Emerging Plasmonic Assemblies Triggered by DNA for Biomedical Applications

Plasmonic gold nanocrystal represents plasmonic metal nanomaterials, and has a variety of unique and beneficial properties, such as optical signal enhancement, catalytic activity, and photothermal properties tuned by local temperature, which are useful in physical, chemical, and biological applications. In addition, the inherent properties of predictable programmability, sequence specificity, and structural plasticity provide DNA nanostructures with precise controllability, spatial addressability, and targeting recognition, serving as ideal ligands to link or position building blocks during the self-assembly process. Self-assembly is a common technique for the organization of prefabricated and discrete nanoparticle blocks for the construction of extremely sophisticated nanocomposites. To this end, the integration of DNA nanotechnology with Au nanomaterials, followed by assembly of DNA-functionalized Au nanomaterials can form novel functional Au nanomaterials that are difficult to obtain through conventional methods. Here, recent progress in DNA-assembled Au nanostructures of various shapes is summarized, and their functions are discussed. The fabrication strategies that employ DNA for the self-assembly of Au nanostructures, including dimers, tetramers, satellites, nanochains, and other nanostructures with more complex geometric configurations are first described. Then, the characteristic optical properties and applications of biosensing, bioimaging, drug delivery, and therapy are discussed. Finally, the remaining challenges and prospects are elucidated.     

相似性度量在基因表达聚类分析中的应用研究

聚类分析是基因表达数据分析研究的主要技术之一,其算法的基本出发点在于根据对象间相似度将对象划分为不同的类,选择适当的相似性度量准则是获得有效聚类结果的关键。采用预处理过的基因数据集在不同相似性度量准则下进行的不同聚类算法的聚类分析,并得到聚类结果评价。其中算法本身的缺陷及距离相似性度量的局限性都是影响结果评价的因素,为了获得更有效的聚类结果,改进相关聚类算法并提出了一种比例相似性度量准则。     

基于DNA折纸基底的与非门计算模型

与非门(NAND)的本质是与门(AND)和非门(NOT)的叠加,先进行与运算,再进行非运算,它是建立DNA计算机的基础。为了实现与非门的计算,该文在DNA折纸基底上建立了一个与非门计算模型,逻辑值的输入是通过在DNA折纸基底上发生有向的杂交链式反应(HCR)来完成的,输入链先经过与门区域再经过非门区域,最后通过DNA折纸基底上是否还保留纳米金颗粒来显示计算结果的真假。利用Visual DSD对该计算模型进行仿真模拟,显示该计算模型具有较好的可行性。     

DNA数据存储

分子数据存储作为一种稳定性强、存储密度高的数据存储方式,表现出巨大的潜力。它有望解决当今日益增长的巨大信息量与存储能力之间差距不断扩大的问题。作为一种典型的分子数据存储方式,DNA数据存储可以作为一种替代性、变革性的存储介质,用于突破现用存储方式的物理极限,满足不断增加的数据存储需求。该综述将对DNA数据存储的历史、工作流程、及当前的发展状态进行概述,同时讨论现今DNA数据存储存在的问题、挑战及发展趋势。     

A new color image encryption scheme based on DNA encoding and spatiotemporal chaotic system

In this paper, a new color image encryption scheme based on DNA operations and spatiotemporal chaotic system is presented. Firstly, to hide the distribution information of the plain image, we convert the plain image into three DNA matrices based on the DNA random encoding rules. Then, the DNA matrices are combined into a new matrix and is permutated by a scramble matrix generated by mixed linear-nonlinear coupled map lattices (MLNCML) system. In which, the key streams are associated with the secret keys and plain image, which can ensure our cryptosystem plain-image-dependent and improve the ability to resist known-plaintext or chosen-plaintext attacks. Thereafter, to resist statistical attacks, the scrambled matrix is decomposed into three matrices and diffused by DNA deletion-insertion operations. Finally, the three matrices are decoded based on DNA random decoding rules and recombined to three channels of the cipher image. Simulation results demonstrate that the proposed image cryptosystem has good security and can resist various potential attacks.     

基于遗传模拟退火算法的DNA多序列比对研究

针对生物信息学中DNA多序列比对问题,提出了一种基于遗传算法和模拟退火算法相结合的求解算法:在遗传模拟退火算法中,利用模拟退火算法针对遗传算子进行改进来提高算法的效率,由遗传算法进行全局搜索,模拟退火算法用于局部寻优,防止遗传算法的早熟收敛。通过与经典比对算法ClustalX和经典遗传算法进行比对研究,结果表明该算法是有效的。     

中功率密度He—Ne激光诱变固体DNA的拉曼光谱分析

中功率密度He—Ne激光照射DNA固体纤维后,在很短的照射时间,激光对DNA磷酸骨架结构和氢键的损伤就达到了最大值,这时不仅有磷酸二酯键的断裂,氢键也发生了断裂;随着照射时间的延长,激光对DNA的损伤程度先是减小,然后再加剧。激光对碱基的影响,先是使碱基谱线强烈减色,随着照射时间的延长,减色效应逐渐减小,然后变为较强的增色效应,再变为减色效应,这也许是激光在损伤碱基后又破坏碱基-碱基间的垂直堆积状况,造成碱基谱线的拉曼增色效应。     

Sentaurus® based modeling and simulation for GFET's characteristic for ssDNA immobilization and hybridization

The graphene field effect transistor (GFET) has been widely studied and developed as sensors and functional devices. The first report about GFET sensing simulation on the device level is proposed. The GFET's characteristics, its responding for single strand DNA (ssDNA) and hybridization with the complimentary DNA (cDNA) are simulated based on Sentaurus, a popular CAD tool for electronic devices. The agreement between the simulated blank GFET feature and the reported experimental data suggests the feasibility of the presented simulation method. Then the simulations of ssDNA immobilization on GFET and hybridization with its cDNA are performed, the results are discussed based on the electron transfer (ET) mechanism between DNA and graphene.     

Healing DNA Self-Assemblies Using Punctures

In self-assembly, individual components (commonly referred to as tiles) have sufficient infor mation to build templates for structures such as lat tices for two-dimensional scaffolds. Tile sets that can heal (fully or partially) an erroneous DNA assembly have been proposed. Healing requires growth to be restarted such that erroneous tiles can be removed and the correct tiles can bind to the aggregate. Punctures have been proposed for this purpose; in this paper, a puncture is intentionally induced in the self-assembly to restart the growth process. The goal of this paper is to characterize an intentionally induced puncture (and its relevant properties) on an erroneous tile site in the grown crystal as part of a healing process. This allows to propagate any newly generated error away from the source of growth (i.e. the seed tile), such that self-assembly can continue along specific directions. Different types of puncture are considered with respect to healing and related features, such as growth direction, error and aggregate types. Punctures are analyzed using a new characterization and metric; different tile sets are investigated in detail for healing of a DNA self-assembly.