DNA计算与DNA密码

DNA在信息科学中的应用,给现代密码学带来了新的挑战和机遇。一方面,DNA计算固有的超大规模并行性给安全性依赖于数学困难问题的现代密码学带来了新的挑战。另一方面, 利用DNA可以实现新的密码技术DNA密码。本文首先介绍了DNA计算,认为在已有的DNA计算模型下,DNA计算不能对现代密码学构成真正的威胁。其次介绍了DNA密码, 并讨论了DNA密码与现代密码学的关系。新生的DNA计算与DNA密码表现出巨大的潜力, 必将会对密码学的未来发展产生深远的影响。     

Nucleic Acid Nanostructures for Chemical and Biological Sensing

The nanoscale features of DNA have made it a useful molecule for bottom‐up construction of nanomaterials, for example, two‐ and three‐dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA‐based nanostructures is in chemical and biological sensing, where they have proven to be cost‐effective, sensitive and have shown promise as point‐of‐care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure‐based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA‐based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.     

Identifying DNA methylation in a nanochannel

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24–96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.     

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids

We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro, and to better understand the role of double-stranded DNA topology during this process.     

DNA功能化碳纳米管电极的制备及与青蒿素相互作用的研究

单壁碳纳米管(SWCNTs)通过羧基和氨基形成酰胺共价键联上了DNA,从而制得DNA生物功能化的碳纳米管修饰电极.傅立叶红外光谱表明DNA共价结合在SWCNTs上,同时用SEM表征了研究电极的形貌.循环伏安法(CV)研究表明,DNA修饰电极反应过程属于扩散控制过程.与青蒿素的相互作用研究结果表明,SWCNTs上的DNA分子具有生物活性,且能与其它生物分子发生相互作用.     

DNA Mold-Based Fabrication of Palladium Nanostructures

DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20–35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.     

金属型与半导体型碳纳米管的分离方法

根据导电性质的不同,碳纳米管可分为金属型和半导体型.在碳纳米管的合成过程中,不同导电性能的碳纳米管总是混合在一起,很难把它们分离开来.分别从物理、化学和生物的角度介绍了目前分离金属型和半导体型碳纳米管的方法,认为DNA自组装分离碳纳米管的方法优于其它的方法,能够将不同类型的碳纳米管分离出来,并且,在分离的数量上优于所有其它的分离方法.     

碳纳米管的DNA修饰研究进展

对碳纳米管生物分子修饰的研究引起了科学家极大的兴趣,将碳纳米管应用到生物体系具有重要的价值.首要的是纳入生物体系的碳纳米管具有生物相容性和特殊的识别功能.因此,利用生物分子功能化碳纳米管是将碳纳米管纳入生物体系必须解决的一个关键问题.综述了DNA功能化碳纳米管的最新研究进展,并阐述了DNA功能化碳纳米管在生物传感器、电化学检测等方面的应用.     

基于碳纳米管的生物传感器研究进展

近年来,纳米材料得到广泛研究与应用,将纳米材料应用于生物传感器可以较大地提高传感器的响应性能,具有特殊结构的一雏纳米材料--碳纳米管为生物传感器的发展开辟了广阔的前景.综述了碳纳米管修饰电化学生物传感器研究中的最新进展,对基于碳纳米管的酶生物传感器、免疫传感器、DNA生物传感器的制备方法、优缺点进行了评述,并展望了碳纳米管修饰生物传感器研究的发展方向.     

Self‐Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms

Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using ‘sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10^?3 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt‐end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction. Heterodimerization yields of gel‐purified monomers are between 98.6% and 99.6%, considerably higher than that of monomers purified using the polyethylene glycol (PEG) method (88.7–96.7%). Depending on the number of PEG purification rounds, these results correspond to about 4‐ to 25‐fold reduction in the number of incorrect structures observed by atomic force microscopy. Furthermore, the analyses of the incorrect structures observed before and after the heterodimerization reactions and comparison of the purification methods provide valuable information on the reaction mechanisms that interfere with heterodimerization.     

Solution‐Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure

Self‐assembled DNA origami nanostructures have a high degree of programmable spatial control that enables nanoscale molecular manipulations. A surface‐tethered, flexible DNA nanomesh is reported herein which spontaneously undergoes sharp, dynamic conformational transitions under physiological conditions. The transitions occur between two major macrostates: a spread state dominated by the interaction between the DNA nanomesh and the BSA/streptavidin surface and a surface‐avoiding contracted state. Due to a slow rate of stochastic transition events on the order of tens of minutes, the dynamic conformations of individual structures can be detected in situ with DNA PAINT microscopy. Time series localization data with automated imaging processing to track the dynamically changing radial distribution of structural markers are combined. Conformational distributions of tethered structures in buffers with elevated pH exhibit a calcium‐dependent domination of the spread state. This is likely due to electrostatic interactions between the structures and immobilized surface proteins (BSA and streptavidin). An interaction is observed in solution under similar buffer conditions with dynamic light scattering. Exchanging between solutions that promote one or the other state leads to in situ sample‐wide transitions between the states. The technique herein can be a useful tool for dynamic control and observation of nanoscale interactions and spatial relationships.     

Vacuum effect on DNA lesion and genetic mutation of cells

DNA topological forms can be changed by environmental factors thus to potentially cause genetic mutation. Vacuum of low pressure is considered to be such a factor. An investigation was carried out to check topological form changes of extracellular plasmid DNA due to lesion in DNA under the vacuum condition. Pumping the experimental stage of biological samples to vacuum may result in three effects on the environment of the sample, namely, low pressure, low temperature and low humidity, all of which may impact DNA. In the experiment, the DNA topological form change and related lesion after plasmid DNA samples were exposed to vacuum with varied time was analyzed with gel electrophoresis and fluorometric assay. The electrophoresis results were quantified to obtain percentages of the supercoiled and relaxed forms but no linear form of DNA. The fluorometer measured concentrations of single strand and double strand DNAs. The results showed that the single strand break was the dominant lesion in DNA. The DNA form change and the lesion were found to depend mainly on the pressure change but not much on the pressure itself. The vacuum-exposed DNA was subsequently transformed into bacteria Escherichia coli (E. coli) for checking mutation occurrence. No observable mutation of the DNA-transformed bacteria was found. This study concluded that certain light lesion in DNA dominated by the single strand break could be induced by vacuum exposure but with negligible risk of genetic mutation.     

Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions

Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality. Our meta-nucleotides are designed to form flexible linear assemblies (single-stranded mDNA (ssmDNA)) analogous to single-stranded DNA. We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA–DNA reactions and the action of various enzymes on DNA. These operations on mDNA include (i) hybridization of ssmDNA into a double-stranded mDNA (dsmDNA) and heat denaturation of a dsmDNA into its component ssmDNA, (ii) strand displacement of one ssmDNA by another, (iii) restriction cuts on the backbones of ssmDNA and dsmDNA, (iv) polymerization reactions that extend ssmDNA on a template to form a complete dsmDNA, (v) synthesis of mDNA sequences via mDNA polymerase chain reaction, (vi) isothermal denaturation of a dsmDNA into its component ssmDNA, and (vii) an isothermal replicator reaction that exponentially amplifies ssmDNA strands and may be modified to allow for mutations.     

Programming Motions of DNA Origami Nanomachines

DNA nanotechnology enables the precise fabrication of DNA‐based machines with nanoscale dimensions. A wide range of DNA nanomachines are designed, which can be activated by specific inputs to perform various movement and functions. The excellent rigidity and unprecedented addressability of DNA origami have made it an excellent platform for manipulating and investigating the motion behaviors of DNA machines at single‐molecule level. In this Concept, power supply, machine actuation, and motion behavior of DNA machines on origami platforms are summarized and classified. The strategies utilized for programming motion behavior of DNA machines on DNA origami are also discussed with representative examples. The challenges and outlook for future development of manipulating DNA nanomachines at the single molecule level are presented and discussed.