Mesoporous Metal-Organic Frameworks for Catalytic RNA Deprotection and Activation

Innovative Chemical Strategies for Advanced CRISPR Modulation

ConspectusOver the past decade, RNA-guided gene editing technologies, particularly those derived from CRISPR systems, have revolutionized life sciences and opened unprecedented opportunities for therapeutic innovation. Despite their transformative potential, achieving precise control over the activity and specificity of these molecular tools remains a formidable challenge, requiring advanced and innovative regulatory strategies. We and others have developed new approaches that integrate chemical ingenuity with bioorthogonal techniques to achieve remarkable precision in CRISPR regulation. One key innovation lies in the chemical modulation of guide RNA (gRNA), significantly expanding the CRISPR toolkit. Strategies such as CRISPR-ON and CRISPR-OFF switches rely on selective chemical masking and demasking of gRNA. These approaches use either bulky chemical groups to preemptively mask RNA or minor, less obstructive groups to fine-tune its function, followed by bioorthogonal reactions to restore or suppress activity. These methodologies have proven to be pivotal for controlled gene editing and expression, addressing the challenges of precision, reversibility, and dynamic regulation.Parallel to these advances, the development of mesoporous metal-organic frameworks (MOFs) has emerged as a promising solution for RNA deprotection and activation. By serving as catalytic tools, MOFs enhance the versatility and efficiency of CRISPR systems, pushing their applications beyond the conventional boundaries. In addition, the synthesis of novel small molecules for regulating CRISPR-Cas9 activity marks a critical milestone in the evolution of gene therapy protocols. Innovative RNA structural control strategies have also emerged, particularly through the engineering of G-quadruplex (G4) motifs and G-G mismatches. These methods exploit the structural propensities of engineered gRNAs, employing small-molecule ligands to induce specific conformational changes that modulate the CRISPR activity. Whether stabilizing G4 formation or promoting G-G mismatches, these strategies demonstrate the precision and sophistication required for the molecular-level control of gene editing.Further enhancing these innovations, techniques like host-guest chemistry and conditional diacylation cross-linking have been developed to directly alter gRNA structure and function. These approaches provide nuanced, reversible, and safe control over CRISPR systems, advancing both the precision and reliability of gene editing technologies. In conclusion, this body of work highlights the convergence of chemistry, materials science, and molecular biology to create integrative solutions for gene editing. By combination of bioorthogonal chemistry, RNA engineering, and advanced materials, these advancements offer unprecedented accuracy and control for both fundamental research and therapeutic applications. These innovations not only advance genetic research but also contribute to developing safer and more effective gene editing strategies, moving us closer to realizing the full potential of these technologies.

Application of Hard and Soft Acid-base Theory to Construct Heterometallic Materials with Metal-oxo Clusters

Heterometallic cluster-based materials offer the potential to incorporate multiple functionalities, leveraging the aggregation effects of clusters and translating this heterogeneity and complexity into unexpected properties that are more than just the sum of their components. However, the rational construction of heterometallic cluster-based materials remains challenging due to the complexity of metal cation coordination and structural unpredictability. This minireview provides insights into a general synthetic strategy based on Hard and Soft Acids and Bases (HSAB) theory, summarizing its advantages in the designed synthesis of discrete heterometallic clusters (intracluster assembly) and infinite heterometallic cluster-based materials (intercluster assembly). Furthermore, it emphasizes the potential to exploit the intrinsic properties of mixed components to achieve breakthroughs across a broad range of applications. The insights from this review are expected to drive the progress of heterometallic cluster-based materials in a controllable and predictable manner.

Space Exploration of Metal-Organic Frameworks in the Mesopore Regime

ConspectusThe past decades have witnessed the proliferation of porous materials offering high surface areas and the revolution in gas storage and separation, where metal-organic frameworks (MOFs) stand out as an important family. Alongside the pursuit of higher surface area, the increase in the size of guests, such as nanoparticles and biomolecules, has also led to the demand for larger space defined by the pores and cages within the MOF structure, from the conventional micropore regime (<2 nm) toward the mesopore regime (2-50 nm). Among the essential elements in the design of MOFs, molecular building blocks, their coordination and spatial arrangement, the chemistry for molecular design, and coordination bonds have become relatively mature, offering precise control of the shape and environment of the molecularly defined 3D cages; however, the correlation between the geometrical parameters and the size of polyhedrons describing the cages, concerning the spatial arrangement of building blocks, is much less explored.In this Account, we made efforts to associate actual cage size with the critical geometrical components, vertices, edges, connectivity, rings, and underlying polyhedrons, as well as the combination of components of various types in the design of MOFs. Several trends were found, such as influence from connectivity and expansion efficiency, offering insights into the construction of 3D cages in MOFs. This enables the creation of extremely large mesoporous cages in MOFs with an internal diameter up to 11.4 nm from relatively small building blocks. Furthermore, we discuss a strategy of partial removal or replacement of organic linkers to construct mesoporous cages from readily known topologies.All of the above efforts urged us to ask the following questions: Is there any limit in the sculpting of the 3D space from molecules? How large an area can one chemical bond support? The answer to these questions will deepen the knowledge of efficient utilization of chemical bonds in the sculpting of 3D spaces and guide the design of larger mesopores. Several general geometrical principals emerged: (1) Expansion efficiency and radius are positively correlated with the number of vertices. (2) Increase in the number of vertices and decrease of their connectivity favor the construction and expansion of large cages. (3) The boundary of the 3D space constructed by the chemical bonds is related to the polyhedron type and determined by the energy involved in crystallinity. Such principals are likely to be applicable also in the design of isolated cages in supramolecular chemistry. In addition to the structural design and synthesis, the applications of these mesoporous cages in MOFs are also summarized.

Chemical diversity of reagents that modify RNA 2'-OH in water: a review

Electrophilic water-soluble compounds have proven versatile in reacting selectively with 2'-OH groups in RNA, enabling structure mapping, probing, caging, labeling, crosslinking, and conjugation of RNAs in vitro and in living cells. While early work focused on one or two types of reagents with limited properties, recent studies have greatly diversified the structure, properties, and applications of these reagents. Here we review the scope of documented RNA hydroxyl-reactive species reported to date, with an eye to the effects of chemical structure on reactivity with RNA and other useful properties. Multiple forms of carbonyl electrophiles are now known to react at the 2'-OH, and recently, sulfonyl and aryl electrophiles have also been documented to form bonds there in high yields as well. In addition to electrophilicity, data also point to significant effects of reagent stability, steric bulk, and chirality on reaction yields and selectivity. Finally, we outline reagent properties and principles that define utility in applications with RNA, with an eye to the design of future reagents.

Chemically Modified Platforms for Better RNA Therapeutics

RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.

Isoreticular Chemistry and Applications of Supramolecularly Assembled Copper-Adenine Porous Materials

The useful concepts of reticular chemistry, rigid and predictable metal nodes together with strong and manageable covalent interactions between metal centers and organic linkers, have made the so-called metal-organic frameworks (MOFs) a flourishing area of enormous applicability. In this work, the extension of similar strategies to supramolecularly assembled metal-organic materials has allowed us to obtain a family of isoreticular compounds of the general formula [Cu7(μ-adeninato-κN3:κN9)6(μ3-OH)6(μ-OH2)6](OOC-R-COO)·nH2O (R: ethylene-, acetylene-, naphthalene-, or biphenyl-group) in which the rigid copper-adeninato entities and the organic dicarboxylate anions are held together not by covalent interactions but by a robust and flexible network of synergic hydrogen bonds and π-π stacking interactions based on well-known supramolecular synthons (SMOFs). All compounds are isoreticular, highly insoluble, and water-stable and show a porous crystalline structure with a pcu topology containing a two-dimensional (2D) network of channels, whose dimensions and degree of porosity of the supramolecular network are tailored by the length of the dicarboxylate anion. The partial loss of the crystallization water molecules upon removal from the mother liquor produces a shrinkage of the unit cell and porosity, which leads to a color change of the compounds (from blue to olive green) if complete dehydration is achieved by means of gentle heating or vacuuming. However, the supramolecular network of noncovalent interactions is robust and flexible enough to reverse to the expanded unit cell and color after exposure to a humid atmosphere. This humidity-driven breathing behavior has been used to design a sensor in which the electrical resistance varies reversibly with the degree of humidity, very similar to the water vapor adsorption isotherm of the SMOF. The in-solution adsorption properties were explored for the uptake and release of the widely employed 5-fluorouracil, 4-aminosalycilic acid, 5-aminosalycilic acid, and allopurinol drugs. In addition, cytotoxicity activity assays were completed for the pristine and 5-fluorouracil-loaded samples.