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- Kang, Zhengzhong, 1990-, et al.
(författare)
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Adsorption and folding of single strand DNA on metal-organic frameworks: a molecular simulation study
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- DNA-MOF nanoparticles based on the loading, release, and conformational change of DNA on MOFs have been frequently explored in gene therapy, drug delivery, and biosensor design. Nevertheless, the mechanism of DNA-MOF interactions, which is a fundamental issue behind these applications, remains largely unclear. Here, we applied molecular simulation methods to study systematically the adsorption and folding of ssDNA with different sequences on ideal and defective UiO-66-NH2 MOFs. We find that the ssDNA prefers to be adsorbed on the surfaces rather than inside the cages due to the size limitation of the cages. It is difficult for the ssDNA to be adsorbed on the ideal MOF surface through van der Waals interactions but it can be stably loaded on the defective MOF surface through electrostatic interactions. The whole process of the ssDNA adsorption onto the defective MOFs includes three stages: fast adsorption, conformational reconfiguration, and lock-down adsorption. The loading state of the ssDNA on UiO-66-NH2 is the coexistence of the adsorbed and dangling nucleotides. The binding of the ssDNA on the MOFs is dominated by the multiple point anchoring of the phosphate groups of the ssDNA on the clusters of UiO-66-NH2. Water layers with complex hydrogen-bond network function as a gate, preventing the ssDNA from approaching to UiO-66-NH2 before adsorption and inhibiting it from leaving UiO-66-NH2 after anchoring. Unlike the circular folding structure in the solution, the adsorbed ssDNA displays a slender conformation or duplex like structure. Our results thus provide a deep understanding of DNA-MOF interactions.
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| 2. |
- Zhengzhong, Kang, 1990-
(författare)
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Understanding Defect Structures and Host-guest Interactions in Metal-organic Frameworks
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Metal-organic frameworks (MOFs) represent a class of crystalline porous materials with prospective applications in molecular capture, separation, storage and catalysis. It has been discovered that there exist various structural defects in MOFs, which can have dramatic impact on their properties. However, the fundamental understanding of the structure and chemistry of the defects in MOFs is still very limited.In this thesis, I focus on the studies of defect structures and host-guest interactions in MOFs by using theoretical chemistry methods. These studies cover the dynamic interplay of water and acetate molecules at the defect sites of linker missing MOFs, host-guest interactions of drug molecules loading in defective MOFs, preparation and triggered release of intrinsically coordinated CpG-MOF conjugate nanoparticles, and the defect-assisted single-strand DNA adsorption and folding on MOFs. The main results of the studies are described below.1. The possible binding structure of acetate and water molecules on defect sites in MOFs are explored. Acetate is coordinated to an unsaturated metal site in a monodentate way, which is accompanied by a water molecule coordinated to the neighboring metal site. The highly flexible acetate molecule performs a fast rotation and undergoes a slow kinetic exchange with a water molecule. Two models, one with insufficient water and the other with excess water, were built to study the role of dynamic hydrogen bonds in the exchange process.2. The loading behavior of drug molecules in MOFs has been studied. The interactions between the drugs and MOFs are fundamentally different for the ideal and defective MOFs. The defects play a key role in the loading of the drugs with phosphate or phosphonate groups on MOFs. The host-guest interactions are dominated by the Coulombic attraction between the phosphate/phosphonate groups and the defect sites, which greatly enhances the loading capacity of the drugs. The conformations of the drugs at the defect sites have also been studied. 3. A new strategy for preparing DNA-MOF conjugates is provided and the interactions between oligonucleotides and MOFs have been studied. Compared to the covalent modification of DNA-MOF nanoparticles, the unmodified oligonucleotides can be densely loaded on the MOFs via the intrinsic, multivalent coordination of the DNA backbone phosphate to the unsaturated zirconium sites on the MOFs. The loading state of CpG on the MOFs is the coexistence of nucleotides in the adsorption state and dangling state. The surface-bound DNA can be efficiently released by free phosphate ions in the acidic environment. 4. The loading and folding of ssDNA on MOFs have been systematically studied. ssDNA prefers to be on the surface of the MOFs rather than inside a cage due to size limitation. The defect-assisted surface adsorption is mainly contributed by the electrostatic interactions between the ssDNA and MOFs. The binding of the ssDNA to the MOFs is dominated by the multiple point anchoring of the phosphate groups of the ssDNA on the MOF clusters. Water layers with complex hydrogen-bond network function as a gate, preventing the DNA from approaching the MOFs before adsorption and inhibiting the DNA from leaving the MOFs after anchoring. Unlike the circular folding structure in the solution, the adsorbed ssDNA display a slender conformation or duplex like structure.
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