Imparting Designer Biorecognition Functionality to Metal–Organic Frameworks by a DNA‐Mediated Surface Engineering Strategy

Surface functionality is an essential component for processing and application of metal–organic frameworks (MOFs). A simple and cost‐effective strategy for DNA‐mediated surface engineering of zirconium‐based nanoscale MOFs (NMOFs) is presented, capable of endowing them with specific molecular recognition properties and thus expanding their potential for applications in nanotechnology and biotechnology. It is shown that efficient immobilization of functional DNA on NMOFs can be achieved via surface coordination chemistry. With this strategy, it is demonstrated that such porphyrin‐based NMOFs can be modified with a DNA aptamer for targeting specific cancer cells. Furthermore, the DNA–NMOFs can facilitate the delivery of therapeutic DNA (e.g., CpG) into cells for efficient recognition of endosomal Toll‐like receptor 9 and subsequent enhanced immunostimulatory activity in vitro and in vivo. No apparent toxicity is observed with systemic delivery of the DNA–NMOFs in vivo. Overall, these results suggest that the strategy allows for surface functionalization of MOFs with different functional DNAs, extending the use of these materials to diverse applications in biosensor, bioimaging, and nanomedicine.     

Synthesis of Branched DNA Scaffolded Super‐Nanoclusters with Enhanced Antibacterial Performance

Metal nanoclusters (NCs) possess unique optical properties, and exhibit a wide variety of potential applications. DNA with robust molecular programmability is demonstrated as an ideal scaffold to regulate the formation of NCs, offering a rational approach to precisely tune the spatial structures of NCs. Herein, the first use of branched DNA as scaffold to regulate the formation of silver nanoclusters (super‐AgNC) is reported, in which the spatial structures are precisely designed and constructed. Super‐AgNC with tunable shapes and arm‐lengths including Y‐, X‐, and (Y–X)‐ shaped super‐AgNC is achieved. The molecular structures and optical properties of super‐AgNCs are systemically studied. As a proof of application, remarkably, super‐AgNCs exhibit superior antibacterial performance. In addition, super‐AgNCs show excellent biocompatibility with three types of tissue cells including 293T (human embryonic kidney cells), SMCs (vascular smooth muscle cells), and GLC‐82 (lung adenocarcinoma cells). These performances enable the super‐AgNCs adaptable in a variety of applications such as biosensing, bioimaging, and antibacterial agents.     

Structural Studies of DNA–Cationic Lipid Complexes Confined in Lithographically Patterned Microchannel Arrays

We have used lithographically patterned microchannel arrays with channel widths ranging from 1 to 20 m, fabricated using electron beam lithography and reactive ion etching, in structural studies of DNA–cationic lipid complexes in confinement. Various techniques have been developed for loading these DNA–membrane complexes into the microchannels or to form the complexes in situ by sequentially depositing DNA and lipid solutions into the microchannels. Optical microscopy studies indicate that such complex formation is strongly influenced by the periodic channel structure even at channel widths much larger than the persistent length of the DNA molecules. Preliminary x-ray diffraction experiments conducted at Stanford Synchrotron Radiation Laboratory (SSRL) yielded only a weak signal from the lipid bilayers in the complexes. The use of a microfocused x-ray beam produced by the newly developed Bragg–Fresnel optics at a third-generation synchrotron facility may dramatically increase the signal-to-noise ratio and allow observation of orientational as well as positional ordering of DNA molecules induced by the microchannels. Structural control of the DNA–membrane complexes has a broad range of potential applications in gene probe technology and as mesoscopic biomolecular composites.     

The effect of DNA probe distribution on the reliability of label-free biosensors

As the design of label-free DNA biosensors matures, and their sizes reduced to enhance their sensitivity, not much has been researched about the variations in the received signal with the positioning of the probes on the sensitive surface. We approach this issue computationally in this paper. By adopting the finite-element model on a three-dimensional biological field-effect transistor (BioFET) slice, and running Monte-Carlo simulations on the positions of the DNA molecules, we extract the expected variations in the signal. Then, we show that signal-to-noise (SNR) ratio can be low enough to hinder the functionality of the device, placing a limitation on how low the sensitivity of a sensor of a certain size can be.     

基于XML的DNA公共数据模型

针对目前DNA数据组织与处理中存在的数据异构问题,提出一个基于XML的DNA公共数据模型（DCDM）。该模型具有很强的可扩展性,能克服一般公共数据模型的作用范围小的缺点,可用于构建DNA研究领域统一的DNA数据描述模式。实验结果表明,该模型能解决DNA数据异构中的语义异构。