A MOF/DNA luminescent sensing platform for detection of potential COVID-19 biomarkers and drugs

COVID-19 has afflicted people's lives worldwide. Interleukin-6 (IL-6) is an important COVID-19 biomarker in human body fluids that can be used as a reference to monitor COVID-19 in real-time and therefore to reduce the risk of virus transmission. On the other hand, oseltamivir is a potential COVID-19 curing drug, but its overuse easily leads to hazardous side effects, calling for its real time monitoring in body fluids. For these purposes, a new yttrium metal–organic framework (Y-MOF) has been synthesized, in which the 5-(4-(imidazole-1-yl)phenyl)isophthalic linker contains a large aromatic backbone capable of strongly interacting with DNA sequences through π–π stacking interactions, which makes it appealing to build a unique sensor based on DNA functionalized MOFs. The MOF/DNA sequence hybrid luminescent sensing platform presents excellent optical properties associated with a high Förster resonance energy transfer (FRET) efficiency. Furthermore, to construct a dual emission sensing platform, a 5′-carboxylfluorescein (FAM) labeled DNA sequence (S2) with a stem-loop structure that can specifically interact with IL-6 has been associated with the Y-MOF. The resulting Y-MOF@S2 exhibits an efficient ratiometric detection of IL-6 in human body fluids with an extremely high Ksv value 4.3 × 108 M−1 and a low detection limit (LOD) of 70 pM. Finally, the Y-MOF@S2@IL-6 hybrid platform allows the detection of oseltamivir with high sensitivity (Ksv value is as high as 5.6 × 105 M−1 and LOD is 54 nM), due to the fact that oseltamivir can disconnect the loop stem structure constructed by S2, leading to a strong quenching effect towards Y-MOF@S2@IL-6. The nature of the interactions between oseltamivir and Y-MOF has been elucidated using density functional theory calculations while the sensing mechanism for the dual detection of IL-6 and oseltamivir has been deciphered based on luminescence lifetime tests and confocal laser scanning microscopy.

one oseltamivir molecule and further geometry-optimized at the Density Functional Theory (DFT) level. To ensure an efficient sampling of the electronic potential energy surface, multiple initial configurations were examined. These DFT calculations were performed using Gaussian 09, [2] employing B3LYP functional [3,4] along with Grimme's D3-BJ correction. [5,6] The 6-31G(d) basis set [7] was employed for H, C, N, and O atoms, while a 28-electron quasi relativistic effective core potentials and the segmented basis sets MWB28 were used for Y 3+ metal ions. [8,9] In order to retain the local geometry of the MOF structure, it was required to maintain the atomic positions of the cluster fixed.
The interaction energy (Eint) between oseltamivir and the Y-MOF cluster for both binding modes was calculated using equation 1: Eint = (Ecluster/oseltamivir) -(Ecluster + Eoseltamivir) (equation 1) where Ecluster/oseltamivir is the energy of the optimized cluster/oseltamivir geometry, and Ecluster and Eoseltamivir are the single point energies of the individual components. The frontier molecular orbital and energy transport analysis for the preferential binding modes were explored further.

Preparation of Y-MOF (1).
A mixture of Yttrium chloride (30.2 mg, 0.1 mmol), and H2L (30.8 mg, 0.1 mmol) was added into the mixture of DMF (1 mL) and sodium acetate aqueous solution (5 mM, 0.5 mL). The mixed solutions were sealed in a 25 mL Teflon reactor, after the reaction mixture had been heated at 120 °C for one day and then cooled to room temperature naturally, colorless bulky crystals of Y-MOF (1). were isolated in 52 % yield based on H2L ligand.

Preparation of Y-MOF (2).
A mixture of Yttrium chloride (30.2 mg, 0.1 mmol), and H2L (30.8 mg, 0.1 mmol) was added into the mixture of DMF (1 mL) and sodium acetate aqueous solution (5 mM, 0.5 mL). The mixed solutions were sealed in a 25 mL Teflon reactor, after the reaction mixture had been heated at 120 °C for one day and then cooled to room temperature naturally, colorless bulky crystals of Y-MOF (2) were isolated in 52 % yield based on H2L ligand.

Preparation of Y-MOF (3).
A mixture of Yttrium chloride (30.2 mg, 0.1 mmol), and H2L (30.8 mg, 0.1 mmol) was added into the mixture of DMF (1 mL) and sodium acetate aqueous solution (10 mM, 0.5 mL). The mixed solutions were sealed in a 25 mL Teflon reactor, after the reaction mixture had been heated at 120 °C for one day and then cooled to room temperature naturally, colorless bulky crystals of Y-MOF (3) were isolated in 53 % yield based on H2L ligand.

Preparation of COVID-19 effective drug solution
In the selective detection process, we prepared lopinavir, oseltamivir, ritonavir, chloroquire phosphate solution with 1 μM solution and DMSO as solvent, respectively.
In the IL-6 titration process, we prepared IL-6 solution with 0.48 μM, PBS as solvent.
To get simulated human body fluid, we mixed creatine, L-LDH, D-dimer, Interleukin-10 into 5% human serum solution and the concentration of creatine is 133 μM, the concentration of L-LDH is 318 U/L, the concentration of D-dimmer is 1 μg/mL and IL-10 is 9.7 pg/mL.