CKAP5 stabilizes CENP-E at kinetochores by regulating microtubule-chromosome attachments.

Stabilization of microtubule plus end-directed kinesin CENP-E at the metaphase kinetochores is important for chromosome alignment, but its mechanism remains unclear. Here, we show that CKAP5, a conserved microtubule plus tip protein, regulates CENP-E at kinetochores in human cells. Depletion of CKAP5 impairs CENP-E localization at kinetochores at the metaphase plate and results in increased kinetochore-microtubule stability and attachment errors. Erroneous attachments are also supported by computational modeling. Analysis of CKAP5 knockout cancer cells of multiple tissue origins shows that CKAP5 is preferentially essential in aneuploid, chromosomally unstable cells, and the sensitivity to CKAP5 depletion is correlated to that of CENP-E depletion. CKAP5 depletion leads to reduction in CENP-E-BubR1 interaction and the interaction is rescued by TOG4-TOG5 domain of CKAP5. The same domain can rescue CKAP5 depletion-induced CENP-E removal from the kinetochores. Interestingly, CKAP5 depletion facilitates recruitment of PP1 to the kinetochores and furthermore, a PP1 target site-specific CENP-E phospho-mimicking mutant gets stabilized at kinetochores in the CKAP5-depleted cells. Together, the results support a model in which CKAP5 controls mitotic chromosome attachment errors by stabilizing CENP-E at kinetochores and by regulating stability of the kinetochore-attached microtubules.

Enzymatic Reaction-Coupled, Cooperative Supramolecular Polymerization.

Nature employs sophisticated mechanisms to precisely regulate self-assembly and functions within biological systems, exemplified by the formation of cytoskeletal filaments. Various enzymatic reactions and auxiliary proteins couple with the self-assembly process, meticulously regulating the length and functions of resulting macromolecular structures. In this context, we present a bioinspired, reaction-coupled approach for the controlled supramolecular polymerization in synthetic systems. To achieve this, we employ an enzymatic reaction that interfaces with the adenosine triphosphate (ATP)-templated supramolecular polymerization of naphthalene diimide monomers (NSG). Notably, the enzymatic production of ATP (template) plays a pivotal role in facilitating reaction-controlled, cooperative growth of the NSG monomers. This growth process, in turn, provides positive feedback to the enzymatic production of ATP, creating an ideal reaction-coupled assembly process. The success of this approach is further evident in the living-growth characteristic observed during seeding experiments, marking this method as the pioneering instance where reaction-coupled self-assembly precisely controls the growth kinetics and structural aspects of supramolecular polymers in a predictive manner, akin to biological systems.

Supramolecular Modulation of Fluid Flow in a Self-Powered Enzyme Micropump.

Regulating macroscopic fluid flow by catalytic harnessing of chemical energy could potentially provide a solution for powerless microfluidic devices. Earlier reports have shown that surface-anchored enzymes can actuate the surrounding fluid in the presence of the respective substrate in a concentration-dependent manner. It is also crucial to have control over the flow speed of a self-powered enzyme micropump in various applications where controlled dosing and mixing are required. However, modulating the flow speed independent of the fuel concentration remains a significant challenge. In a quest to regulate the fluid flow in such a system, a supramolecular approach has been adopted, where reversible regulation of enzyme activity was achieved by a two-faced synthetic receptor bearing sulfonamide and adamantane groups. The bovine carbonic anhydrase (BCA) enzyme containing a single binding site favorable to the sulfonamide group was used as a model enzyme, and the enzyme activity was inhibited in the presence of the two-faced inhibitor. The same effect was reflected when the immobilized enzyme was used as an engine to actuate the fluid flow. The flow velocity was reduced up to 53% in the presence of 100 µM inhibitor. Later, upon addition of a supramolecular "host" CB[7], the inhibitor was sequestered from the enzyme due to the higher binding affinity of CB[7] with the adamantane functionality of the inhibitor. As a result, the flow velocity was restored to ∼72%, thus providing successful supramolecular control over a self-powered enzyme micropump.

Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies.

In a three-dimensional (3D) representation, each protein molecule displays a specific pattern of chemical and topological features, which are altered during its misfolding and aggregation pathway. Generating a recognizable fingerprint from such features could provide an enticing approach not only to identify these biomolecules but also to gain clues regarding their folding state and the occurrence of pathologically lethal misfolded aggregates. We report here a universal strategy to generate a fluorescent fingerprint from biomolecules by employing the pan-selective molecular recognition feature of a cucurbit[7]uril (CB[7]) macrocyclic receptor. We implemented a direct sensing strategy by covalently tethering CB[7] with a library of fluorescent reporters. When CB[7] recognizes the chemical and geometrical features of a biomolecule, it brings the tethered fluorophore into the vicinity, concomitantly reporting the nature of its binding microenvironment through a change in their optical signature. The photophysical properties of the fluorophores allow a multitude of probing modes, while their structural features provide additional binding diversity, generating a distinct fluorescence fingerprint from the biomolecule. We first used this strategy to rapidly discriminate a diverse range of protein analytes. The macrocyclic sensor was then applied to probe conformational changes in the protein structure and identify the formation of oligomeric and fibrillar species from misfolded proteins. Notably, the sensor system allowed us to differentiate between different self-assembled forms of the disease-specific amyloid-ß (Aß) aggregates and segregated them from other generic amyloid structures with a 100% identification accuracy. Ultimately, this sensor system predicted clinically relevant changes by fingerprinting serum samples from a cohort of pregnant women.

Measuring mRNA translation in neuronal processes and somata by tRNA-FRET.

In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. Here, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and transport of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA mobility in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of long-term potentiation (LTP) in culture revealed up-regulation of mRNA translation with a similar effect in dendrites and somata, which appeared to be GluR-dependent 6 h post-activation. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.

Stereoselective Primary and Secondary Nucleation Events in Multicomponent Seeded Supramolecular Polymerization.

Bioinspired, kinetically controlled seeded growth has been recently shown to provide length, dispersity, and sequence control on the primary structure of dynamic supramolecular polymers. However, command over the molecular organization at all hierarchical levels for the modulation of higher order structures of supramolecular polymers remains a formidable task. In this context, a surface-catalyzed secondary nucleation process, which plays an important role in the autocatalytic generation of amyloid fibrils and also during the chiral crystallization of small monomers, offers exciting possibilities for topology control in synthetic macromolecular systems by introducing secondary growth pathways compared to the usual primary nucleation-elongation process. However, mechanistic insights into the molecular determinants and driving forces for the secondary nucleation event in synthetic systems are not yet realized. Herein, we attempt to fill this dearth by showing an unprecedented molecular chirality control on the primary and secondary nucleation events in seed-induced supramolecular polymerization. Comprehensive kinetic experiments using in situ spectroscopic probing of the temporal changes of the monomer organization during the growth process provide a unique study to characterize the primary and secondary nucleation events in a supramolecular polymerization process. Kinetic analyses along with various microscopic studies further reveal the remarkable effect of stereoselective nucleation and seeding events on the (micro)structural aspects of the resulting multicomponent supramolecular polymers.

Tricomponent Supramolecular Multiblock Copolymers with Tunable Composition via Sequential Seeded Growth.

Synthesis of supramolecular block co-polymers (BCP) with small monomers and predictive sequence requires elegant molecular design and synthetic strategies. Herein we report the unparalleled synthesis of tri-component supramolecular BCPs with tunable microstructure by a kinetically controlled sequential seeded supramolecular polymerization of fluorescent π-conjugated monomers. Core-substituted naphthalene diimide (cNDI) derivatives with different core substitutions and appended with ß-sheet forming peptide side chains provide perfect monomer design with spectral complementarity, pathway complexity and minimal structural mismatch to synthesize and characterize the multi-component BCPs. The distinct fluorescent nature of various cNDI monomers aids the spectroscopic probing of the seeded growth process and the microscopic visualization of resultant supramolecular BCPs using Structured Illumination Microscopy (SIM). Kinetically controlled sequential seeded supramolecular polymerization presented here is reminiscent of the multi-step synthesis of covalent BCPs via living chain polymerization. These findings provide a promising platform for constructing unique functional organic heterostructures for various optoelectronic and catalytic applications.

Self-Sorted, Random, and Block Supramolecular Copolymers via Sequence Controlled, Multicomponent Self-Assembly.

Multicomponent supramolecular copolymerization promises to construct complex nanostructures with emergent properties. However, even with two monomeric components, various possible outcomes such as self-sorted supramolecular homopolymers, a random (statistical) supramolecular copolymer, an alternate supramolecular copolymer, or a complex supramolecular block copolymer can occur, determined by their intermolecular interactions and monomer exchange dynamics and hence structural prediction is extremely challenging. Herein, we target this challenge and demonstrate unprecedented two-component sequence controlled supramolecular copolymerization by manipulating thermodynamic and kinetic routes in the pathway complexity of self-assembly of the constitutive monomers. Extensive molecular dynamics simulations provided useful mechanistic insights into the monomer exchange rates and free energy of interactions between the monomers that dictate the self-assembly pathway and sequence. The fluorescent nature of core-substituted naphthalene diimide monomers has been further utilized to characterize the three sequences via Structured Illumination Microscopy (SIM).

Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures.

Supramolecular block copolymerzation with optically or electronically complementary monomers provides an attractive bottom-up approach for the non-covalent synthesis of nascent axial organic heterostructures, which promises to deliver useful applications in energy conversion, optoelectronics, and catalysis. However, the synthesis of supramolecular block copolymers (BCPs) constitutes a significant challenge due to the exchange dynamics of non-covalently bound monomers and hence requires fine microstructure control. Furthermore, temporal stability of the segmented microstructure is a prerequisite to explore the applications of functional supramolecular BCPs. Herein, we report the cooperative supramolecular block copolymerization of fluorescent monomers in solution under thermodynamic control for the synthesis of axial organic heterostructures with light-harvesting properties. The fluorescent nature of the core-substituted naphthalene diimide (cNDI) monomers enables a detailed spectroscopic probing during the supramolecular block copolymerization process to unravel a nucleation-growth mechanism, similar to that of chain copolymerization for covalent block copolymers. Structured illumination microscopy (SIM) imaging of BCP chains characterizes the segmented microstructure and also allows size distribution analysis to reveal the narrow polydispersity (polydispersity index (PDI) ≈ 1.1) for the individual block segments. Spectrally resolved fluorescence microscopy on single block copolymerized organic heterostructures shows energy migration and light-harvesting across the interfaces of linearly connected segments. Molecular dynamics and metadynamics simulations provide useful mechanistic insights into the free energy of interaction between the monomers as well as into monomer exchange mechanisms and dynamics, which have a crucial impact on determining the copolymer microstructure. Our comprehensive spectroscopic, microscopic, and computational analyses provide an unambiguous structural, dynamic, and functional characterization of the supramolecular BCPs. The strategy presented here is expected to pave the way for the synthesis of multi-component organic heterostructures for various functions.

Synthesis and Localized Photoluminescence Blinking of Lead-Free 2D Nanostructures of Cs3 Bi2 I6 Cl3 Perovskite.

Two-dimensional (2D) lead-free halide perovskites have generated enormous perception in the field of optoelectronics due to their fascinating optical properties. However, an in-depth understanding on their shape-controlled charge-carrier recombination dynamics is still lacking, which could be resolved by exploring the photoluminescence (PL) blinking behaviour at the single-particle level. Herein, we demonstrate, for the first time, the synthesis of nanocrystals (NCs) and 2D nanosheets (NSs) of layered mixed halide, Cs3 Bi2 I6 Cl3 , by solution-based method. We applied fluorescence microscopy and super-resolution optical imaging at single-particle level to investigate their morphology-dependent PL properties. Narrow emission line widths and passivation of non-radiative defects were evidenced for 2D layered nanostructures, whereas the activation of shallow trap states was recognized at 77 K. Interestingly, individual NCs were found to display temporal intermittency (blinking) in PL emission. On the other hand, NS showed temporal PL intensity fluctuations within localized domains of the crystal. In addition, super-resolution optical image of the NS from localization-based method showed spatial inhomogeneity of the PL intensity within perovskite crystal.

Quantitative super-resolution imaging with qPAINT.

Counting molecules in complexes is challenging, even with super-resolution microscopy. Here, we use the programmable and specific binding of dye-labeled DNA probes to count integer numbers of targets. This method, called quantitative points accumulation in nanoscale topography (qPAINT), works independently of dye photophysics for robust counting with high precision and accuracy over a wide dynamic range. qPAINT was benchmarked on DNA nanostructures and demonstrated for cellular applications by quantifying proteins in situ and the number of single-molecule FISH probes bound to an mRNA target.

Solvent Adaptive Dynamic Metal-Organic Soft Hybrid for Imaging and Biological Delivery.

A solvent responsive dynamic nanoscale metal-organic framework (NMOF) [Zn(1 a)(H2 O)2 ] has been devised based on the self-assembly of ZnII and asymmetric bola-amphiphilic oligo-(p-phenyleneethynylene) (OPE) dicarboxylate linker 1 a having dodecyl and triethyleneglycolmonomethylether (TEG, polar) side chains. In THF solvent, NMOF showed nanovesicular morphology (NMOF-1) with surface decorated dodecyl chains. In water and methanol, NMOF exhibited inverse-nanovesicle (NMOF-2) and nanoscroll (NMOF-3) morphology, respectively, with surface projected TEG chains. The pre-formed NMOFs also unveiled reversible solvent responsive transformation of different morphologies. The flexible NMOF showed cyan emission and no cytotoxicity, allowing live cell imaging. Cisplatin (14.4 wt %) and doxorubicin (4.1 wt %) were encapsulated in NMOF-1 by non-covalent interactions and, in vitro and in vivo drug release was studied. The drug loaded NMOFs exhibited micromolar cytotoxicity.

Synthetic Host-Guest Assembly in Cells and Tissues: Fast, Stable, and Selective Bioorthogonal Imaging via Molecular Recognition.

Bioorthogonal strategies are continuing to pave the way for new analytical tools in biology. Although a significant amount of progress has been made in developing covalent reaction based bioorthogonal strategies, balanced reactivity, and stability are often difficult to achieve from these systems. Alternatively, despite being kinetically beneficial, the development of noncovalent approaches that utilize fully synthetic and stable components remains challenging due to the lack of selectivity in conventional noncovalent interactions in the living cellular environment. Herein, we introduce a bioorthogonal assembly strategy based on a synthetic host-guest system featuring Cucurbit[7]uril (CB[7]) and adamantylamine (ADA). We demonstrate that highly selective and ultrastable host-guest interaction between CB[7] and ADA provides a noncovalent mechanism for assembling labeling agents, such as fluorophores and DNA, in cells and tissues for bioorthogonal imaging of molecular targets. Additionally, by combining with covalent reaction, we show that this CB[7]-ADA based noncovalent interaction enables simultaneous bioorthogonal labeling and multiplexed imaging in cells as well as tissue sections. Finally, we show that interaction between CB[7] and ADA fulfills the demands of specificity and stability that is required for assembling molecules in the complexities of a living cell. We demonstrate this by sensitive detection of metastatic cancer-associated cell surface protein marker as well as by showing the distribution and dynamics of F-actin in living cells.

Cucurbit[7]uril-Directed Assembly of Colloidal Membrane and Stimuli-Responsive Microcapsules at the liquid-liquid Interface.

Colloidal microcapsules based on supramolecular architectures feature attractive properties and offer new opportunities in diverse areas such as delivery, sensing, and catalysis. Herein, we report a new strategy to fabricate the colloidal membrane and stimuli-responsive microcapsules by utilizing cucurbit[7]uril-mediated interfacial host-guest molecular recognition. In contrast to the traditionally used cross-linking approach, this method exploits the engineered interaction between a nanoparticle ligand and cucurbit[7]uril to tune the interfacial energy and stabilize the colloidal assembly at the interface. These capsules provide a versatile platform for simultaneous encapsulation of dual cargos. Additionally, the dynamic nature of the supramolecular interactions allows triggered release of the encapsulated cargos through the orthogonal presentation of a high affinity guest molecule.

Synthesis of Ultrathin Few-Layer 2D Nanoplates of Halide Perovskite Cs3Bi2I9 and Single-Nanoplate Super-Resolved Fluorescence Microscopy.

The discovery of new two-dimensional (2D) perovskite halides has created sensation recently because of their structural diversity and intriguing optical properties. The toxicity of Pb-based perovskite halides led to the development of Pb-free halides. Herein, we have demonstrated a one-pot solution-based synthesis of 2D ultrathin (∼1.78 nm) few-layer (2-4 layers) nanoplates (300-600 nm lateral dimension), nanosheets (0.6-1.5 µm), and nanocrystals of layered Cs3Bi2I9 by varying the reaction temperature from 110 to 180 °C. We have established a mechanistic pathway for the variation of morphology of Cs3Bi2I9 with temperature in the presence of organic capping ligands. Further, we have synthesized the bulk powder of Cs3Bi2I9 by mechanochemical synthesis and liquid-assisted grinding and crystalline ingot by vacuum-sealed tube melting. 2D nanoplates and bulk Cs3Bi2I9 demonstrate optical absorption edge along with excitonic transition. Photoluminescence properties of individual nanoplates were studied by super-resolution fluorescence imaging, which indicated the blinking behavior down to the level of an individual Cs3Bi2I9 nanoplate along with its emission at the far-red region and high photostability.

Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.

To decipher the molecular mechanisms of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit but are not widely adopted due to the common limitation of requiring multirounds of slow (typically over 2 h at room temperature to overnight at 4 °C in practice) immunostaining. We present here a practical and robust method, which we call DNA Exchange Imaging (DEI), for rapid in situ spectrally unlimited multiplexing. This technique overcomes speed restrictions by allowing for single-round immunostaining with DNA-barcoded antibodies, followed by rapid (less than 10 min) buffer exchange of fluorophore-bearing DNA imager strands. The programmability of DEI allows us to apply it to diverse microscopy platforms (with Exchange Confocal, Exchange-SIM, Exchange-STED, and Exchange-PAINT demonstrated here) at multiple desired resolution scales (from ∼300 nm down to sub-20 nm). We optimized and validated the use of DEI in complex biological samples, including primary neuron cultures and tissue sections. These results collectively suggest DNA exchange as a versatile, practical platform for rapid, highly multiplexed in situ imaging, potentially enabling new applications ranging from basic science, to drug discovery, and to clinical pathology.

Autofluorescence-spectral imaging for rapid and invasive characterization of soybean for pre-germination anaerobic stress tolerance.

The autofluorescence-spectral imaging (ASI) technique is based on the light-emitting ability of natural fluorophores. Soybean genotypes showing contrasting tolerance to pre-germination anaerobic stress can be characterized using the photon absorption and fluorescence emission of natural fluorophores occurring in seed coats. In this study, tolerant seeds were efficiently distinguished from susceptible genotypes at 405 nm and 638 nm excitation wavelengths. ASI approach can be employed as a new marker for the detection of photon-emitting compounds in the tolerant and susceptible soybean seed coats. Furthermore, the accuracy of rapid characterization of genotypes using this technique can provide novel insights into soybean breeding.

Regulation of microtubule dynamics and function in living cells via cucurbit[7]uril host-guest assembly.

Living systems utilize sophisticated biochemical regulators and various signal transduction mechanisms to program bio-molecular assemblies and their associated functions. Creating synthetic assemblies that can replicate the functional and signal-responsive properties of these regulators, while also interfacing with biomolecules, holds significant interest within the realms of supramolecular chemistry and chemical biology. This pursuit not only aids in understanding the fundamental design principles of life but also introduces novel capabilities that contribute to the advancements in medical and therapeutic research. In this study, we present a cucurbit[7]uril (CB[7]) host-guest system designed to regulate the dynamics and functions of microtubules (MTs) in living cells. To establish communication between MTs and CB[7] and to reversibly control MT function through host-guest recognition, we synthesized a two-faced docetaxel-p-xylenediamine (Xyl-DTX) derivative. While Xyl-DTX effectively stabilized polymerized MTs, inducing MT bundling and reducing dynamics in GFP-α-tubulin expressing cells, we observed a significant reduction in its MT-targeted activity upon threading with CB[7]. Leveraging the reversible nature of the host-guest complexation, we strategically reactivated the MT stabilizing effect by programming the guest displacement reaction from the CB[7]·Xyl-DTX complex using a suitable chemical signal, namely a high-affinity guest. This host-guest switch was further integrated into various guest activation networks, enabling 'user-defined' regulatory control over MT function. For instance, we demonstrated programmable control over MT function through an optical signal by interfacing it with a photochemical guest activation network. Finally, we showcased the versatility of this supramolecular system in nanotechnology-based therapeutic approaches, where a self-assembled nanoparticle system was employed to trigger the MT-targeted therapeutic effect from the CB[7]·Xyl-DTX complex.

Multistep Array-Based Sensing of Bioanalytes Using Modified MoS2, Fluorescence Proteins, and Cucurbituril.

One pot sensor by multiplexing in the array is an attractive system for rapid discrimination of multiple analytes. Multiplexing can be achieved in two ways, i.e., using multiple signal transducers or adding sequential agents to the sensor media. Herein, we have used a combination of both multichannel and sequential ON-OFF strategies for the discrimination of different bioanalytes. The sensor array was constructed by implementing positively charged MoS2 as a receptor and different fluorescent proteins possessing distinguishable emission profiles as signal transducers. The sensing setup was constructed with the interaction between oppositely charged MoS2 and the host-guest combination between a cationic headgroup of MoS2 and Cucurbit [7] uril (CB7) to alter the fluorescence of signal transducers in situ noncovalently. Electrodynamic analysis and optical assays suggest that the electrostatic interaction played a major role in the modulation of the fluorescence outcomes in the array. Both cationic and anionic proteins were discriminated at a 50 nM concentration. The detection limit of the sensor array by using ß-gal protein was found to be 1 nM. The sensor array was further implemented for the discrimination of normal and diseased cell lines and lysates, which indicates the versatile detection ability of this reported sensor array.

Supramolecular Guest Exchange in Cucurbit[7]uril for Bioorthogonal Fluorogenic Imaging across the Visible Spectrum.

Fluorogenic probes that unmask fluorescence signals in response to bioorthogonal reactions are a powerful new addition to biological imaging. They can significantly reduce background fluorescence and minimize nonspecific signals, potentially enabling real-time, high-contrast imaging without the need to wash out excess fluorophores. While diverse classes of highly refined synthetic fluorophores are now readily available, integrating them into a bioorthogonal fluorogenic scheme still requires extensive design efforts and customized structural alterations to optimize quenching mechanisms for each specific fluorophore scaffold. Herein, we present a highly generalizable strategy that can produce an efficient bioorthogonal fluorogenic response from essentially any readily available fluorophore without further structural alterations. We designed this strategy based on the macrocyclic cucurbit[7]uril (CB7) host, where a fluorogenic response is achieved by programming a guest exchange reaction within the macrocyclic cavity. We employed this strategy to rapidly create fluorogenic probes across the visible spectrum from diverse fluorophore scaffolds, which enabled no-wash imaging in live cells and tissues with minimal background signal. Finally, we demonstrated that this strategy can be combined with metabolic labeling for fluorogenic detection of metabolically tagged mycobacteria under no-wash conditions and paired with covalently clickable probes for high-contrast super-resolution and multiplexed imaging in cells and tissues.