This thesis will focus on the computational design of structural and dynamic nucleic acid systems, particularly for new type of DNA structure design and high precision control of gene expression in vivo. Firstly, a new type of fundamental DNA structural motif, the layered-crossover motif, will be introduced. The layered-crossover allow non-parallel alignment of DNA helices with precisely controlled angle. By using the layered-crossover motif, the scaffold can go through the 3D framework DNA origami structures. The properties of precise angle control of the layered-crossover tiles can also be used to assemble 2D and 3D crystals. One the dynamic control part, a de-novo-designed riboregulator is developed that can recognize single nucleotide variation. The riboregulators can also be used to develop paper-based diagnostic devices.
In a series of experiments in the late 1970s, Alec J. Jeffreys in the UK and Richard A. Flavell in the Netherlands developed a technique to detect variations in the DNA of different individuals. They compared fragments of DNA from individuals’ beta-globin genes, which produce a protein in hemoglobin. Previously, to identify biological material, scientists focused on proteins rather than on genes. But evidence about proteins enabled scientists only to exclude, but not to identify, individuals as the sources of the biological samples. By 1979, Jeffrey’s experiments on beta-globin genes shifted the analytical approach of scientific identification from proteins to genes to identify an individual’s genetic identity. The ability to match a person to a biological sample developed in the 1980s and impacted many fields including paternity testing, forensics, immigration, and body identification.