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Nursing reagent-American scientists develop self-assembled DNA nanostructure gene detection platform
U.S. scientists have developed a self-assembling DNA nanostructure gene detection platform. Scientists at the Arizona State University Biodesign Institute have developed the world ’s first gene detection platform made entirely of self-assembling DNA nanostructures. "We started with the most famous structure in biology, that is, DNA, and then used it as a nano-scale building material," a member of the Institute's single-molecule biophysics center, assistant professor of chemistry and biochemistry at the College of Arts and Sciences HaoYan said. HaoYan is a researcher in a rapidly developing field called structural DNA nanotechnology. The technology assembles biomolecules into various nanostructures and has applications in many fields from human health to nanoelectronics. An interdisciplinary research group at Arizona State University led by HaoYan has developed a method that uses structural DNA nanotechnology to target genetic chemical messengers called RNA. The members of this research group include: the first author of the paper, Yonggang Ke, a graduate student in chemistry and biochemistry; Yan Liu, assistant professor of chemistry and biochemistry; Stuart Lindsay, director of the Center for Single Molecular Biophysics and professor of physics; and Yung Chang, associate professor at the School of Life Sciences. "This is one of the first practical applications of a powerful technology. Previously, the technology was mainly a subject of research and demonstration," Lindsay said. "There have been very exciting developments in the field of structural DNA nanotechnology recently, that is, Ned Seeman, Erik Winfree and colleagues first demonstrated the use of tile DNA self-assembly to construct geometric and topological nanostructures," Hao Yan said. The recent breakthrough in the manufacture of space-addressable DNA nanoarrays came from Paul Rothemund ’s research on scaffolding DNA origami technology, in which a long single-stranded viral DNA scaffold can be synthesized by a large number of short “auxiliary strands†Folded and nailed to the nanostructure, showing a complicated pattern. "But the potential of structural DNA nanotechnology in biological applications is underestimated. If we look at the process of DNA self-assembly, you will be surprised to find that trillions of DNA nanostructures can be formed simultaneously in a few microliters of solution, Very importantly, they are biocompatible and easily soluble in water, "Hao Yan said. DNA chip and microarray technology has become a multi-billion dollar industry. Scientists can use this technology to simultaneously check for mutations in thousands of genes or find clues to diseases. However, since the DNA probe is fixed on the solid surface of the microarray chip, finding the probe by the target is a slow process. Moreover, it is difficult to control the distance between the probes to nanometer accuracy. "In this study, we developed a water-soluble nanoarray that can take advantage of the DNA self-assembly process and also has advantages that macroscopic DNA chip arrays do not have," Hao Yan said. "Unlike solid surface chips, this array is itself a reactant." In order to make RNA probes for DNA origami technology, Hao Yan used the basic pairing rules of DNA chemical letters ("A" can only form a similar to "T" Due to the chemical bond of the zipper, "G" can only be paired with "C"). By controlling the exact position of these bases in a copy of synthetic DNA, Hao Yan compiled a single-stranded genomic DNA, called M13, to make nanotiles containing probes for specific gene expression targets. Hao Yan calls these self-assembled DNA nanoarrays nucleic acid probe tiles, and they look like nanometer-sized stamps. In just one step, the M13 scaffolding system can produce 100 trillion tiles with a yield of nearly 100%. Hao Yan's team designed three different DNA probe tiles for detecting three different RNA genes, and also designed a barcode index to distinguish different tiles. "Each probe can be identified by its own barcode, so we mix them in the same solution, and then we use it for multiple detection," Hao Yan said. The research team used a powerful instrument called an atomic force microscope (AFM). This instrument allows scientists to take images of tiles at the single molecule level. There is a dangling single-stranded DNA fragment on the surface of each DNA probe tile, which can be combined with the target RNA target. "Each probe actually contains two half-probes. When the target RNA arrives, it will hybridize with the half-probe, turning the single-stranded hanging probe into a rigid structure," Hao Yan said. "When it hardens, it will be felt by the cantilever of the atomic force microscope, and you will see a bright line that represents an increase in height. The result is a mechanical, label-free detection." This technology can also Detect trace amounts of RNA. "Since the affinity of DNA-RNA hybridization is so strong in principle, only one molecule can hybridize to the probe tiles," Hao Yan said. Although there are many technical obstacles to be overcome, this research group is excited about the possible application of this technology. "Our method provides water-soluble probe tile reactants, so the sample volume may be reduced to the level of single cell capacity. Our ultimate goal is to detect RNA gene expression at the single cell level."