Docking of Antibodies into the Cavities of DNA Origami Structures

Immobilized antibodies are extensively employed for medical diagnostics, such as in enzyme‐linked immunosorbent assays. Despite their widespread use, the ability to control the orientation of immobilized antibodies on surfaces is very limited. Herein, we report a method for the covalent and orientation‐selective immobilization of antibodies in designed cavities in 2D and 3D DNA origami structures. Two tris(NTA)‐modified strands are inserted into the cavity to form NTA–metal complexes with histidine clusters on the Fc domain. Subsequent covalent linkage to the antibody was achieved by coupling to lysine residues. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) confirmed the efficient immobilization of the antibodies in the origami structures. This increased control over the orientation of antibodies in nanostructures and on surfaces has the potential to direct the interactions between antibodies and targets and to provide more regular surface assemblies of antibodies.     

Near‐Infrared Light‐Initiated Hybridization Chain Reaction for Spatially and Temporally Resolved Signal Amplification

Precise control over signal amplification provides unparalleled opportunities for diverse applications. However, spatiotemporally controlled amplification has not been realized because of the lack of a design methodology. The aim of this study was thus to develop a conceptual approach for remote control over signal amplification at a chosen time and site in living cells. This system was constructed by re‐engineering the functional units of the hybridization chain reaction (HCR) and combination with upconversion photochemistry, thus resulting in an activatable HCR with the high spatial and temporal precision of near‐infrared (NIR) light. As a proof of concept, we demonstrate the spatially and temporally resolved amplified imaging of messenger RNA (mRNA) with ultrahigh sensitivity in vitro and in vivo. Furthermore, by using a system targeting subcellular sites we have developed a new technique for NIR‐initiated amplified imaging of mRNA exclusively within a specific organelle.     

Programmable Assembly of Nano-architectures through Designing Anisotropic DNA Origami Patches

Programmable assembly of nanoparticles (NPs) into well-defined architectures has attracted attention because of tailored properties resulting from coupling effects. However, general and precise approaches to control binding modes between NPs remain a challenge owing to the difficulty in manipulating the accurate positions of the functional patches on the surface of NPs. Here, a strategy is developed to encage spherical NPs into pre-designed octahedral DNA origami frames (DOFs) through DNA base-pairings. The DOFs logically define the arrangements of functional patches in three dimensions, owing to the programmability of DNA hybridization, and thus control the binding modes of the caged nanoparticle with designed anisotropy. Applying the node-and-spacer approach that was widely used in crystal engineering to design coordination polymers, patchy NPs could be rationally designed with lower symmetry encoded to assemble a series of nano-architectures with high-order geometries.     

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.     

表面引发的DNA杂交链式反应的石英晶体微天平研究

通过石英晶体振荡技术研究了杂交链式反应这种核酸扩增的方法. 石英晶体微天平可以表征在晶体和溶液的界面上的DNA层, 并获得粘性穿透深度这一重要参数. 根据石英晶体表面吸附质量和振荡频率之间的关系, 我们测量了表面引发的杂交链式反应的动力学过程, 并获得界面上的粘度、剪切模量等参数. 这一工作为研究固液界面上核酸反应过程, 特别是杂交链式反应的机制提供了新的途径.     

Hyperbranched Hybridization Chain Reaction for Triggered Signal Amplification and Concatenated Logic Circuits

A hyper‐branched hybridization chain reaction (HB‐HCR) is presented herein, which consists of only six species that can metastably coexist until the introduction of an initiator DNA to trigger a cascade of hybridization events, leading to the self‐sustained assembly of hyper‐branched and nicked double‐stranded DNA structures. The system can readily achieve ultrasensitive detection of target DNA. Moreover, the HB‐HCR principle is successfully applied to construct three‐input concatenated logic circuits with excellent specificity and extended to design a security‐mimicking keypad lock system. Significantly, the HB‐HCR‐based keypad lock can alarm immediately if the “password” is incorrect. Overall, the proposed HB‐HCR with high amplification efficiency is simple, homogeneous, fast, robust, and low‐cost, and holds great promise in the development of biosensing, in the programmable assembly of DNA architectures, and in molecular logic operations.     

基于杂交链式反应信号放大和磁分离技术荧光检测端粒酶活性

端粒酶是由RNA和蛋白质组成的一种核糖核蛋白酶, 它一般在癌细胞中被激活. 它与端粒DNA的不断复制以及癌细胞的不断增殖密切相关. 所以检测端粒酶的活性对癌症的早期诊断以及以端粒酶为靶标分子的抗癌药物的开发具有重要意义. 利用杂交链式反应(HCR)无酶放大检测信号, 建立了一种简单、快速的端粒酶活性检测方法. 端粒酶延伸产物是一条末端具有(ggttag)_n重复序列的DNA. 在实验过程中, 通过链霉亲合素与生物素的特异性作用将端粒酶延伸产物连接在磁性微球上. 设计一条端粒酶延伸产物特异性的DNA探针I作为杂交链式反应的引发探针. DNA探针I的3'-端与端粒酶延伸产物的重复序列匹配, 通过杂交, DNA探针I被固定在磁球上; DNA探针I的5'-端引发DNA探针II和探针III发生杂交链式反应. DNA探针II和探针III上都标记有荧光基团, 可以利用荧光直接进行信号检测. 在反应过程中, 通过磁分离去除多余未反应的三种DNA探针. 在优化条件下, 可以检测到1.0×10⁵个Hela细胞中的端粒酶活性. 该方法简单、快速、检测成本低, 分析全程无酶参与, 在肿瘤或癌症的临床诊断以及以端粒酶为靶标分子的抗癌药物的筛选上具有广阔的应用前景.     

Assembly and Purification of Enzyme‐Functionalized DNA Origami Structures

The positioning of enzymes on DNA nanostructures for the study of spatial effects in interacting biomolecular assemblies requires chemically mild immobilization procedures as well as efficient means for separating unbound proteins from the assembled constructs. We herein report the exploitation of free‐flow electrophoresis (FFE) for the purification of DNA origami structures decorated with biotechnologically relevant recombinant enzymes: the S‐selective NADP⁺/NADPH‐dependent oxidoreductase Gre2 from S. Cerevisiae and the reductase domain of the monooxygenase P450 BM3 from B. megaterium. The enzymes were fused with orthogonal tags to facilitate site‐selective immobilization. FFE purification yielded enzyme–origami constructs whose specific activity was quantitatively analyzed. All origami‐tethered enzymes were significantly more active than the free enzymes, thereby suggesting a protective influence of the large, highly charged DNA nanostructure on the stability of the proteins.     

基于杂交链式反应辅助多重信号放大的端粒酶灵敏检测

端粒酶是真核细胞维持端粒长度的关键逆转录酶,其生物活性的高低可以为多种癌症的临床诊断和预后治疗提供有价值的信息.本研究以人宫颈癌细胞(HeLa细胞)裂解液中的端粒酶为研究对象,通过借助杂交链式反应辅助多重信号放大策略,提出了一种新颖、灵敏的检测端粒酶电化学方法.首先将端粒酶的延伸引物自组装在金电极表面,当端粒酶存在时,端粒酶能够催化引物的延伸,产生与发卡环探针H1部分互补的序列,进而引发杂交链式反应,形成由两个发卡环探针(H1和H2)交替杂交而形成的DNA长链.由于H1和H2末端均修饰有生物素,加入链霉亲和素修饰辣根过氧化物酶后,辣根过氧化物酶被被连接到电极表面,催化邻苯二胺氧化生成2,3-二氨基吩嗪,产生显著的电化学信号.实验结果表明,本研究建立的端粒酶电化学检测方法高效、可行,线性范围宽,灵敏度高,可以检测每毫升10个HeLa细胞裂解液中的端粒酶.本方法具有较好的选择性,能有效区分端粒酶和对照蛋白.     

Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters

miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.     

两种异金属链状配位聚合物的合成和晶体结构

在甲醇溶液中,将K2NiL·H2O和M(OAC)2(M = Co,Zn)按1:1的摩尔比进行组装反应,得到了镍、钴和镍、锌两种异金属一维链状配位聚合物,其化学组成分别为{[Ni2Co2L2(H2O)2]·CH3OH·3H2O}n（1）和{[Ni2Zn2L2 (H2O)2]·2CH3OH·H2O}n（2）,（H4L=2-羟基-3-[(E)-({2-(2-羟基苯甲酰胺基)乙基}亚氨基)甲基]苯甲酸,OAC- = CH3COO-）。通过IR谱,元素分析的方法对其进行了表征,利用X-射线单晶衍射方法对其晶体结构进行了测定,结构分析表明：它们都是由不对称四核单元组成链状配位聚合物。     

Synthesis and Crystal Structures of Two Cadmium Coordination Chain Polymers

Hydrothermal reactions of cadmium precursors with 2, 2′‐bipyridine, fumaric acid or NaN₃ in basified aqueous solutions gave rise to two cadmium complexes [Cd(bipy)(fum)(H₂O)]_n ( 1 ), and [Cd(bipy)(μ_{1, 1}‐N₃)₂]_n ( 2 ) (fum = fumarate dianion), which were characterized by X‐ray crystallography. Complex [Cd(bipy)(fum)(H₂O)]_n ( 1 ) crystallizes in the orthorhombic system, space group Pbca, with a = 9.0488(8), b = 16.246(3), c = 19.810(4) Å, and Z = 8 while complex [Cd(bipy)(μ_{1, 1}‐N₃)₂]_n ( 2 ) in the monoclinic system, space group C2/c, with a = 12.378(3), b = 14.788(3), c = 6.6139(13) Å, β = 91.49(3)°, and Z = 4. The photoluminescence spectra for compounds 1 and 2 have also been studied.     

Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame

The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.     

Clamped Hybridization Chain Reactions for the Self‐Assembly of Patterned DNA Hydrogels

DNA hydrogels hold great potential for biological and biomedical applications owing to their programmable nature and macroscopic sizes. However, most previous studies involve spontaneous and homogenous gelation procedures in solution, which often lack precise control. A clamped hybridization chain reaction (C‐HCR)‐based strategy has been developed to guide DNA self‐assembly to form macroscopic hydrogels. Analogous to catalysts in chemical synthesis or seeds in crystal growth, we introduced DNA initiators to induce the gelation process, including crosslinked self‐assembly and clamped hybridization in three dimensions with spatial and temporal control. The formed hydrogels show superior mechanical properties. The use of printed, surface‐confined DNA initiators was also demonstrated for fabricating 2D hydrogel patterns without relying on external confinements. This simple method can be used to construct DNA hydrogels with defined geometry, composition, and order for various bioapplications.     

Gold‐Nanoparticle‐Mediated Jigsaw‐Puzzle‐like Assembly of Supersized Plasmonic DNA Origami

DNA origami has rapidly emerged as a powerful and programmable method to construct functional nanostructures. However, the size limitation of approximately 100 nm in classic DNA origami hampers its plasmonic applications. Herein, we report a jigsaw‐puzzle‐like assembly strategy mediated by gold nanoparticles (AuNPs) to break the size limitation of DNA origami. We demonstrated that oligonucleotide‐functionalized AuNPs function as universal joint units for the one‐pot assembly of parent DNA origami of triangular shape to form sub‐microscale super‐origami nanostructures. AuNPs anchored at predefined positions of the super‐origami exhibited strong interparticle plasmonic coupling. This AuNP‐mediated strategy offers new opportunities to drive macroscopic self‐assembly and to fabricate well‐defined nanophotonic materials and devices.     

Multiplexed Immunosensing Platform Coupled to Hybridization Chain Reaction for Electrochemical Determination of MicroRNAs in Clinical Samples

There is an urgent need for development of rapid and inexpensive techniques for detection of microRNAs (miRNAs), which are potential biomarkers of various types of cancer. In this paper, we describe a multiplexed electrochemical platform for determination of three cancer‐relevant miRNAs: miR‐21, let‐7a and miR‐31. The strategy combines the use of magnetic beads (MBs) modified with a commercial antibody for the efficient capture of the heteroduplexes formed by hybridization of the target miRNA with DNA probe. Free non‐hybridized region of the DNA probe was thereafter hybridized with two biotin‐labeled auxiliary DNA probes in a process of hybridization chain reaction (HCR), resulting in a long hybrid bearing a large number of biotin molecules. Labeling of these multiple biotin units with streptavidin‐peroxidase conjugates allowed an amplification of the amperometric signal measured after capturing the modified MBs at a screen‐printed carbon electrode array of eight electrodes. The combined strategy demonstrated in a similar assay time significantly higher sensitivity than those previously described using modified MBs with the same capture antibody (without amplification by HCR) or a HCR strategy implemented on the surface of MBs, respectively. The methodology exhibits a good selectivity for discriminating single mismatches and was applied to the determination of the three target miRNAs in total RNA (RNA_t) extracted from various cancer cell lines and from cervical precancerous lesions.     

指数线性聚合酶链式反应法制备焦磷酸测序反应的单链模板

建立了一种简单的焦磷酸测序用单链模板制备方法,以包含SNP6位点一段78bp序列为对象,采用非热启动Taq酶进行指数线性PCR扩增,通过加入甘油、BSA等PCR增强剂增加反应的效率和特异性,设计反应液A和B处理PCR产物中干扰焦测序的限制性引物、未完全反应的产物、焦磷酸和dNTPs等杂质, 处理后1～2 μL PCR产物就可直接用于焦测序检测.测定了BRCA1基因中5个乳腺癌相关的SNP位点,获得的图谱无非特异性信号,测得序列与参考序列一致,能够进行SNP分析,表明本方法可以制备高质量焦测序单链模板,且使焦测序的成本显著降低,操作更为简便,减少了操作过程中样本间的交叉污染,有利于焦测序样品预处理的自动化.     

Solvothermal Synthesis,Crystal Structures,and Magnetic Properties of Two Organically Templated Iron Sulfates with Chain Structures

Two new one‐dimensional (1D) organically templated iron(III) sulfates [C₂NH₈]₃ [Fe₃(μ₃‐O)₂(SO₄)₄] ( 1 ) and [C₂N₂H₁₀][C₂NH₇]_0.5[FeF(SO₄)₂] ( 2 ) were synthesized under solvothermal conditions and characterized by single‐crystal X‐ray diffraction, powder X‐ray diffraction (XRD), FT‐IR spectroscopy, elemental analyses, ICP analyses, and thermogravimetric analyses. Single‐crystal structure analysis reveals that both compounds show linear‐chain structures, involving FeO₆ (FeF₂O₄) octahedra and SO₄ tetrahedra. The magnetic properties of the two compounds have also been investigated.