DNA directed self-assembly of anisotropic plasmonic nanostructures

Programmable positioning of one-dimensional (1D) gold nanorods (AuNRs) was achieved by DNA directed self-assembly. AuNR dimer structures with various predetermined inter-rod angles and relative distances were constructed with high efficiency. These discrete anisotropic metallic nanostructures exhibit unique plasmonic properties, as measured experimentally and simulated by the discrete dipole approximation method.     

Compaction and multiple chain assembly of DNA with the cationic polymer poly(aluminum chloride) (PAC)

Assembly of DNA molecules by the addition of poly(aluminum chloride) (PAC) was studied. In the absence of PAC, electron microscopy indicated the formation of elongated coiled DNA molecules. In the presence of PAC, multiple doughnut-like structures, 8-15 nm thick, formed and fused together. When salt was added, the doughnut-like structures tended to be thinner and the morphology of the fused doughnuts became irregular. We obtained a view of a single DNA structure by fluorescent microscopy, which revealed that individual DNA molecules undergo a discrete transition from an elongated to compacted state with an increase in PAC concentration. Electron microscopic observation showed that a regular doughnut is the typical structure seen under low salt conditions. At high salt concentrations, the doughnut shape deformed, yielding results similar to those produced by the salt effect on DNA assembly at high DNA concentrations.     

DNA与非离子糖基表面活性剂相互作用的研究

用动态表面张力法、键合等温线、紫外光谱及荧光光谱等方法研究了不同链长烷基葡萄糖苷(APG)与DNA的相互作用．研究发现APG对DNA键合可分为两阶段,第一阶段：多苷依靠多羟基结构与DNA形成动力学稳定的复合物;第二阶段：随时间延长,单苷由于其较小的空间位阻而与DNA形成能量更低的热力学稳定复合物．由平衡渗析法得到的单苷与DNA相互作用键合等温线显示,APG与DNA键合为一非协同过程．证实了其非离子氢键吸附的本质,同时也支持了DNA对胶束及预胶束的缠绕模型．紫外光谱结果证明了在APG与DNA作用过程中疏水作用的重要性．以溴化乙锭为探针,荧光光谱法研究证明,随APG链长增加,DNA构象缩拢程度加大,但即使是C2APG也仅能使DNA构象部分缩拢,推测DNA仅是部分链段对APG胶束进行包裹,其它链段仍处于伸展状态．与阳离子表面活性剂十六烷基三甲基溴化铵(CTAB)可使DNA构象强烈缩拢的事实相比,证明了静电作用在大分子与表面活性剂相互作用中的主导性．     

DNA modified with metal complexes: Applications in the construction of higher order metal–DNA nanostructures

DNA has recently emerged as a useful building block for higher order nanostructures, such as extended two-dimensional surfaces and discrete two- and three-dimensional structures. Transition metal complexes can introduce functionality to these otherwise passive nanostructures. This review examines the synthetic strategies used to introduce metals in a site-specific manner to DNA: either by attaching preformed metal complexes to DNA, or by metal coordination to unmodified or modified DNA. The applications of metal–DNA complexes in building higher order nanostructures and the utility of attaching luminescent or electrochemical labels are discussed.     

Elongation/compaction of giant DNA caused by depletion interaction with a flexible polymer

Structural changes in giant DNA induced by the addition of the flexible polymer Polyethylene Glycol (PEG) were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule transition, whereas in concentrated solution, DNA molecules exhibit an extended conformation via macroscopic phase segregation. The long-axis length of the stretched state in DNA is about 10(3) times larger than that of the compact state. Phase segregation at high DNA concentrations occurs at lower PEG concentrations than the compaction at low DNA concentrations. These opposite changes in the conformation of DNA molecule are interpreted in terms of the free energy, including depletion interaction.     

Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules

It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 microM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 microM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.     

Effect of headgroup on DNA-cationic surfactant interactions

The interaction behavior of DNA with different types of hydroxylated cationic surfactants has been studied. Attention was directed to how the introduction of hydroxyl substituents at the headgroup of the cationic surfactants affects the compaction of DNA. The DNA-cationic surfactant interaction was investigated at different charge ratios by several methods like UV melting, ethidium bromide exclusion, and gel electrophoresis. Studies show that there is a discrete transition in the DNA chain from extended coils (free chain) to a compact form and that this transition does not depend substantially on the architecture of the headgroup. However, the accessibility of DNA to ethidium bromide is preserved to a significantly larger extent for the more hydrophilic surfactants. This was discussed in terms of surfactant packing. Observations are interpreted to reflect that the surfactants with more substituents have a larger headgroup and therefore form smaller micellar aggregates; these higher curvature aggregates lead to a less efficient, "patch-like" coverage of DNA. The more hydrophilic surfactants also presented a significantly lower cytotoxicity, which is important for biotechnological applications.     

Transfer of Two‐Dimensional Oligonucleotide Patterns onto Stereocontrolled Plasmonic Nanostructures through DNA‐Origami‐Based Nanoimprinting Lithography

The precise functionalization of self‐assembled nanostructures with spatial and stereocontrol is a major objective of nanotechnology and holds great promise for many applications. Herein, the nanoscale addressability of DNA origami was exploited to develop a precise copy‐machine‐like platform that can transfer two‐dimensional oligonucleotide patterns onto the surface of gold nanoparticles (AuNPs) through a deliberately designed toehold‐initiated DNA displacement reaction. This strategy of DNA‐origami‐based nanoimprinting lithography (DONIL) demonstrates high precision in controlling the valence and valence angles of AuNPs. These DNA‐decorated AuNPs act as precursors in the construction of discrete AuNP clusters with desired chirality.     

DNA-templated three-branched nanostructures for nanoelectronic devices

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.     

Capillary electrophoresis of DNA damage after irradiation: apoptosis and necrosis

Apoptosis is a type of cellular death but also directly regulates tumorigenesis through different gene expression. This phenomenon is often used as end-point in studies of radio- and chemosensitivity of cancer cells. Restriction DNA fragments have been separated quickly, efficiently and successfully by capillary gel electrophoresis (CGE). In this study CGE has been applied to distinguish between the discrete pattern of degraded DNA produced by apoptosis and randomized DNA breaks produced by ionizing radiation. The influence of different variables has been discussed and an example of fast separation by CGE of the apoptotic fragments produced by UV light treatment is shown.     

DNA与两性表面活性剂相互作用研究

本文综述了DNA与两性表面活性剂相互作用的研究进展,主要介绍了利用荧光显微镜、动静态光散射、相图及浊度等方法对DNA与两性表面活性剂相互作用的观察与形成复合物的表征。由于两性表面活性剂所具有的独特性质,可以实现在特定pH范围通过静电作用诱导DNA构象发生线圈状向小球状的不连续转变,并可通过调节溶液pH值、离子强度等实现对DNA-两性表面活性剂复合物的稳定性的调控。DNA与两性表面活性剂相互作用形成的复合物在非病毒基因载体研究方面具有潜在的应用价值。     

Discrete DNA three-dimensional nanostructures: the synthesis and applications

Structural DNA nanotechnology, an emerging technique that utilizes the nucleic acid molecule as generic polymer to programmably assemble well-defined and nano-sized architectures, holds great promise for new material synthesis and constructing functional nanodevices for different purposes. In the past three decades, rapid development of this technique has enabled the syntheses of hundreds and thousands of DNA nanostructures with various morphologies at different scales and dimensions. Among them, discrete three-dimensional (3D) DNA nanostructures not only represent the most advances in new material design, but also can serve as an excellent platform for many important applications. With precise spatial addressability and capability of arbitrary control over size, shape, and function, these nanostructures have drawn particular interests to scientists in different research fields. In this review article, we will briefly summarize the development regarding the synthesis of discrete DNA 3D nanostructures with various size, shape, geometry, and topology, including our previous work and recent progress by other groups. In detail, three methods majorly used to synthesize the DNA 3D objects will be introduced accordingly. Additionally, the principle, design rule, as well as pros and cons of each method will be highlighted. As functions of these discrete 3D nanostructures have drawn great interests to researchers, we will further discuss their cutting-edge applications in different areas, ranging from novel material synthesis, new device fabrication, and biomedical applications, etc. Lastly, challenges and outlook of these promising nanostructures will be given based on our point of view.     

Silver nanoparticle-DNA bionanoconjugates bearing a discrete number of DNA ligands

Silver nanoparticles (AgNPs), which are stable in strongly ionic solutions and appear as a single sharp band during gel electrophoresis, are synthesized by a facile one-pot process, allowing for the first time realization of AgNP-DNA bio-nano-conjugates bearing a discrete number of DNA ligands.     

Damage to rat retinal DNA induced in vivo by visible light

Intense visible light can damage retinal photoreceptor cells by photochemical or thermal processes, leading to cell death. The precise mechanism of light-induced damage is unknown; however, oxidative stress is thought to be involved, based on the protective effect of antioxidants on the light-exposed retina. To explore the in vivo effects of light on retinal DNA, rats were exposed to intense visible light for up to 24 h and the time courses of single-strand breaks in restriction fragments containing the opsin, insulin 1 and interleukin-6 genes were measured. All three gene fragments displayed increasing single-strand modifications with increasing light exposure. Treatment with the antioxidant dimethylthiourea prior to light exposure delayed the development of net damage. The time course of double-strand DNA damage was also examined in specific genes and in repetitive DNA. The appearance of discrete 140-200 base-pair DNA fragments after 20 h of light exposure implicated a nonrandom, possibly enzymatic damaging mechanism. The generation of nucleosome core-sized DNA fragments, in conjunction with single-strand breaks, suggests two phases of light-induced retinal damage, with random attack on DNA by activated oxygen species preceding enzymatic degradation.     

Characterization and modulation of the hierarchical self-assembly of nanostructured DNA tiles into supramolecular polymers

We present a set of DNA supramolecular architectures based on the polymerization of discrete DNA tiles having the shape of parallelograms and designed to have a one-dimensional inter-tile connectivity. Tiles bind to each other with two connections, which have different thermal stabilities. We discuss how this difference in stability implies that the same monomeric tile can yield supramolecular polymers of different shapes just by changing the polymerization conditions. We show how this system reacts to external stimuli by interconverting between some of its possible states. Concurrently, we show how performing the polymerization on a surface can influence its outcome.     

Attenuation of Biologically Effective UV Radiation in Tropical Atlantic Waters Measured with a Biochemical DNA Dosimeter

Abstract— A biochemical dosimeter was developed to study the attenuation of biologically effective UV radiation in marine tropical waters. Small quartz vials were used containing a solution of DNA molecules; the vials were incubated at discrete water depths. Subsequently, DNA damage was determined in these samples, using an antibody directed against thymine dimers followed by chemiluminescent detection. Measurements of DNA damage were compared with calculated biologically effective doses, as derived from spectroradiometer measurements. The biodosimeter was found to be a reliable and easy tool to determine levels of harmful UV radiation in marine waters. The highest attenuation coefficient (1.60 m^-l) measured with the biochemical dosimeter was found in eutrophic waters, at a coastal station off Curabcao, Netherlands Antilles. At the other stations attenuation coefficients ranged from 0.18 m^-1 in central Atlantic waters to 0.43 m^-1 close to the Curapcao coast line. Latter results indicate that biologically effective UV radiation may easily reach ecologically significant depths, e.g. coral reef communities.     

DNA amplification fingerprinting using arbitrary oligonucleotide primers

DNA amplification fingerprinting (DAF) is a strategy for genetic typing and mapping that uses one or more very short (≥5 nt) arbitrary oligonucleotides to direct the enzymatic amplification of discrete portions of a DNA template resulting in a spectrum of products characteristic of the DNA starting material. Polymorphisms from simple banding patterns are useful as genetic markers while more complex and informative patterns are suitable for DNA fingerprinting. The use of polyacrylamide gel electrophoresis and silver staining can adequately resolve the spectrum of DAF products into detailed and reproducible patterns.     

Milestones in graphical bioinformatics

After reviewing the field of graphical bioinformatics, we have selected two dozen of the most significant publications that represent milestones of graphical bioinformatics. These publications can be viewed as forming the backbone of graphical bioinformatics, the branch of bioinformatics that initiates analysis of DNA, RNA, and proteins by considering various graphical representations of these sequences. Graphical bioinformatics, a division of bioinformatics that analyzes sequences of DNA, RNA, proteins, and proteomics maps by developing and using tools of discrete mathematics and graph theory in particular, has expanded since the year 2000, although pioneering contributions date back to Hamory (1983) and Jeffrey (1990). We chronologically follow the development of graphical bioinformatics, without assuming that readers are familiar with discrete mathematics or graph theory. Readers unfamiliar with graph theory may even have some advantage over those who have been only superficially exposed to graph theory, inview of wide misconceptions and misinformation about chemical graph theory among quantum chemists, physical chemists, and medicinal chemists in past decades. © 2013 Wiley Periodicals, Inc.