E. coli K-12琥珀酸脱氢酶sdhC基因纳米锥的设计及自组装

采用DAEDALUS软件，以E. coli K-12 MG1655的琥珀酸脱氢酶复合体C亚基编码酶基因sdhC的双链DNA为脚手架链，进行一个边长为17.68 nm的正四面锥设计，并最终通过核酸自组装反应获得了sdhC基因的纳米锥聚合体。利用琼脂糖凝胶电泳、扫描电子显微镜和透射电子显微镜对多组样品进行化学组分和形貌分析，同时利用原子力显微镜液下成像法测定了核酸聚合体的三维尺度。结果表明：DAEDALUS软件设计出的16条订书钉链，确实将624 bp的sdhC双链DNA中的一条链折叠成了平均边长为19.05nm的正四面锥，与预设模型仅相差1.37nm，证明普通基因的双链DNA可以替代M13mp18单链核酸作为DNA折纸的核酸材料，为构建核酸纳米材料提供了一种新方法。     

DNA折纸术制备纳米结构-研究进展及应用

DNA折纸术是2006年Rothemund提出的一种DNA自组装方法,它通过一条长链DNA(脚手架链)与预设计的短链DNA片段(订书钉链)碱基互补配对,能得到二维图案或者三维立体结构。相对于其他DNA自组装技术,它可控性高,实验要求低,方便快捷,操作简单,成功率高且在建立二维或三维晶体材料方面有着得天独厚的优势。得到的DNA组装体可以作为模板与功能纳米粒子进行组合,也可用来制作有特殊性能的纳米器件,因而其在各个领域都有极大的潜在应用价值。本文主要综述了DNA折纸术的发展、应用以及对DNA折纸技术的展望。     

双亲纳米颗粒在选择性溶剂中的自组装行为：耗散粒子动力学模拟

接枝聚合物纳米颗粒在构筑多级功能性纳米材料方面具有很大潜力,但其在选择性溶剂中自组装相图却鲜见报道。利用耗散粒子动力学模拟研究了溶剂选择性、接枝聚合物链长度以及亲水、疏水聚合物链比例等因素对双亲纳米颗粒自组装行为的影响,并绘制了自组装形态相图。结果显示,随着浓度的增大,双亲纳米颗粒逐渐自组装成球状、棒状、二维膜、纳米膜孔等丰富纳米结构。不仅如此,溶剂与亲水、疏水聚合物相容性差异较小时（a_S-HL=40k_BT/R_c,a_S-HB=50k_BT/R_c）,双亲纳米颗粒自组装形成层状纳米结构,在较高浓度时,形成规则的多孔网络结构。研究发现,双亲纳米颗粒浓度和接枝聚合物的链长以及亲水、疏水聚合物链比例是调控双亲纳米颗粒自组装形态的关键因素。鉴于双亲纳米颗粒丰富的自组装行为,它在气体分离、检测、载药、催化剂载体等领域有着很大的潜在应用价值。     

四苯基卟啉锰纳米材料的制备及其性能研究

利用自组装方法在水/二甲基亚砜(DMSO)混合溶液体系中使5,10,15,20-四苯基卟啉锰(MnTPP)分子聚集成纳米材料,其最适宜温度为50℃。通过场发射扫描电子显微镜(FE-SEM)对MnTPP纳米材料的表面形貌进行了研究,可获得平均宽度在200 nm左右的均匀分布的锰卟啉纳米环或半环。通过使用紫外可见光谱分析了锰卟啉单体与纳米材料的光学性质的差别,在紫外-可见光谱中,锰卟啉纳米分散体系468 nm处的Soret带吸收峰明显变宽并且红移到477 nm处,其吸光值也明显减小。利用紫外可见光谱对锰卟啉的光学检测性能进行了研究,对比锰卟啉单体和纳米溶液体系对低浓度甲基膦酸二甲酯(DMMP)的检测效果,结果显示锰卟啉纳米溶液体系的检测效果优于单体。     

生物化工

纳米科技研究中的新热点 ——纳米生物化学研究 最近,生物大分子DNA、多聚核苷酸被用来作为分子模板,通过改变DNA分子大小、形状和组合来控制半导体纳米材料的大小、形状、取向和组装等,合成半导体纳米线、量子环、量子点。Murply等研究了DNA与CdS纳米族的相互作用,目的是发展DNA探针诊断技术,一旦取得突破将对DNA芯片生物信息技术,建立快速高效的基因疾病诊断技术起到巨大推动作用。(李哲元)     

以生物蛋白为模板控制合成MnO_2纳米颗粒

利用生物模拟矿化技术原位合成金属氧化物纳米颗粒。利用超分子蛋白纳米空腔结构作为反应模板矿化组装纳米材料,马脾铁蛋白作为限制性反应器控制金属离子水解、氧化还原等反应组装成单分散的纳米粒子。在碱性条件下脱铁铁蛋白限制性合成Mn氧化物纳米颗粒,通过透射电子显微镜(TEM)、EDX元素分析对产品的结构和组成进行表征,产品为球形颗粒状,直径分布在3～8nm范围。此外,采用紫外、可见吸收光谱分析对蛋白组装过程做了实验研究并对纳米材料形成机理进行了讨论。     

双亲纳米颗粒在选择性溶剂中的自组装行为:耗散粒子动力学模拟

接枝聚合物纳米颗粒在构筑多级功能性纳米材料方面具有很大潜力,但其在选择性溶剂中自组装相图却鲜见报道。利用耗散粒子动力学模拟研究了溶剂选择性、接枝聚合物链长度以及亲水、疏水聚合物链比例等因素对双亲纳米颗粒自组装行为的影响,并绘制了自组装形态相图。结果显示,随着浓度的增大,双亲纳米颗粒逐渐自组装成球状、棒状、二维膜、纳米膜孔等丰富纳米结构。不仅如此,溶剂与亲水、疏水聚合物相容性差异较小时(a _(S-HL)=40k _BT/R_c,a _(S-HB)=50k _BT/R_c),双亲纳米颗粒自组装形成层状纳米结构,在较高浓度时,形成规则的多孔网络结构。研究发现,双亲纳米颗粒浓度和接枝聚合物的链长以及亲水、疏水聚合物链比例是调控双亲纳米颗粒自组装形态的关键因素。鉴于双亲纳米颗粒丰富的自组装行为,它在气体分离、检测、载药、催化剂载体等领域有着很大的潜在应用价值。     

自组装肽基纳米材料运载药物和基因的研究进展

肽基分子自组装以其丰富的自组装驱动力、新颖的自组装体纳米结构、自组装体的特殊功能及良好的生物相容性等,在纳米生物材料、护肤和化妆产品、药物传输释放、组织工程支架材料等方面有着广泛的应用前景。由天然氨基酸组成的自组装短肽具有良好的低细胞毒性,可控的降解性能,高的运载效率及细胞摄取率,同时还具有降低药物的毒副作用等优点。因此,它在作为药物和基因的纳米载药材料方面有着巨大的发展前景。使用自组装肽基材料形成的纳米载体对疏水性抗癌药物、蛋白质药物及基因等进行传递释放已成为生物医药学领域的研究重点,因此,对近年来自组装肽基纳米材料作为药物和基因载体在生物医药学上的研究进展做了综述。     

基于蛋白及其组装体的金属纳米复合材料构建

将蛋白分子及其自组装体作为模板用于功能性金属纳米材料合成吸引了研究者的广泛关注。蛋白质及其自组装体形态结构独特多样,具有特异性分子识别及仿生矿化能力,在纳米材料形成过程中可发挥结构导向及形貌控制作用,以其为模板构建的蛋白-金属纳米复合材料在催化转化、生物传感、医学成像等领域具有广阔的应用前景。本文基于蛋白质及其组装体的结构特征差异,综述了近些年在以蛋白质单亚基结构、蛋白多亚基超组装结构及蛋白三维晶体结构为模板的金属纳米复合材料构建研究方面取得的进展,并对其未来的研究发展方向进行了展望。     

噬菌体展示技术在纳米材料合成中的应用

建立在化学、生物学和材料学等交叉学科基础上的噬菌体展示技术,为合成、组装新颖纳米材料提供了一条新的途径.噬菌体作为一种信息载体,能模拟自然进化过程产生特异性多肽,从而在分子水平上识别靶材料并进行自组装.噬菌体的单分散性和长杆状外形,造就了特定的识别部位,使各种纳米材料有序地组装成规则的层次结构.通过噬菌体展示技术筛选出来的特异性识别肽,可以指导多肽介导的矿化过程,从而合成具有应用价值的一系列无机和有机纳米材料,进一步制成的纳米装置将应用于电子、光学、生物技术和医学领域.     

DNA Three‐Way Junctions Stabilized by Hydrophobic Interactions for Creation of Functional Nanostructures

The construction of nanomaterials from oligonucleotides by modular assembly invariably requires the use of branched nucleic acid architectures such as three‐ and four‐way junctions (3WJ and 4WJ). We describe the stabilization of DNA 3WJ by using non‐nucleotide lipophilic spacers to create a hydrophobic pocket within the junction space. Stabilization of nucleic acid junctions is of particular importance when constructing nanostructures in the “ultra‐nano” size range (<20 nm) with shorter double‐stranded regions. UV thermal melting studies show that lipophilic spacers strategically placed within the junction space significantly increased thermal stability. For a 3WJ with eight base pair arms, thermal stability was increased from 30.5 °C for the unmodified junction to a maximum stability of 55.0 °C. The stability of the junction can be modulated within this temperature range by using the appropriate combinations of spacers.     

Aptamer-Functionalized Hybrid Nanostructures for Sensing,Drug Delivery,Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO₂ nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions “nucleoapzymes”. In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.     

Strategies for Stabilizing DNA Nanostructures to Biological Conditions

DNA is one of the most promising building blocks for creating functional nanostructures for applications in biology and medicine. However, these highly programmable nanomaterials (e.g., DNA origami) often require supraphysiological salt concentrations for stability, are degraded by nuclease enzymes, and can elicit an inflammatory response. Herein, three key strategies for stabilizing DNA nanostructures to conditions required for biological applications are outlined: 1) tuning the buffer conditions or nanostructure design; 2) covalently crosslinking the strands that make up the structures; and 3) coating the structures with polymers, proteins, or lipid bilayers. Taken together, these approaches greatly expand the chemical diversity and future applicability of DNA nanotechnology both in vitro and in vivo.     

基于分子动力学水分和离子在水化硅酸钙纳米孔道中的传输特性研究

水化硅酸钙凝胶是水泥水化产物中最基本的粘结相,水分子和离子在凝胶孔中的传输从根本上决定着水泥混凝土材料的服役寿命.采用分子动力学方法系统地研究了水分子、氯离子和钠离子在1nm、2nm、3nm和4nm的水化硅酸钙凝胶孔中的传输过程.基于径向分布函数和均方位移的离子轨迹分析发现在纳米孔道中离子和水分子展现出异于毛细水的分子结构和动力学特性:水分子有序性排布、离子大量在界面吸附和扩散速度急剧下降.这种分子结构与动力学的特性是因为水化硅酸钙界面处硅链中的非桥接氧会与水分子形成稳定的氢键连接,而钠离子可以形成Na-O化学键,同时表面的钙离子也可以与氯离子形成CaCl2团簇体.此外,随着孔径的增大,离子和水分子的扩散系数逐渐由0.15×10-9m2/s、0.7×10-9m2/s增大到1.3×10-9m2/s、3×10-9m2/s,这很接近于实验测得的毛细水的扩散系数,说明在纳米尺度上,孔径的约束和界面化学键作用是决定离子和水分子传输的关键因素.     

核酶在病毒基因治疗中的研究进展

核酶是一类具有催化功能的核酸分子,能够与双链DNA或RNA分子结合,从而抑制其转录或翻译。由于核酶能够在相应位点切割核酸序列,具有酶的活性,使其在病毒的基因治疗中具有广阔的应用前景。随着有效的转运和表达方法的建立及核酸化学的进步,核酶有望成为基因治疗中最有效的工具之一。本文就核酶在病毒基因治疗中的研究进展作一综述。     

Nanopore-Based Analysis of Chemically Modified DNA and Nucleic Acid Drug Targets

Nucleic acids are central figures in many of life’s key molecular processes, e.g., enzymatic activity, epigenetics/gene regulation, viral replication, aging, cancer, and other diseases. Over the past two decades, nanopores have emerged as a new tool for studying the properties of nucleic acids at the single-molecule level. In this review, we summarize the use of nanopores as sensors of nucleic acid structure, particularly for studying chemically modified and damaged DNA, and for probing the interactions of small-molecule drugs with nucleic acid targets.     

Structure-Dependent Electrical Conductance of DNA Origami Nanowires

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si₃N₄) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si₃N₄ substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼10¹³ ohms) than on native Si₃N₄ substrates without HMDS (∼10¹⁴ ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si₃N₄ substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.     

How We Make DNA Origami

DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know‐how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know‐how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage‐free preparation of DNA origami. These methods are agarose‐gel purification, filtration through molecular cut‐off membranes, PEG precipitation, size‐exclusion chromatography, and ultracentrifugation‐based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.