF) has gained considerable research attention owing to its powerful rigid structure which could be precisely adjusted by controlling the base sequence [ [26] , [27] , [28] , [29] , [30] ]. TDF as surface immobilized substrate can achieve precise regulation of ligands in well-defined orientation and spacing, which could improve the sensitivity of biosensors [ [31] , [32] , [33] ].…”

A highly sensitive electrochemical biosensor for Hg2+ based on entropy-driven DNA walker-based amplification

“…Among them, the electrochemical methods have received particular attention due to their sensitivity, simplicity, low cost, fast response, miniaturization, and portability. 15 Although the electrochemical methods have many advantages, their selectivity restricts the detection of metal ions. Consequently, it is still a great challenge to develop a sensitive, selective and environmentally friendly electrochemical method for Hg 2+ detection.…”