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.     

AutoProc: An automatic proactive replication scheme for P2P storage

Due to the prevalence of peer departures, P2P storage systems need to constantly generate replicas for high durability. However, few existing systems are able to select the right replication rate that balances replication cost and durability, e.g., minimizing replication cost without threatening the durability target. In this paper, we propose a method called AutoProc to automate the replication process in P2P storage systems. AutoProc employs two key techniques to enable cost-effective replication: correct...     

Optimizing write operation on replica in data grid

Replication technique can improve access performance and data availability of data grid systems. So far,most related work on data replication in data grid systems focuses on read-only dataset.Though write operations have been widely used in practice,its optimization problem has not been suciently studied.In this paper,we show that write requests from users can be processed by a nearest site,regardless of the location of latest written replicas.The policy of write nearby instead of write to the latest replic...     

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。     

基于数据块的关系数据库日志挖掘技术

在关系型数据库中数据库通过Redo日志来实现事物的快速提交,并记录事物的操作过程与操作内容.通过对Redo日志的分析与变化数据内容的捕获,将变化数据传送到灾备端,并在灾备端实现变化数据的写入,是目前数据库复制最主要实现原理.本文分析了oralce数据库Redo日志文件结构,阐述了日志文件头标志位信息.结合Redo 日志文件头定位分析技术,给出了一种基于数据块的数据库Redo日志挖掘算法.通过测试分析,验证了该Redo日志挖掘技术的可行性与可靠性.最后展望了下一步的研究方向.     

Similarity/dissimilarity calculation methods of DNA sequences: A survey

DNA sequence similarity/dissimilarity analysis is a fundamental task in computational biology, which is used to analyze the similarity of different DNA sequences for learning their evolutionary relationships. In past decades, a large number of similarity analysis methods for DNA sequence have been proposed due to the ever-growing demands. In order to learn the advances of DNA sequence similarity analysis, we make a survey and try to promote the development of this field. In this paper, we first introduce the related knowledge of DNA similarities analysis, including the data sets, similarities distance and output data. Then, we review recent algorithmic developments for DNA similarity analysis to represent a survey of the art in this field. At last, we summarize the corresponding tendencies and challenges in this research field. This survey concludes that although various DNA similarity analysis methods have been proposed, there still exist several further improvements or potential research directions in this field.     

基于NaOH刻蚀玻碳电极的电化学传感器在检测膀胱癌DNA中的应用

制备了一种基于活化的玻碳电极的新型电化学DNA生物传感器,可用于膀胱癌DNA的检测.通过循环伏安法(CV)实现玻碳电极在NaOH溶液中的刻蚀,使电极表面负载大量官能团,为DNA提供连接位点,由Laviron方程计算得到玻碳电极表面的羧基浓度为 1.022×10-6 mol/cm2.亚甲基蓝(MB)作为电化学检测的杂交指示剂.采用原子力显微镜(AFM)对刻蚀后的电极进行了形貌表征.在最优杂交条件下,通过差分脉冲法(DPV)计算出最佳检测限为5.677×10-13 mol/L(n=5),适用目标 DNA浓度范围1×10-8 mol/L~1×10-12 mol/L.该传感器有望用于实际样品中膀胱癌DNA的快速检测.