Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

NEW METHODOLOGY FOR FEEDER RECONFIGURATION IN DISTRIBUTION NETWORKS WITH DISTRIBUTED ENERGY RESOURCES

This doctoral Thesis defines and develops a new methodology for feeder reconfiguration in distribution networks with Distributed Energy Resources (DER). The proposed methodology is based on metaheuristic Ant Colony Optimization (ACO) algorithms. The methodology is called Item Oriented Ant System (IOAS) and the doctoral Thesis also defines three variations of the original methodology, Item Oriented Ant Colony System (IOACS), Item Oriented Max-min Ant System (IOMMAS) y Item Oriented Max-min Ant Colony System (IOACS). All methodologies pursue a twofold objective, to minimize the power losses and maximize DER penetration in distribution networks. The aim of the variations is to find the algorithm that adapts better to the present optimization problem, solving it most efficiently. The main feature of the methodology lies in the fact that the heuristic information and the exploitation information (pheromone) are attached to the item not to the path. Besides, the doctoral Thesis proposes to use feeder reconfiguration in order to increase the distribution network capacity of accepting a major degree of DER. The proposed methodology and its three variations have been tested and verified in two distribution networks well documented in the existing bibliography. These networks have been modeled and used to test all proposed methodologies for different scenarios with various DER penetration degrees.