DNA纳米自组装技术研究进展及应用

本文总结了DNA纳米自组装技术在近20年来的研究,归纳了DNA纳米结构的优势及三种组装技术的原理和发展历程。阐述该技术在纳米材料制造、药物靶向递送、DNA计算等方面的应用。最后,探讨了DNA纳米技术的发展前景,并对其相关应用进行展望。     

羧酸甜菜碱甲基丙烯酸酯与DNA组装体系的耗散粒子动力学模拟

采用耗散粒子动力学模拟方法(DPD)研究了聚羧酸甜菜碱甲基丙烯酸酯(PCBMA)在不同浓度及pH下在水中的自组装与解组装情况,以及PCBMA与DNA的组装情况。模拟结果显示,不同浓度下,聚合物在水中依次形成球状、柱状、层状纳米粒子。pH下降时,DNA能被释放出来。     

DNA生物传感器金薄膜电极的制备及性能

用两种不同溅射工艺制备金薄膜电极。利用扫描电子显微镜、拉曼光谱法和循环伏安法对这两种电极的表面形貌、单链DNA在电极表面的自组装性能和其电化学行为进行了研究。发现不同工艺条件制作的电极性能差异较大;特别是金电极表面有其它金属存在互扩散时,对电极的电化学行为和单链DNA自组装性能具有直接影响。     

pH/退火方式控制DNA纳米笼的选择性组装

通过调控溶液的pH、选择不同速率热退火方式,以四点星DNA分子瓦为建筑模块,根据沃森-克里克碱基互补配对原则和Hoogsteen氢键配对连接,选择性地组装成不同的DNA多面体结构。非变性聚丙烯酰胺凝胶电泳表征结果表明,在酸性条件(pH 5. 5)及退火时间5. 0 h下,分子瓦自组装成DNA变形四面体(tTET)结构;在中性条件(pH 8. 0)及退火时间24. 0 h下,自组装形成DNA八面体(OCT)结构。在中性条件(pH 8. 0)下,只改变分子瓦黏性末端碱基的数目,直至形成不同数目的碱基对来产生不同强度的作用力,也能类似地组装成不同的DNA多面体结构。该结果也由非变性聚丙烯酰胺凝胶电泳进行了表征。     

链置换反应触发G-四链体DNA酶双向自组装用于高灵敏均相比色生物传感

结合高特异性核酸适配体识别及链置换作用触发杂交链反应,成功实现了大量G-四链体DNA酶活性结构的双向自组装,进一步利用该DNA酶优良的类过氧化物酶性质发展了一种凝血酶(Tb)均相比色生物传感新方法。基于链置换辅助的目标物循环作用以及杂交链反应引起的DNA酶双向自组装信号放大,该方法可在3个数量级线性范围内实现对Tb的高灵敏检测,检测限为0.82 pmol·L~(-1)。     

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。     

上海应物所在DNA纳米泵研究方面取得进展

正近期,中国科学院上海应用物理研究所研究人员基于界面精确自组装技术实现了质子驱动的DNA纳米泵。分子级别的纳米泵在生物体内发挥着重要的生物学功能,如细胞内外水分子的输运以及离子的输运等。模拟并构建纳米泵及其功能实现是纳米技术领域的重要挑战之一。DNA纳米技术为解决这一挑战性问题提供了可能。上海应物所樊春海团队基于DNA纳米技术发展了三维、动态DNA纳米结构,并对DNA纳米器件以及生物分子的界面可控组装开展了系统的研究。     

DNA金属化及其应用

由于DNA自身的导电性尚存在争议,研究人员试图通过金属化途径来提高DNA双螺旋结构的导电性,从而使其能够在纳米电子学方面发挥重要作用。本文简要综述了静电吸附、无电沉积、DNA自组装、金属蒸镀等常用的DNA金属化方法,介绍了这些金属化DNA结构在纳米电子学、催化、传感等相关领域的应用,在此基础上对DNA金属化技术的进一步发展和存在的挑战进行了展望,揭示了其广阔的基础和应用研究前景。     

基于DNA支持的脂质膜工程化研究进展

脂质膜表面的工程化修饰是指通过在脂质膜表面引入附加的活性位点来调控脂质囊泡的理化性质,进而赋予其更广泛生物化学功能的过程。简单介绍了DNA与脂质膜的相互作用,重点阐述了基于DNA或DNA纳米结构支持的脂质膜工程化研究进展,包括脂质膜结构的构建、合成、自组装行为等,指出了该领域所面临的挑战,并对未来的应用前景进行了展望。     

自组装及其在分析化学等方面的应用

自组装技术主要是通过自发反应过程,从而改变粒子的排列方式,以形成新型有序结构。近些年来自组装技术发展很快,涌现出了各种自组装方法。结合具体实例,介绍了近年来几种比较常见的自组装方法:超分子自组装合成方法、层层自组装、水热自组装、反胶束法、一锅法自组装等方法,这些方法各具特色。随着各种简便高效的自组装方法出现,自组装技术在各类学科领域的应用发展空间也得到了更进一步的开发,举例介绍了自组装在分析化学、电化学及能源等领域的具体应用,并在最后简略概括了自组装技术在发展中遇到的一些挑战。     

Regulating DNA Self‐assembly by DNA–Surface Interactions

DNA self‐assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA–DNA interactions. When confined to surfaces, DNA–surface interactions become an additional, important factor to DNA self‐assembly. However, the way in which DNA–surface interactions influence DNA self‐assembly is not well studied. In this study, we showed that weak DNA–DNA interactions could be stabilized by DNA–surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds.     

Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass

The DNA replisome inevitably encounters DNA damage during DNA replication. The T7 DNA replisome contains a DNA polymerase (gp5), the processivity factor thioredoxin (trx), a helicase‐primase (gp4), and a ssDNA‐binding protein (gp2.5). T7 protein interactions mediate this DNA replication. However, whether the protein interactions could promote DNA damage bypass is still little addressed. In this study, we investigated strand‐displacement DNA synthesis past 8‐oxoG or O⁶‐MeG lesions at the synthetic DNA fork by the T7 DNA replisome. DNA damage does not obviously affect the binding affinities between helicase, polymerase, and DNA fork. Relative to unmodified G, both 8‐oxoG and O⁶‐MeG—as well as GC‐rich template sequence clusters—inhibit strand‐displacement DNA synthesis and produce partial extension products. Relative to the gp4 ΔC‐tail, gp4 promotes DNA damage bypass. The presence of gp2.5 also promotes it. Thus, the interactions of polymerase with helicase and ssDNA‐binding protein facilitate DNA damage bypass. Accessory proteins in other complicated DNA replisomes also facilitate bypassing DNA damage in similar manner. This work provides new mechanistic information relating to DNA damage bypass by the DNA replisome.     

miR-29 Represses the Activities of DNA Methyltransferases and DNA Demethylases

Members of the microRNA-29 (miR-29) family directly target the DNA methyltransferases, DNMT3A and DNMT3B. Disturbances in the expression levels of miR-29 have been linked to tumorigenesis and tumor aggressiveness. Members of the miR-29 family are currently thought to repress DNA methylation and suppress tumorigenesis by protecting against de novo methylation. Here, we report that members of the miR-29 family repress the activities of DNA methyltransferases and DNA demethylases, which have opposing roles in control of DNA methylation status. Members of the miR-29 family directly inhibited DNA methyltransferases and two major factors involved in DNA demethylation, namely tet methylcytosine dioxygenase 1 (TET1) and thymine DNA glycosylase (TDG). Overexpression of miR-29 upregulated the global DNA methylation level in some cancer cells and downregulated DNA methylation in other cancer cells, suggesting that miR-29 suppresses tumorigenesis by protecting against changes in the existing DNA methylation status rather than by preventing de novo methylation of DNA.     

Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking

DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole (^CNVK) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy.     

Using archaeal histones for precise DNA fragmentation

The fragmentation of DNA is a useful procedure for many molecular biology procedures. However, most methods used to fragment DNA are poorly controllable, and cannot be used to create small fragments. We describe a method to generate random DNA fragments of a predictable size to be cloned in expression vectors for the construction of display libraries. The DNA is allowed to form complexes with archaeal histones from Methanothermus fervidus (HMf) and the HMf/DNA core complex is naturally protected from nuclease DNaseI activity, giving rise to DNA fragments of approximately 60 bp and multiples thereof. We found that by varying the wt/wt ratio between DNA and HMf, the concentration of DNA and the incubation time with DNaseI, DNA fragments of desired size can be obtained. This approach should be applicable to the efficient fragmentation of DNA for the construction of phage display polypeptide libraries, as well as any other molecular biology procedures in which small DNA fragments of defined size are required.     

Plant DNA Repair and Agrobacterium T−DNA Integration

Agrobacterium species transfer DNA (T−DNA) to plant cells where it may integrate into plant chromosomes. The process of integration is thought to involve invasion and ligation of T-DNA, or its copying, into nicks or breaks in the host genome. Integrated T−DNA often contains, at its junctions with plant DNA, deletions of T−DNA or plant DNA, filler DNA, and/or microhomology between T-DNA and plant DNA pre-integration sites. T−DNA integration is also often associated with major plant genome rearrangements, including inversions and translocations. These characteristics are similar to those often found after repair of DNA breaks, and thus DNA repair mechanisms have frequently been invoked to explain the mechanism of T−DNA integration. However, the involvement of specific plant DNA repair proteins and Agrobacterium proteins in integration remains controversial, with numerous contradictory results reported in the literature. In this review I discuss this literature and comment on many of these studies. I conclude that either multiple known DNA repair pathways can be used for integration, or that some yet unknown pathway must exist to facilitate T−DNA integration into the plant genome.     

Visual characterization and quantitative measurement of artemisinin-induced DNA breakage

DNA conformational change and breakage induced by artemisinin, a traditional Chinese herbal medicine, have been visually characterized and quantitatively measured by the multiple tools of electrochemistry, UV-vis absorption spectroscopy, atomic force microscopy (AFM), and DNA electrophoresis. Electrochemical and spectroscopic results confirm that artemisinin can intercalate into DNA double helix, which causes DNA conformational changes. AFM imaging vividly demonstrates uneven DNA strand breaking induced by QHS interaction. To assess these DNA breakages, quantitative analysis of the extent of DNA breakage has been performed by analyzing AFM images. Basing on the statistical analysis, the occurrence of DNA breaks is found to depend on the concentration of artemisinin. DNA electrophoresis further validates that the intact DNA molecules are unwound due to the breakages occur at the single strands. A reliable scheme is proposed to explain the process of artemisinin-induced DNA cleavage. These results can provide further information for better understanding the anticancer activity of artemisinin.     

The Role of Topoisomerase II in DNA Repair and Recombination in Arabidopsis thaliana

DNA entanglements and supercoiling arise frequently during normal DNA metabolism. DNA topoisomerases are highly conserved enzymes that resolve the topological problems that these structures create. Topoisomerase II (TOPII) releases topological stress in DNA by removing DNA supercoils through breaking the two DNA strands, passing a DNA duplex through the break and religating the broken strands. TOPII performs key DNA metabolic roles essential for DNA replication, chromosome condensation, heterochromatin metabolism, telomere disentanglement, centromere decatenation, transmission of crossover (CO) interference, interlock resolution and chromosome segregation in several model organisms. In this study, we reveal the endogenous role of Arabidopsis thaliana TOPII in normal root growth and cell cycle, and mitotic DNA repair via homologous recombination. Additionally, we show that the protein is required for meiotic DSB repair progression, but not for CO formation. We propose that TOPII might promote mitotic HR DNA repair by relieving stress needed for HR strand invasion and D-loop formation.     

Assessing the differential affinity of small molecules for noncanonical DNA structures

The targeting of higher-order DNA structures has been thoroughly developed with G-quadruplex DNA but not with other structures like branched DNA (also known as DNA junctions). Because these alternative higher-order DNA architectures might be of high biological relevance, we implemented a high-throughput version of the FRET melting assay that enabled us to map the interactions of a candidate with four different DNA structures (duplex- and quadruplex DNA, three- and four-way junctions) in a rapid and reliable manner. We also introduce a novel index, the BONDS (branched and other noncanonical DNA selectivity) index, to conveniently quantify this differential affinity.