Efficient fluorescence quenching and low-limit detection of HIV-1 DNA via morphology controlled ZIF-8 crystals

ZIF-8 (zinc-methylimidazolate framework-8) has shown promising applications as a fluorescence sensing platform, particularly in fluorescence quenching sensors for various biological and chemical analyses and detections. However, the impact of the morphology of ZIF-8 crystals on their performance of biomolecule detection, especially DNA detection, remains to be explored. In this study, six types of ZIF-8 crystals with different morphology (cubic, rough octahedral, flakes, rhombic, dodecahedral, and hexapod) are successfully synthesized by incorporating different concentrations of the surfactant/end-capping agent, namely cetyltrimethylammonium bromide (CTAB) and/or tris(hydroxymethyl)aminomethane (TRIS). These crystals are characterized in terms of morphology, crystal structure, specific surface area, and electrostatic adsorption capacity. Subsequently, these morphologically different ZIF-8 crystals are combined with fluorophore carboxyfluorescein (FAM)-labeled single-stranded DNA (ss-DNA) to form FAM-DNA@ZIF-8 biosensor. Then, their fluorescence quenching efficiency is characterized by using the fluorescence spectroscopy. The measurement results show that, due to its higher external specific surface area and zeta potential thereby higher electrostatic adsorption capacity, the cubic ZIF-8 crystal can effectively capture more FAM-DNA molecules through the electrostatic adsorption and achieve high fluorescence quenching efficiency via the fluorescence resonance energy transfer mechanism. Thus, the fluorescence quenching efficiency of the cubic FAM-DNA@ZIF-8 reaches up to 98.1 %. Finally, the cubic FAM-DNA@ZIF-8 biosensor is used to detect the complementary target HIV-1 DNA via the fluorescence recovery. The experimental results show that the fluorescence recovery efficiency of the FAM-DNA@ZIF-8 reaches up to 40.8 upon the addition of complementary target ssDNA, significantly higher than the recovery efficiency when non-complementary target DNA is introduced. Also, both fluorescence quenching efficiency and recovery efficiency of the cubic FAM-DNA@ZIF-8 are much higher than those of the reported biosensors based on ZIF-8 crystals with non-optimal morphology. Additionally, the fluorescence recovery sensitivity of the biosensor is 0.536/(nM⋅mL), with a detection limit as low as 1.37 nM. In addition, its detection performance remains almost unchanged after ten days of storage. These findings provide valuable insights for optimizing ZIF-8-based DNA biosensor.