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.     

A Biomimetic Approach for Spatially Controlled Cell Membrane Engineering Using Fusogenic Spherical Nucleic Acid

Engineering of the cell plasma membrane using functional DNA is important for studying and controlling cellular behaviors. However, most efforts to apply artificial DNA interactions on cells are limited to external membrane surface due to the lack of suitable synthetic tools to engineer the intracellular side, which impedes many applications in cell biology. Inspired by the natural extracellular vesicle-cell fusion process, we have developed a fusogenic spherical nucleic acid construct to realize robust DNA functionalization on both external and internal cell surfaces via liposome fusion-based transport (LiFT) strategy, which enables applications including the construction of heterotypic cell assembly for programmed signaling pathway and detection of intracellular metabolites. This approach can engineer cell membranes in a highly efficient and spatially controlled manner, allowing one to build anisotropic membrane structures with two orthogonal DNA functionalities.     

Nanoparticle‐Assisted Alignment of Carbon Nanotubes on DNA Origami

Aligning carbon nanotubes (CNTs) is a key challenge for fabricating CNT‐based electronic devices. Herein, we report a spherical nucleic acid (SNA) mediated approach for the highly precise alignment of CNTs at prescribed sites on DNA origami. We find that the cooperative DNA hybridization occurring at the interface of SNA and DNA‐coated CNTs leads to an approximately five‐fold improvement of the positioning efficiency. By combining this with the intrinsic positioning addressability of DNA origami, CNTs can be aligned in parallel with an extremely small angular variation of within 10°. Moreover, we demonstrate that the parallel alignment of CNTs prevents incorrect logic functionality originating from stray conducting paths formed by misaligned CNTs. This SNA‐mediated method thus holds great potential for fabricating scalable CNT arrays for nanoelectronics.     

Single‐Particle Tracking and Modulation of Cell Entry Pathways of a Tetrahedral DNA Nanostructure in Live Cells

DNA is typically impermeable to the plasma membrane due to its polyanionic nature. Interestingly, several different DNA nanostructures can be readily taken up by cells in the absence of transfection agents, which suggests new opportunities for constructing intelligent cargo delivery systems from these biocompatible, nonviral DNA nanocarriers. However, the underlying mechanism of entry of the DNA nanostructures into the cells remains unknown. Herein, we investigated the endocytotic internalization and subsequent transport of tetrahedral DNA nanostructures (TDNs) by mammalian cells through single‐particle tracking. We found that the TDNs were rapidly internalized by a caveolin‐dependent pathway. After endocytosis, the TDNs were transported to the lysosomes in a highly ordered, microtubule‐dependent manner. Although the TDNs retained their structural integrity within cells over long time periods, their localization in the lysosomes precludes their use as effective delivery agents. To modulate the cellular fate of the TDNs, we functionalized them with nuclear localization signals that directed their escape from the lysosomes and entry into the cellular nuclei. This study improves our understanding of the entry into cells and transport pathways of DNA nanostructures, and the results can be used as a basis for designing DNA‐nanostructure‐based drug delivery nanocarriers for targeted therapy.     

Designed Intercalators for Modification of DNA Origami Surface Properties

The modification of the backbone properties of DNA origami nanostructures through noncovalent interactions with designed intercalators, based on acridine derivatized with side chains containing esterified fatty acids or oligo(ethylene glycol) residues is reported. Spectroscopic analyses indicate that these intercalators bind to DNA origami structures. Atomic force microscopy studies reveal that intercalator binding does not affect the structural intactness but leads to altered surface properties of the highly negatively charged nanostructures, as demonstrated by their interaction with solid mica or graphite supports. Moreover, the noncovalent interaction between the intercalators and the origami structures leads to alteration in cellular uptake, as shown by confocal microscopy studies using two different eukaryotic cell lines. Hence, the intercalator approach offers a potential means for tailoring the surface properties of DNA nanostructures.     

DNA codes for nanoscience

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.     

DNA Framework-based Topological Aptamer for Differentiating Subtypes of Hepatocellular Carcinoma Cells

Hepatocellular carcinoma(HCC) remains a global health challenge with a growing incidence worldwide. The accurate identification of liver HCC cell subtypes plays crucial roles in precision medicine and prognosis. Nevertheless, simple and efficient methods for cell subtype discrimination still remain an issue to be studied. In this study, we construct topological probes by using a tetrahedral DNA framework(TDF) to topologically engineer the spatial orientations of the aptamers. The three vertexes of a TDF were algebraic topologically anchored with aptamers targeting epithelial cell adhesion molecule(EpCAM), which may express differently on different subtypes of HCC cells. Using the TDF-based topological aptamer(TDF-TA), we accomplish the differentiation of HCC cell subtypes, including high-metastatic, low-metastatic HCC and normal cells based on flow cytometry(FCM) and fluorescence microscope imaging. By replacing the fluorescent indicator modified on aptamers with photoacoustic dyes, we achieve the discrimination of different HCC cells using photoacoustic imaging technology, further demonstrating the feasibility of the TDF-based topological probe for HCC cell subtype discrimination. This TDF-based topolo-gical engineering strategy thus provides a flexible means for subtype cell discrimination, which may provide new ideas for achieving accurate diagnosis of HCC.     

Switchable Enzyme/DNAzyme Cascades by the Reconfiguration of DNA Nanostructures

Mimicking cellular transformations and signal transduction pathways by means of biocatalytic cascades proceeding in organized media is a scientific challenge. We describe two DNA machines that enable the “ON/OFF” switchable activation and deactivation of three‐component biocatalytic cascades. One system consists of a reconfigurable DNA tweezers‐type structure, whereas in the second system the catalytic cascade proceeds on a switchable DNA clamp scaffold. The three‐component catalytic cascades consist of β‐galactosidase (β‐Gal), glucose oxidase (GOx), and the K⁺‐ion‐stabilized hemin‐G‐quadruplex horseradish peroxidase (HRP)‐mimicking DNAzyme. The hemin‐G‐quadruplex‐bridged closed structure of the tweezers or clamp allows the biocatalytic cascades to operate (switched “ON′′), whereas separation of the hemin‐G‐quadruplex by means of 18‐crown‐6‐ether opens the tweezers/clamp structures, thus blocking the catalytic cascade (switched ”OFF“). This study is complemented by two‐component, switchable biocatalytic cascades composed of GOx and hemin‐G‐quadruplex assembled on hairpin‐bridged DNA tweezers or clamp nanostructures.     

Framework Nucleic Acids for Cell Imaging and Therapy

Over the past decade,structural DNA nanotechnology has been well developed to be a promising and powerful technique to generate various nanostructures with programmability,spatial organization and biocompatibi-lity.With the advent of computer-aided tools,framework nucleic acids have been employed in a series of biomedical applications,ranging from biosensing,bioimaging,diagnosis,to therapeutics.In this review,we summarized recent advances in the construction of precisely assembled DNA nanostructures,and DNA-engineered biomimetics.We also outlined the challenges and opportunities for the translational applications of framework nucleic acids.     

Engineering Substrate Topography at the Micro‐ and Nanoscale to Control Cell Function

The interaction of mammalian cells with nanoscale topography has proven to be an important signaling modality in controlling cell function. Naturally occurring nanotopographic structures within the extracellular matrix present surrounding cells with mechanotransductive cues that influence local migration, cell polarization, and other functions. Synthetically nanofabricated topography can also influence cell morphology, alignment, adhesion, migration, proliferation, and cytoskeleton organization. We review the use of in vitro synthetic cell–nanotopography interactions to control cell behavior and influence complex cellular processes, including stem‐cell differentiation and tissue organization. Future challenges and opportunities in cell–nanotopography engineering are also discussed, including the elucidation of mechanisms and applications in tissue engineering.     

DNA电化学传感器在DNA损伤研究中的应用

利用单链DNA分子共价固定在石墨电极表面,采用核酸分子杂交技术,以道诺霉素作为杂交指示剂形成DNA电化学传感器.研究了在不同致突变剂的作用下,特定碱基序列的DNA在电极表面能否杂交及杂交程度的差异,探讨了DNA突变情况及可能的突变机理.     

Turning DNA Binding Motifs into a Material for Flow Cells

Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.     

Magnetic–Fluorescent Colloidal Nanobeads: Preparation and Exploitation in Cell Separation Experiments

Nanostructures displaying fluorescence and magnetic properties at the same time are potentially useful for achieving simultaneous bio‐separation and bio‐sensing (e.g., magnetic separation coupled with multiplexing optical detection of different tumour cell populations). Spherical nanobeads that display both fluorescent and magnetic features are reported; they are fabricated by grafting fluorescent oligothiophene molecules to an amphiphilic polymer that is then used to enwrap iron oxide nanoparticles, which acts as the magnetic domain. By tuning experimental conditions, control over the number of magnetic nanoparticles per bead and over the bead diameter (30–400 nm) was achieved. A cell separation efficiency of the level required for cell sorting applications is also reported.

     

基于DNA的细胞膜功能化

细胞膜在细胞与外界环境间的物质运输、能量转换和信息传递等过程中起着重要作用,研究和控制细胞膜上的分子的相互作用,对理解和操控细胞的生理功能具有重要意义。脱氧核糖核酸(Deoxyribonucleic acid, DNA)分子具有精确自组装和可编程的特性,是一种研究生物膜分子相互作用的新工具。本综述中,我们概括了DNA分子修饰细胞膜的方法,随后介绍了基于DNA分子的监测、控制细胞膜分子相互作用的工作以及DNA分子介导细胞连接的研究,并分析了上述研究的局限性。最后,我们对基于DNA的细胞膜功能化研究进行总结与展望,以期促进对细胞膜功能的新认识,获得控制细胞功能的新方法。