A modified uridine for the synthesis of branched DNA

Branched DNA constructs have found wide application in DNA-based nanotechnology. Several reports describe the generation of branched DNA structures with variable numbers of arms to self-assemble with pre-designed architectures. Branched DNA is generated by using designed rigid crossover DNA molecules as building blocks. Alternatively, branched DNAs can also be generated by using synthetic branch points derived either from nucleoside or non-nucleoside building blocks. Herein, we report the synthesis of modified uridine derivatives as branching monomer for the synthesis of branched DNA and first studies of their self-assembling properties.     

New branched DNA constructs

The Watson-Crick base pairing of DNA is an advantageous phenomenon that can be exploited when using DNA as a scaffold for directed self-organization of nanometer-sized objects. Several reports have appeared in the literature that describe the generation of branched DNA (bDNA) with variable numbers of arms that self-assembles into predesigned architectures. These bDNA units are generated by using cleverly designed rigid crossover DNA molecules. Alternatively, bDNA can be generated by using synthetic branch points derived from either nucleoside or non-nucleoside building blocks. Branched DNA has scarcely been explored for use in nanotechnology or from self-assembling perspectives. Herein, we wish to report our results for the synthesis, characterization, and assembling properties of asymmetrical bDNA molecules that are able to generate linear and circular bDNA constructs. Our strategy for the generation of bDNA is based on a branching point that makes use of a novel protecting-group strategy. The bDNA units were generated by means of automated DNA synthesis methods and were used to generate novel objects by employing chemical and biological techniques. The entities generated might be useful building blocks for DNA-based nanobiotechnology.     

Nanoparticle-DNA conjugates bearing a specific number of short DNA strands by enzymatic manipulation of nanoparticle-bound DNA

Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.     

Bioconjugated nanoparticles for DNA protection from cleavage

We have developed a novel method to protect DNA from cleavage using bioconjugated nanoparticles. Positively charged amino-modified silica nanoparticles have been directly prepared using water-in-oil microemulsion. Plasmid DNA can be easily enriched onto the positively charged nanoparticle surface, and the DNA strands are well protected from enzymatic cleavage. When incubated with nuclease enzyme for enzymatic cleavage, free plasmid DNA strands are completely cleaved, while those on the nanoparticle surfaces are intact. Our results clearly demonstrate unique properties of nanomaterials when combined with biomolecules. Our simple bionanotechnology will be highly useful in DNA separation, manipulation, and detection, and possibly in genetic engineering and gene therapy, as plasmid DNA can be protected in cellular environments without any change in its property.     

Plasmid DNA hydrogels for biomedical applications

In the last few years, our research group has focused on the design and development of plasmid DNA (pDNA) based systems as devices to be used therapeutically in the biomedical field. Biocompatible macro and micro plasmid DNA gels were prepared by a cross-linking reaction. For the first time, the pDNA gels have been investigated with respect to their swelling in aqueous solution containing different additives. Furthermore, we clarified the fundamental and basic aspects of the solute release mechanism from pDNA hydrogels and the significance of this information is enormous as a basic tool for the formulation of pDNA carriers for drug/gene delivery applications. The co-delivery of a specific gene and anticancer drugs, combining chemical and gene therapies in the treatment of cancer was the main challenge of our research. Significant progresses have been made with a new p53 encoding pDNA microgel that is suitable for the loading and release of pDNA and doxorubicin. This represents a strong valuable finding in the strategic development of systems to improve cancer cure through the synergetic effect of chemical and gene therapy.     

Self-assembled peptide nanostructures: the design of molecular building blocks and their technological utilization

In this tutorial review the process and applications of peptide self-assembly into nanotubes, nanospheres, nanofibrils, nanotapes, and other ordered structures at the nano-scale are discussed. The formation of well-ordered nanostructures by a process of self-association represents the essence of modern nanotechnology. Such self-assembled structures can be formed by a variety of building blocks, both organic and inorganic. Of the organic building blocks, peptides are among the most useful ones. Peptides possess the biocompatibility and chemical diversity that are found in proteins, yet they are much more stable and robust and can be readily synthesized on a large scale. Short peptides can spontaneously associate to form nanotubes, nanospheres, nanofibrils, nanotapes, and other ordered structures at the nano-scale. Peptides can also form macroscopic assemblies such as hydrogels with nano-scale order. The application of peptide building blocks in biosensors, tissue engineering, and the development of antibacterial agents has already been demonstrated.     

DNA-based supramolecular hydrogels: From construction strategies to biomedical applications

DNA-based supramolecular hydrogels are important and promising biomaterials for various applications due to their inherent biocompatibility and tunable physicochemical properties. The three-dimensional supramolecular matrix of DNA formed by non-covalently dynamic cross-linking provides exceptional adaptability, self-healing, injectable and responsive properties for hydrogels. In addition, DNA hydrogels are also ideal bio-scaffold materials owing to their tissue-like mechanics and intrinsic biological functions. Technically, DNA can assemble into supramolecular networks by pure complementary base pairing; it can also be combined with other building blocks to construct hybrid hydrogels. This review focuses on the development and construction strategies of DNA hydrogels. Assembly and synthesis methods, diverse responsiveness and biomedical applications are summarized. Finally, the challenges and prospects of DNA-based supramolecular hydrogels are discussed.     

Enzymatic synthesis of phosphoroselenoate DNA using thymidine 5'-(alpha-P-seleno)triphosphate and DNA polymerase for X-ray crystallography via MAD

We report here the first study of enzymatic synthesis of two phosphoroselenoate (PSe) DNAs using the two alpha-Se-TTP diastereomers (Sp and Rp) and DNA polymerase. The experimental results indicate that Klenow equally recognizes the two individual diastereomers at the same level as natural TTP. The incorporations of the PSe groups at the expected sites have been confirmed by the digestion resistance to exonuclease III, and the different patterns of the digestion resistance of DNA I and II indicate the configurational differences of the PSe centers (Sp or Rp). Unlike chemical synthesis, which is limited to short DNAs and where the separation of the PSe DNA diastereomers is necessary, this enzymatic method can be used to prepare longer DNAs without diastereomer separation. This quantitative enzymatic approach is particular valuable for the synthesis of longer DNAs with multiple PSe groups in large scale for their X-ray crystal structure determination by the MAD phasing technique.     

Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions

Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site‐specific inhibition and timed removal. S‐Adenosyl‐L‐methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC‐ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC‐ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC‐MATs were compatible with DNA‐ and RNA‐MTases, enabling sequence‐specific modification (“writing”) of plasmid DNA and light‐triggered removal (“erasing”).     

Rational design of DNA nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.     

烷氧磺酸盐功能化的聚乙撑二氧噻吩水凝胶

通过氧化偶联聚合方法成功地制备出一种基于烷氧磺酸盐功能化的聚乙撑二氧噻吩水凝胶, 揭示了零维单体胶束向二维纳米片层及三维水凝胶的转变过程, 发现通过改变反应温度或初始单体浓度, 可以诱导水凝胶网络结构单元的维度变化, 即由零维纳米粒子向二维纳米片层进行转化. 提出了一种导电高分子水凝胶的合成方法, 即采用一种氧化剂与一种多价金属盐的混合物作为引发剂, 其中前者用于诱导单体聚合, 后者则充当离子交联试剂, 并发现可以通过引入不同金属离子来改变凝胶的形貌. 此外, 导电高分子水凝胶具有良好的电化学电容, 并具有选择性吸附与可控脱附某些染料分子的特性.     

Encoded dendrimers with defined chiral composition via'click' reaction of enantiopure building blocks

Dendrimers with end-groups of defined chiral composition have been prepared from alkyne functional enantio-pure building blocks obtained by selective enzymatic (ADH) ketone reductions using click chemistry. Optical rotation and enantioselective enzymatic modification is in agreement with the chiral composition of the dendrimers and permits unique molecular-level encoding of stereoisomeric dendritic libraries.     

Controlled assembly of mesoscale structures using DNA as molecular bridges

Mesoscale polyhedral structures from binary mixtures of microspheres of specific size ratios were prepared by using DNA as a molecular bridge. Carboxy-modified polystyrene beads were decorated with fluorescently labeled single-stranded DNA via carboxydiimide chemistry. Fluorescent resonance electron transfer in a confocal microscopy setting was utilized to corroborate DNA hybridization. Tetrahedrons were made by combining DNA-containing 0.818 and 0.211 mum beads, while octahedrons were obtained by bridging 0.818 and 0.364 mum beads. Confocal data in the reflection mode and SEM provide evidence for the formation of mesoscale building blocks.     

DNA hydrogels: New functional soft materials

Deoxyribonucleic acid (DNA) hydrogel is a network of crosslinked DNA strands swollen in aqueous solutions. The crosslinks may be physical or chemical, such as the hydrogen bonds or ethylene glycol units, respectively, connecting the strands belonging to different double‐helical DNA molecules. As DNA network strands in the hydrogels exhibit properties similar to those of the individual DNA molecules, such soft materials are a good candidate to make use of the characteristics of DNA such as coil‐globule transition, biocompatibility, selective binding, and molecular recognition. Physical DNA hydrogels with an elastic modulus in the order of megapascals can be prepared by subjecting semidilute aqueous solutions of DNA to successive heating–cooling cycles between below and above the melting temperature of DNA. Chemical DNA hydrogels can be prepared by connecting the amino groups on the nucleotide bases through covalent bonds to form a three‐dimensional DNA network in aqueous solutions. In this article, we summarize the preparation strategies of DNA hydrogels with a wide range of tunable properties. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Controlling the chirality of DNA nanocages

Playing DNA Twister: By using asymmetric DNA building blocks, self-assembled DNA nanocages that are chiral on the nanoscale have been designed. The resulting DNA nanocages have been characterized with a variety of methods. Such chiral control could be useful for tuning the photonic/optical properties of DNA-templated nanostructures.     

Fluorescent Dynamic Covalent Polymers for DNA Complexation and Templated Assembly

Dynamic covalent polymers (DCPs) offer opportunities as adaptive materials of particular interest for targeting, sensing and delivery of biological molecules. In this view, combining cationic units and fluorescent units along DCP chains is attractive for achieving optical probes for the recognition and delivery of nucleic acids. Here, we report on the design of acylhydrazone-based DCPs combining cationic arginine units with π-conjugated fluorescent moieties based on thiophene-ethynyl-fluorene cores. Two types of fluorescent building blocks bearing neutral or cationic side groups on the fluorene moiety are considered in order to assess the role of the number of cationic units on complexation with DNA. The (chir)optical properties of the building blocks, the DCPs, and their complexes with several types of DNA are explored, providing details on the formation of supramolecular complexes and on their stability in aqueous solutions. The DNA-templated formation of DCPs is demonstrated, which provides new perspectives on the assembly of fluorescent DCP based on the nucleic acid structure.     

Preparation of DNA Markers Based on E. Coli Plasmid DNA

DNA fragments of various length were produced by enzymatic restriction of plasmid DNA from various strains of E. coli. A molecular DNA marker was constructed based on the DNA restricts.     

Multiple Light Control Mechanisms in ATP-Fueled Non-equilibrium DNA Systems

Fuel-driven self-assemblies are gaining ground for creating autonomous systems and materials, whose temporal behavior is preprogrammed by a reaction network. However, up to now there has been a lack of simple external control mechanisms of the transient behavior, at best using remote and benign light control. Even more challenging is to use different wavelengths to modulate the reactivity of different components of the system, for example, as fuel or building blocks. Success would enable such systems to navigate along different trajectories in a wavelength-dependent fashion. Herein, we introduce the first examples of light control in ATP-fueled, dynamic covalent DNA polymerization systems organized in an enzymatic reaction network of concurrent ATP-powered ligation and restriction. We demonstrate concepts for light activation and modulation by introducing caged ATP derivatives and caged DNA building blocks, making it possible to realize light-activated fueling, self-sorting in structure and behavior, and transition across different wavelength-dependent dynamic steady states.     

3'-nitrophenylpropyloxycarbonyl (NPPOC) protecting groups for high-fidelity automated 5' --> 3' photochemical DNA synthesis

[structure: see text]. The most powerful DNA microarrays would be prepared by photolithography with free 3'-ends that could be processed enzymatically. A photoremovable group that could be removed in quantitative yield would ensure high purity of the synthesized probes. We have developed new pyrimidine building blocks for 5' --> 3' DNA synthesis with high cycle yields using the NPPOC (3'-nitrophenylpropyloxycarbonyl) protecting group. These phosphoramidites were proved in automated photochemical DNA synthesis on a modified synthesizer.