Sequence and Structure Dual-Dependent Interaction between Small Molecules and DNA for the Detection of Residual...

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.