Interaction of Nucleic Acids with Metal–Organic Framework Nanosheets by Fluorescence Spectroscopy and Molecular Dynamics Simulations

The integration of nanomaterials and nucleic acids has attracted great attention in various research fields, especially biomedical applications. Designing two-dimensional nanomaterials and studying the mechanism of their interaction with nucleic acids are still attractive tasks. Herein, we designed and prepared a class of ultrathin two-dimensional metal-organic framework (MOF) nanosheets, named Zr-BTB MOF nanosheets, composed of Zr-O clusters and 1,3,5-benzenetribenzoate by a bottom-up synthesis strategy. The Zr-BTB MOF nanosheets possessed inherent excellent performance such as a high specific surface area, porosity, and biocompatibility. In addition, we clarified the interaction difference between the Zr-BTB MOF nanosheets and fluorophore-labeled double-stranded DNA and single-stranded DNA via molecular dynamics simulations and fluorescence measurement. Through molecular dynamics simulations, specific interactions between DNA and nanosheets such as forces, binding energies, and binding modes were deeply analyzed and clearly presented. Based on the affinity difference, the system showed the biosensing potential for target DNA detection with considerable specificity, sensitivity, and linearity. Our research results presented the Zr-BTB MOF nanosheet as a platform for nucleic acid detection, showing the potential for hybridization-based biosensing and related biological applications.