DNA Framework-Based Topological Cell Sorters

Molecular recognition in cell biological process is characterized with specific locks-and-keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically-engineered ligand systems enable the exploration of the binding strength between ligand-receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10-fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands.     

DNA Framework‐Based Topological Cell Sorters

Molecular recognition in cell biological process is characterized with specific locks‐and‐keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically‐engineered ligand systems enable the exploration of the binding strength between ligand‐receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10‐fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands.     

Virus-sized DNA nanoparticles for gene delivery based on micelles of cationic calixarenes

Macrocyclic amphiphilic molecules based on calix[4]arenes are highly attractive for controlled supramolecular assembly of DNA into small nanoparticles, since they present a unique conical architecture and can bear multiple charged groups. In the present work, we synthesized new amphiphilic calixarenes bearing cationic groups at the upper rim and alkyl chains at the lower rim. Their self-assembly in aqueous solution was characterized by fluorescent probes, fluorescence correlation spectroscopy, dynamic light scattering, gel electrophoresis and atomic force microscopy. We found that calixarenes bearing long alkyl chains (octyl) self-assemble into micelles of 6 nm diameter at low critical micellar concentration and present the unique ability to condense DNA into small nanoparticles of about 50 nm diameter. In contrast, the short-chain (propyl) analogues that cannot form micelles at low concentrations failed to condense DNA, giving large polydisperse DNA complexes. Thus, formation of small DNA nanoparticles is hierarchical, requiring assembly of calixarenes into micellar building blocks that further co-assemble with DNA into small virus-sized particles. The latter showed much better gene transfection efficiency in cell cultures relative to the large DNA complexes with the short-chain analogues, which indicates that gene delivery of calixarene/DNA complexes depends strongly on their structure. Moreover, all cationic calixarenes studied showed low cytotoxicity. Thus, this work presents a two-step hierarchical assembly of small DNA nanoparticles for gene delivery based on amphiphilic cone-shaped cationic calixarenes.     

pH-Responsive Reversible DNA Self-assembly Mediated by Zwitterion

pH-Responsive DNA assembles have drawn growing attentions owing to their great potential in diverse areas.However,pH-responsive motifs are limited to specific DNA sequences and annealing is usually needed for DNA assemblies;therefore,sequence-independent pH-responsive DNA assembly at room temperature is highly desired as a more general way.Here,we propose a reversible pH-responsive DNA assembly strategy at room-temperature using zwitterion,glycine betaine(GB),as charge-regulation molecules.The reversible assembly and disassembly of DNA nanostructures could be achieved by alternatively regulating the acidic and basic environments in the presence of GB,respectively.In an acidic environment,carboxylate group in GB was protonated and GB was positively charged,which facilitated to shield the inherent electrostatic repulsion of DNA strands.Molecular simulation showed that the newly formed carboxyl group in protonated GB could form hydrogen bonds with bases in DNA to promote the assembly of DNA strands.In a basic solution,carboxylate group in GB was deprotonated and GB was neutral,thus inducing the dissociation of DNA assembly.     

DNA-templated assembly of droplet-derived PEG microtissues

Patterning multiple cell types is a critical step for engineering functional tissues, but few methods provide three-dimensional positioning at the cellular length scale. Here, we present a "bottom-up" approach for fabricating multicellular tissue constructs that utilizes DNA-templated assembly of 3D cell-laden hydrogel microtissues. A flow focusing-generated emulsion of photopolymerizable prepolymer is used to produce 100 μm monodisperse microtissues at a rate of 100 Hz (10(5) h(-1)). Multiple cell types, including suspension and adherently cultured cells, can be encapsulated into the microtissues with high viability (~97%). We then use a DNA coding scheme to self-assemble microtissues "bottom-up" from a template that is defined using "top-down" techniques. The microtissues are derivatized with single-stranded DNA using a biotin-streptavidin linkage to the polymer network, and are assembled by sequence-specific hybridization onto spotted DNA microarrays. Using orthogonal DNA codes, we achieve multiplexed patterning of multiple microtissue types with high binding efficiency and >90% patterning specificity. Finally, we demonstrate the ability to organize multicomponent constructs composed of epithelial and mesenchymal microtissues while preserving each cell type in a 3D microenvironment. The combination of high throughput microtissue generation with scalable surface-templated assembly offers the potential to dissect mechanisms of cell-cell interaction in three dimensions in healthy and diseased states, as well as provides a framework for templated assembly of larger structures for implantation.     

Acid-Activatable Transmorphic Peptide-Based Nanomaterials for Photodynamic Therapy

Inspired by the dynamic morphology control of molecular assemblies in biological systems, we have developed pH-responsive transformable peptide-based nanoparticles for photodynamic therapy (PDT) with prolonged tumor retention times. The self-assembled peptide–porphyrin nanoparticles transformed into nanofibers when exposed to the acidic tumor microenvironment, which was mainly driven by enhanced intermolecular hydrogen bond formation between the protonated molecules. The nanoparticle transformation into fibrils improved their singlet oxygen generation ability and enabled high accumulation and long-term retention at tumor sites. Strong fluorescent signals of these nanomaterials were detected in tumor tissue up to 7 days after administration. Moreover, the peptide assemblies exhibited excellent anti-tumor efficacy via PDT in vivo. This in situ fibrillar transformation strategy could be utilized to design effective stimuli-responsive biomaterials for long-term imaging and therapy.     

A flexible rapid self-assembly scaffold-net DNA hydrogel exhibiting cell mobility control

DNA hydrogels have unique properties, such as specific identifiable molecular structures, programmable self-assembly, and excellent biocompatibility, which have led to increasing researches in the field of nanomaterials and biomedical over the past two decades. However, effective methods to regulate the microstructure of DNA hydrogels still lack, which limits their applications in tissue engineering. By introducing DNA scaffolds into rolling circle amplification (RCA) products and implementing rapid self-assembly strategy, we can produce a regulable new type scaffold-net DNA hydrogel in a short time. Scaffolds concentration and RCA time can regulate the microcharacteristics and physical properties of hydrogels. Scaffold-net DNA hydrogels will be a promising bionic platform for the studies of cancer cell metastatic and microenvironment biophysics.     

Fluorescent and Biocompatible Ruthenium-Coordinated Oligo(p-phenylenevinylene) Nanocatalysts for Transfer Hydrogenation in the Mitochondria of Living Cells

It is challenging to design metal catalysts for in situ transformation of endogenous biomolecules with good performance inside living cells. Herein, we report a multifunctional metal catalyst, ruthenium-coordinated oligo(p-phenylenevinylene) (OPV-Ru), for intracellular catalysis of transfer hydrogenation of nicotinamide adenine dinucleotide (NAD⁺) to its reduced format (NADH). Owing to its amphiphilic characteristic, OPV-Ru possesses good self-assembly capability in water to form nanoparticles through hydrophobic interaction and π–π stacking, and numerous positive charges on the surface of nanoparticles displayed a strong electrostatic interaction with negatively charged substrate molecules, creating a local microenvironment for enhancing the catalysis efficiency in comparison to dispersed catalytic center molecule (TOF value was enhanced by about 15 fold). OPV-Ru could selectively accumulate in the mitochondria of living cells. Benefiting from its inherent fluorescence, the dynamic distribution in cells and uptake behavior of OPV-Ru could be visualized under fluorescence microscopy. This work represents the first demonstration of a multifunctional organometallic complex catalyzing natural hydrogenation transformation in specific subcellular compartments of living cells with excellent performance, fluorescent imaging ability, specific mitochondria targeting and good chemoselectivity with high catalysis efficiency.     

基于微流控芯片的乳腺癌细胞微环境酸化检测

建立了基于微流控芯片的乳腺癌微环境酸化模型和动态检测微环境酸化情况的分析方法。设计了一种多层复合式微流控芯片,将乳腺癌细胞悬液引入含有水凝胶前体的芯片培养室后,在硝酸纤维素薄膜上固化形成3D培养支架。芯片通道连续灌流模拟血流供应,并将非电化学的pH检测器引入芯片,通过图像分析得到实时的pH变化。通过观察癌细胞的存活率、增殖率、乳酸水平及pH值,分析微环境的酸化情况,同时与正常细胞进行比较。结果表明,连续灌流培养7 d,乳腺癌细胞的存活率保持在90%以上;随着培养天数的增加,芯片上癌细胞微环境的pH值逐渐降低,且灌流速度越低,pH值下降越明显,而正常细胞微环境的pH值无明显变化。基于微流控芯片的微环境酸化检测平台可实时动态检测微环境的pH值,有望成为相关肿瘤研究的有力工具。     

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich “toolbox” of structures used to develop DNA‐based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH‐induced, switchable assembly and dissociation of triplex‐DNA‐bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH‐responsive systems and materials are described. Examples include semiconductor‐loaded DNA‐stabilized microcapsules, DNA‐functionalized dye‐loaded metal–organic frameworks (MOFs), and the pH‐induced release of the loads. Furthermore, the design of stimuli‐responsive DNA‐based hydrogels undergoing reversible pH‐induced hydrogel‐to‐solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape‐memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.     

Pericellular Hydrogel/Nanonets Inhibit Cancer Cells

Fibrils formed by proteins are vital components for cells. However, selective formation of xenogenous nanofibrils of small molecules on mammalian cells has yet to be observed. Here we report an unexpected observation of hydrogel/nanonets of a small D ‐peptide derivative in pericellular space. Surface and secretory phosphatases dephosphorylate a precursor of a hydrogelator to trigger the self‐assembly of the hydrogelator and to result in pericellular hydrogel/nanonets selectively around the cancer cells that overexpress phosphatases. Cell‐based assays confirm that the pericellular hydrogel/nanonets block cellular mass exchange to induce apoptosis of cancer cells, including multidrug‐resistance (MDR) cancer cells, MES‐SA/Dx5. Pericellular hydrogel/nanonets of small molecules to exhibit distinct functions illustrates a fundamentally new way to engineer molecular assemblies spatiotemporally in cellular microenvironment for inhibiting cancer cell growth and even metastasis.     

A Preloaded Amorphous Calcium Carbonate/Doxorubicin@Silica Nanoreactor for pH‐Responsive Delivery of an Anticancer Drug

Biomedical applications of nontoxic amorphous calcium carbonate (ACC) nanoparticles have mainly been restricted because of their aqueous instability. To improve their stability in physiological environments while retaining their pH‐responsiveness, a novel nanoreactor of ACC–doxorubicin (DOX)@silica was developed for drug delivery for use in cancer therapy. As a result of its rationally engineered structure, this nanoreactor maintains a low drug leakage in physiological and lysosomal/endosomal environments, and responds specifically to pH 6.5 to release the drug. This unique ACC–DOX@silica nanoreactor releases DOX precisely in the weakly acidic microenvironment of cancer cells and results in efficient cell death, thus showing its great potential as a desirable chemotherapeutic nanosystem for cancer therapy.     

Inducible biosynthetic nanoscaffolds as recruitment platforms for detecting molecular target interactions inside living cells

We present a novel phenotypic readout using inducible, biosynthetic nanoscaffolds to directly visualize dynamic molecular interactions within living cells at the single-cell level with high sensitivity and selectivity. Labeled ferritin is used to form biological nanoparticles inside cells. Specific supramolecular assembly of ferritin-derived nanoparticles induces highly clustered nanoscaffolds. These inducible biosynthetic nanoscaffolds are used as the artificial recruitment/redistribution platform for monitoring interactions of a small molecule with its target protein(s) inside living cells.     

Photo- and electropatterning of hydrogel-encapsulated living cell arrays

Living cells have the potential to serve as sensors, naturally integrating the response to stimuli to generate predictions about cell fate (e.g., differentiation, migration, proliferation, apoptosis). Miniaturized arrays of living cells further offer the capability to interrogate many cells in parallel and thereby enable high-throughput and/or combinatorial assays. However, the interface between living cells and synthetic chip platforms is a critical one wherein the cellular phenotype must be preserved to generate useful signals. While some cell types retain tissue-specific features on a flat (2-D) surface, it has become increasingly apparent that a 3-D physical environment will be required for others. In this paper, we present two independent methods for creating living cell arrays that are encapsulated within a poly(ethylene glycol)-based hydrogel to create a local 3-D microenvironment. First, 'photopatterning' selectively crosslinks hydrogel microstructures containing living cells with approximately 100 microm feature size. Second, 'electropatterning' utilizes dielectrophoretic forces to position cells within a prepolymer solution prior to crosslinking, forming cell patterns with micron resolution. We further combine these methods to obtain hierarchical control of cell positioning over length scales ranging from microns to centimeters. This level of microenvironmental control should enable the fabrication of next-generation cellular microarrays in which robust 3-D cultures of cells are presented with appropriate physical and chemical cues and, consequently, report on cellular responses that resemble in vivo behavior.     

Chitosan‐induced synthesis of magnetite nanoparticles via iron ions assembly

Superparamagnetic magnetite nanoparticles were synthesized induced by chitosan hydrogel under ambient conditions via iron ions assembly, and the inducing effect of chitosan hydrogel was discussed. Results of X‐ray diffraction and transmission electron microscopy indicate that the nanoparticles were inverse cubic spinel structure magnetite with diameter about 16 nm, and the superparamagnetic nanoparticles with narrow size distribution dispersed uniformly in chitosan. The magnetization measurements indicated that the nanoparticles showed the typical superparamagnetic behavior. The crystallinity, morphology, and magnetic properties of magnetite nanoparticles were remarkably influenced by the pH values of iron ion solutions. The interaction between magnetite and chitosan was illustrated by FT‐IR and thermogravimetric analysis, which concluded that the magnetite nanoparticles were coated by a chitosan layer via the amino groups of chitosan. The chitosan hydrogel assisted in the synthesis of superparamagnetic magnetite nanoparticles through chelation by amino groups. Copyright © 2008 John Wiley & Sons, Ltd.     

Adaptive Chemoenzymatic Microreactors Composed of Inorganic Nanoparticles and Bioinspired Intrinsically Disordered Proteins

The assembly of protein and inorganic nanoparticles represents an attractive approach to generate composite materials with multiple functions. Herein, we functionalize inorganic nanoparticles with intrinsically disordered protein domains associated with the formation of membraneless compartments in cells. These protein sequences, defined as low complexity domains (LCDs), encode intermolecular interactions that drive highly controlled, dynamic self‐assembly in response to environmental changes. We show that the properties of the LCDs can be transferred to inorganic nanoparticles, inducing controlled phase separation that is dynamic and responsive to ionic strength and pH. Specifically, we hybridize magnetic nanoparticles with multi‐domain proteins consisting of LCD domains and a globular enzyme, generating dynamic protein‐composite compartments that locally confine hybrid chemoenzymatic reactions and respond to external magnetic fields and changes in solution conditions.     

Reconfigurable Bioinspired Framework Nucleic Acid Nanoplatform Dynamically Manipulated in Living Cells for Subcellular Imaging

In nature, the formation of spider silk fibers begins with dimerizing the pH‐sensitive N‐terminal domains of silk proteins (spidroins) upon lowering pH, and provides a natural masterpiece for programmable assembly. Inspired by the similarity of pH‐dependent dimerization behaviors, introduced here is an i‐motif‐guided model to mimic the initial step of spidroin assembly at the subcellular level. A framework nucleic acid (FNA) nanoplatform is designed using two tetrahedral DNA nanostructures (TDNs) with different branched vertexes carrying a bimolecular i‐motif and a split ATP aptamer. Once TDNs enter acidic lysosomes within living cells, they assemble into a heterodimeric architecture, thereby enabling the formation of a larger‐size framework and meanwhile subcellular imaging in response to endogenous ATP, which can be dynamically manipulated by adjusting intracellular pH and ATP levels with external drug stimuli.     

Structural Transformation: Assembly of an Otherwise Inaccessible DNA Nanocage

A strategy of structural transformation for the assembly of DNA nanocages that can not be assembled directly is described. In this strategy, a precursor DNA nanocage is assembled first and then is isothermally transformed into a desired, complicated nanocage. A dramatic, conformational change accompanies the transformation. This strategy has been proven to be successful by native polyacrylamide gel electrophoresis (PAGE) and cryogenic electron microscopy (cryoEM) imaging. We expect that the strategy of structural transformation will be useful for the assembly of many otherwise inaccessible DNA nanostructures and help to increase the structural complexity of DNA nanocages.     

Autonomous Growth of a Spatially Localized Supramolecular Hydrogel with Autocatalytic Ability

Autocatalysis and self‐assembly are key processes in developmental biology and are involved in the emergence of life. In the last decade both of these features were extensively investigated by chemists with the final goal to design synthetic living systems. Herein, we describe the autonomous growth of a self‐assembled soft material, that is, a supramolecular hydrogel, able to sustain its own formation through an autocatalytic mechanism that is not based on any template effect and emerges from a peptide (hydrogelator) self‐assembly. A domino sequence of events starts from an enzymatically triggered peptide generation followed by self‐assembly into catalytic nanofibers that induce and amplify their production over time, resulting in a 3D hydrogel network. A cascade is initiated by traces (10^?18 m ) of a trigger enzyme, which can be localized allowing for a spatial resolution of this autocatalytic buildup of hydrogel growth, an essential condition on the route towards further cell‐mimic designs.     

Switchable Hydrolase Based on Reversible Formation of Supramolecular Catalytic Site Using a Self‐Assembling Peptide

The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH‐switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH‐responsive peptide. The peptide exhibits a conformational transition from random coil to β‐sheet by changing the pH from acidic to alkaline. The β‐sheet self‐assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity. Catalytic activity can be reversible switched by pH‐induced assembly/disassembly of the fibrils into random coils. At higher concentrations, the peptide forms a hydrogel which is also catalytically active and maintains its reversible (de‐)activation.