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

Zhang, Huinan; Luo, Bin; An, Peng; Zhan, Xiaowei; Lan, Fang; Wu, Yao

doi:10.1021/acsabm.2c00431

Cited by 10 publications

(4 citation statements)

References 34 publications

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“…Such interactions may lead to bending, twisting, or structural deformation of nucleic acid chains, potentially affecting the double-helix structure of DNA/RNA. For example, Zhang et al designed and prepared a class of ultrathin two-dimensional MOF nanosheets, named Zr-BTB MOF nanosheets, composed of Zr − O clusters and 1,3,5-benzenetribenzoate by a bottom-up synthesis strategy [ 103 ]. The nano-bio interaction between DNA and Zr-BTB MOF nanosheets was deeply investigated by systematic molecular dynamics simulations and fluorescence spectroscopic analysis.…”

Section: Effects Of Nano-bio Interfacial Interactions By 2d Nmsmentioning

confidence: 99%

Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment

Wang,

Zhang,

Yue

2024

J Nanobiotechnol

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Two-dimensional nanomaterials (2D NMs), characterized by a large number of atoms or molecules arranged in one dimension (typically thickness) while having tiny dimensions in the other two dimensions, have emerged as a pivotal class of materials with unique properties. Their flat and sheet-like structure imparts distinctive physical, chemical, and electronic attributes, which offers several advantages in biomedical applications, including enhanced surface area for efficient drug loading, surface-exposed atoms allowing precise chemical modifications, and the ability to form hierarchical multilayer structures for synergistic functionality. Exploring their nano-bio interfacial interactions with biological components holds significant importance in comprehensively and systematically guiding safe applications. However, the current lack of in-depth analysis and comprehensive understanding of interfacial effects on cancer treatment motivates our ongoing efforts in this field. This study provides a comprehensive survey of recent advances in utilizing 2D NMs for cancer treatment. It offers insights into the structural characteristics, synthesis methods, and surface modifications of diverse 2D NMs. The investigation further delves into the formation of nano-bio interfaces during their in vivo utilization. Notably, the study discusses a wide array of biomedical applications in cancer treatment. With their potential to revolutionize therapeutic strategies and outcomes, 2D NMs are poised at the forefront of cancer treatment, holding the promise of transformative advancements. Graphical Abstract

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Section: Effects Of Nano-bio Interfacial Interactions By 2d Nmsmentioning

confidence: 99%

Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment

Wang,

Zhang,

Yue

2024

J Nanobiotechnol

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“…The influenza A virus subtype H5N1 gene hybridized with ssDNA to form dsDNA, thus recovering the fluorescence. Recently, Zhang et al investigated the interaction between ultrathin 2D Zr-BTB MOF nanosheets and fluorophore-labeled dsDNA as well as ssDNA by molecular dynamics simulations ( Figure 12 A) [ 174 ]. The nanosheets composed of Zr-O clusters and 1,3,5-benzenetribenzoate were prepared by a bottom-up method.…”

Section: Biosensorsmentioning

confidence: 99%

“… ( A ) Schematic illustration of preparation of Zr-BTB MOF nanosheets and projected interaction between nanosheets with ssDNA and dsDNA. Reproduced with permission [ 174 ]. Copyright 2020, American Chemical Society.…”

Section: Biosensorsmentioning

confidence: 99%

An Overview of the Design of Metal-Organic Frameworks-Based Fluorescent Chemosensors and Biosensors

et al. 2022

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Taking advantage of high porosity, large surface area, tunable nanostructures and ease of functionalization, metal-organic frameworks (MOFs) have been popularly applied in different fields, including adsorption and separation, heterogeneous catalysis, drug delivery, light harvesting, and chemical/biological sensing. The abundant active sites for specific recognition and adjustable optical and electrical characteristics allow for the design of various sensing platforms with MOFs as promising candidates. In this review, we systematically introduce the recent advancements of MOFs-based fluorescent chemosensors and biosensors, mainly focusing on the sensing mechanisms and analytes, including inorganic ions, small organic molecules and biomarkers (e.g., small biomolecules, nucleic acids, proteins, enzymes, and tumor cells). This review may provide valuable references for the development of novel MOFs-based sensing platforms to meet the requirements of environment monitoring and clinical diagnosis.

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“…10 Early generations of MON-based biosensors have typically involved fluorescence quenching of dye-labeled single-stranded DNA, functionalization with bioreceptors and nanozyme behavior. 3,[11][12][13][14][15][16] In these examples, much of the sensitivity and selectivity is conferred by other components, such as aptamers and antibodies, enzymes, nanoparticles or other two-dimensional materials. 9 To the best of our knowledge, there are currently no studies investigating the interaction of specific sequences of amino acids with MONs, although several studies have investigated their interactions with their three-dimensional analogs, MOFs.…”

Section: Introductionmentioning

confidence: 99%

Phage display against two-dimensional metal-organic nanosheets as a new route to highly selective biomolecular recognition surfaces

Wood,

Johnson,

Prasad

et al. 2023

Preprint

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Peptides are important biomarkers for a range of diseases, however distinguishing different amino-acid sequences using artificial receptors remains a major challenge in biomedical sensing. Here we present a new approach to creating highly selective recognition surfaces using phage display biopanning against metal-organic nanosheets (MONs) and demonstrate their use as the next-generation of biomolecular recognition surfaces. Three MONs (ZIF-7, ZIF-7-NH2 and Hf-BTB-NH2) were chosen as initial targets to demonstrate how simple synthetic modifications can enhance selectivity towards specific amino acid sequences. Each MON system was added to a solution containing every possible combination of 7-residue peptides attached to bacteriophage hosts and the highest affinity binding peptides for each system was identified via successive biopanning rounds. In each case only a single peptide sequence was isolated (YNYRNLL – ZIF-7, NNWWAPA – ZIF-7-NH2 and FTVRDLS – Hf-BTB-NH2). This indicates that these MONs are highly selective, which is attributed to their 2D nanosheet structure. Zeta potential and contact angle measurements were conducted on each MON and combined with calculated properties for the peptide sequences and binding studies to provide insights into the relative importance of electrostatic, hydrophobic and co-ordination bonding interactions. A quartz crystal microbalance (QCM) was used to model phage binding and the Hf-BTB-NH2 MON coated QCM produced a 5-fold higher signal for FTVRDLS functionalised phage compared to phage with generic peptide sequences. Further studies focusing on Hf-BTB-NH2 confirmed that the VRDL sequence was highly conserved, and on-target binding exhibited equilibrium dissociation constants that are comparable to natural recognition materials. Surface plasmon resonance (SPR) studies indicated a 4600-fold higher equilibrium dissociation constant (KD) for FTVRDLS compared to those obtained for off-target sequences, comparable to those of antibodies (KD = 4 x10-10). We anticipate that the highly tunable nature of MONs will enhance our understanding of binding interactions and enable molecular recognition of biomedically important peptides.

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

Cited by 10 publications

References 34 publications

Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment

Two-dimensional nanomaterials induced nano-bio interfacial effects and biomedical applications in cancer treatment

An Overview of the Design of Metal-Organic Frameworks-Based Fluorescent Chemosensors and Biosensors

Phage display against two-dimensional metal-organic nanosheets as a new route to highly selective biomolecular recognition surfaces

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