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The role of DNA as structuring or templating agent has become more significant with the development of nanobiotechnology. Although short single and double stranded DNA have extensively been used as immobilization tool, as a template for nanoparticle preparation and in design of various devices such as nanomotors and biosensors, DNA from natural sources has an advantage of being abundant, cheap and...
DNA nanotechnology is a powerful tool to fabricate nanoscale motors, but the DNA nanomotors to date are largely limited to the simplistic burn-the-bridge design principle that prevents re-use of a fabricated motor-track system and is unseen in biological nanomotors. Here we propose and experimentally demonstrate a scheme to implement a conceptually new design principle by which a symmetric bipedal...
Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry...
In this review, we introduce the biophysical and biochemical methods currently used to investigate the structures and stabilities of tetramolecular DNA G-quadruplexes containing chemical modifications. We hope this paper will guide others as they perform similar experiments leading to more information about the effects of chemical modifications on G-quadruplex formation. The structures of tetramolecular...
The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the...
The functionalized DNA has been widely developed and played a more and more important role in life science and material science during last decades. Therefore, methods to effectively endue DNA new functions by modifying DNA have been developed quickly. In this review, we will give an introduction in the methods for covalent terminal functionalization of DNA, including solid-phase functionalization...
The addressable DNA nanostructures offer ideal platforms to construct organized assemblies of multiple protein molecules. Sequence-specific DNA binding proteins that target defined sites on DNA nanostructures would act as orthogonal adaptors to carry individual protein molecules to the programmed addresses. We have recently developed a protein-based adaptor by utilizing the sequence-specific DNA binding...
In the last decade, in vivo studies have revealed that even subtle differences in size, concentration of components, cell cycle stage, make the cells in a population respond differently to the same stimulus. In order to characterize such complexity of behavior and shed more light on the functioning and communication amongst cells, researchers are developing strategies to study single live cells in...
In living organisms, the integration of signals from the environment and the molecular computing leading to a cellular response are orchestrated by Gene Regulatory Networks (GRN). However, the molecular complexity of in vivo genetic regulation makes it next to impossible to describe in a quantitative manner. Reproducing, in vitro, reaction networks that could mimic the architecture and behavior of...
DNA nanostructures facilitating drug delivery are likely soon to be realized. In the past few decades programmed self-assembly of DNA building blocks have successfully been employed to construct sophisticated nanoscale objects. By conjugating functionalities to DNA, other molecules such as peptides, proteins and polymers can be precisely positioned on DNA nanostructures. This exceptional ability to...
Over more than 20years of development has led to the substantial progress made in the wet chemical synthesis of elementary nanoparticle building blocks including metal nanoparticles, quantum dots, and magnetic particles. However, it remains challenging to rationally assemble them into well-defined molecule-like architectures. DNA was first used to program nanomaterials synthesis in 1996, and more...
DNA is the most exploited biopolymer for the programmed self-assembly of objects and devices that exhibit nanoscale-sized features. One of the most useful properties of DNA nanostructures is their ability to be functionalized with additional non-nucleic acid components. The introduction of such a component is often achieved by attaching it to an oligonucleotide that is part of the nanostructure, or...
Precise structure switching between all of the three forms of three-state nanomechanical DNA origami devices has been accomplished. A nanomechanical DNA origami device called DNA origami pliers, which consists of two levers of 170-nm long, 20-nm wide, and 2-nm thick connected at a Holliday-junction fulcrum, takes three conformations: closed parallel, closed antiparallel, and open cross forms. They...
DNA nanostructures have recently emerged as a type of drug delivery nanocarriers due to their suitable sizes, well-defined structures and low-toxicity. Here, we present a protocol for the assembly of DNA nanoribbon structures with rolling circle amplification (RCA) and delivery of CpG oligonucleotide. DNA nanoribbons with different dimensions and patterns were assembled with long RCA strands and several...
The stabilities, structures, and functions of nucleic acids are responsive to surrounding conditions. Living cells contain biomolecules, including nucleic acids, proteins, polysaccharides, and other soluble and insoluble low-molecular weight components, that occupy a significant fraction of the cellular volume (up to 40%), resulting in a highly crowded intracellular environment. We have proven that...
DNA nanostructures are finding diverse applications as scaffolds for molecular organization. In general, components such as nucleic acids, proteins, and nanoparticles are attached to addressable DNA nanostructures via hybridization, and there is interest in exploiting hybridization for localized computation on DNA nanostructures. This report details two fluorescence microscopy methods, single-particle...
Nanoscale assemblies of metal nanoparticles in one dimension (1D) to three dimensions (3D) can exhibit novel phenomena that are not observed in the amorphous state. Bottom-up assembly technique is expected to overcome the resolution limit of top-down method and casts a new light on the nanofabrication field. DNA origami, which is mainly used to construct discrete and addressable nanostructures, can...
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