X-ray Scattering from Immunostimulatory Tetrapod-Shaped DNA in Aqueous Solution To Explore Its Biological Activity–Conformation Relationship

Anisotropically Functionalized Aptamer-DNA Nanostructures for Enhanced Cell Proliferation and Target-Specific Adhesion in 3D Cell Cultures

The development of supramolecular hydrogel scaffolds for the precise positioning of biochemical cues is paramount for applications such as tissue engineering. Nucleic acid engineering allows fabrication of three-dimensional (3D) nanostructures with high variability and nanoscale precision. In this study, aptamers were anisotropically functionalized onto branched DNA nanostructures to control their cell adhesion capability, and their efficiency as biological signal inducers for 3D cell cultivation was investigated. Each arm of the X-shaped DNA nanostructure (X-DNA) was functionalized with photo-cross-linkable or cell adhesion moieties, and the steric hindrance of the 3D DNA nanostructures on a cell was optimized. X-DNA nanostructures with cell-positioning parameters were rapidly photopolymerized to form hybrid hydrogels, and their effects on cell behaviors and positions were investigated. We observed that aptamer-functionalized X-DNA nanostructures exhibited significantly enhanced cell proliferation and provided homogeneous distribution and target-specific adhesion of encapsulated cells within hydrogel matrices. Overall, the anisotropic functionalization of DNA nanostructures provides a controllable function for the advancement of conventional 3D culture platforms.

Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications

The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.

Nanostructured DNA for the delivery of therapeutic agents

DNA and RNA, the nucleic acids found in every living organism, are quite crucial, because not only do they store the genetic information, but also they are used as signals through interaction with various molecules within the body. The nature of nucleic acids, especially DNA, to form double-helix makes it possible to design nucleic acid-based nanostructures with various shapes. Because the shapes as well as the physicochemical properties determine their interaction with proteins or cells, nanostructured DNAs will have different features in the interaction compared with single- or double-stranded DNA. Some of these unique features of nanostructured DNA make ways for efficient delivery of therapeutic agents to specific targets. In this review, we begin with the factors affecting the properties of nanostructured DNA, followed by summarizing the methods for the development of nanostructured DNA. Further, we discuss the characteristics of nanostructured DNA and their applications for the delivery of bioactive compounds.

Polypod-Shaped DNAs: Small-Angle X-ray Scattering and Immunostimulatory Activity

We explored in detail the relationship between the structure in aqueous solution and immunostimulatory activity of polypod-shaped DNAs, called polypodnas. The polypodnas were constructed using 3-6 oligodeoxynucleotides (ODNs) to obtain tri-, tetra-, penta-, and hexapodna, each of which had 3, 4, 5, and 6 arms made of double-stranded DNA, respectively. A highly potent immunostimulatory CpG sequence was included into each of the polypodnas. Synchrotron X-ray scattering analysis showed that the double-stranded DNA arms of all of the polypodnas adopted a B-form DNA conformation. The analysis also suggested that some nucleotides in the central parts of pentapodna and hexapodna did not form base pairs, whereas those of tripodna and tetrapodna all formed base pairs. This difference would occur because of an increase in steric hindrance and electrical repulsion with increasing number of arms. The pentapodna and hexapodna induced a large amount of tumor necrosis factor α-release from macrophage-like cells compared with the tripodna and tetrapodna, suggesting that the partly loosened DNA in polypodna with many arms is advantageous for exposing the immunostimulatory sequences of the polypodna.