Sequence and Structure Dual-Dependent Interaction between Small Molecules and DNA for the Detection of Residual Silver Ions in As-Prepared Silver Nanomaterials

Investigations on interaction between small molecules and DNA are the basis of designing advanced bioanalytical systems. We herein propose a novel interaction between heterocyclic aromatic compounds (HACs) and single-stranded DNA (ssDNA). Taking methylene blue (MB) as a typical HAC, it is found that MB can interact with cytosine (C)-rich ssDNA in an enthalpy-driven process. The interaction between MB and C-rich ssDNA is sequence and structure dual-dependent: at least three consecutive C and single-stranded structure are necessary, affecting the fluorescence response of metal nanoparticles. With the exception of the single-stranded structure, double-stranded, i-motif, and C-Ag-C mismatch structures will remarkably impede the interaction with MB. UV-vis absorption, fluorescent, and electrochemical curves demonstrate that the conjugated system, electron transition, and electron transfer of MB are remarkably affected by MB-C-rich ssDNA interaction. In particular, the absorption peak of MB at 664 nm decreases, and a new peak at 538 nm emerges. Therefore, the interaction can be characterized by a colorimetric and ratiometric signal. Relying on the inhibition of C-Ag-C mismatch and the enhanced analytical performances of the ratiometic signal, the MB-C-rich ssDNA interaction is further employed to quantify silver ions (Ag⁺) selectively and sensitively. In addition, since silver nanomaterials cannot introduce C-Ag-C mismatch, the fabricated biosensor is able to sense residual Ag⁺ in silver nanoparticles and silver nanowires, which is of great value in the precise and economical preparation of silver nanomaterials.