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.

Determining the role of linear and nonlinear interactions in records of climate change: possible solar influences in annual to century-scale records

Time series analysis methods have traditionally helped in identifying the role of various forcing mechanisms in influencing climate change. A challenge to understanding decadal and century-scale climate change has been that the linkages between climate changes and potential forcing mechanisms such as solar variability are often uncertain. However, most studies have focused on the role of climate forcing and climate response within a strictly linear framework. Nonlinear time series analysis procedures provide the opportunity to analyze the role of climate forcing and climate responses between different time scales of climate change. An example is provided by the possible nonlinear response of paleo-ENSO-scale climate changes as identified from coral records to forcing by the solar cycle at longer time scales.

Global linear and nonlinear stability of viscous confined plane wakes with co-flow

The global stability of confined uniform density wakes is studied numerically, using two-dimensional linear global modes and nonlinear direct numerical simulations. The wake inflow velocity is varied between different amounts of co-flow (base bleed). In accordance with previous studies, we find that the frequencies of both the most unstable linear and the saturated nonlinear global mode increase with confinement. For wake Reynolds number Re = 100 we find the confinement to be stabilising, decreasing the growth rate of the linear and the saturation amplitude of the nonlinear modes. The dampening effect is connected to the streamwise development of the base flow, and decreases for more parallel flows at higher Re. The linear analysis reveals that the critical wake velocities are almost identical for unconfined and confined wakes at Re ≈ 400. Further, the results are compared with literature data for an inviscid parallel wake. The confined wake is found to be more stable than its inviscid counterpart, whereas the unconfined wake is more unstable than the inviscid wake. The main reason for both is the base flow development. A detailed comparison of the linear and nonlinear results reveals that the most unstable linear global mode gives in all cases an excellent prediction of the initial nonlinear behaviour and therefore the stability boundary. However, the nonlinear saturated state is different, mainly for higher Re. For Re = 100, the saturated frequency differs less than 5% from the linear frequency, and trends regarding confinement observed in the linear analysis are confirmed.

Linear and nonlinear model large-eddy simulations of a plane jet

The nonlinear Kosovic, and mixed Leray and α subgrid scale models are contrasted with linear Smagorinsky and Yoshizawa Large Eddy Simulations for a Re = 4000 plane jet simulation. Comparisons are made with Direct Numerical Simulation data and measurements. Global properties of the jet such as the spreading and centreline velocity decay rates are investigated. The mean-flow and turbulence parameters in the self-similar region are also studied. All models generally give encouraging agreement with the Direct Numerical Simulation data and reliable measurements. Solution differences for the models are relatively minor, none giving clear improvements for all data comparisons.

Linear and nonlinear intersubband optical properties in a step quantum well with an applied electric field

Within the framework of the effective-mass envelope-function theory, the field-dependent intersubband optical properties of a Al0.4Ga0.6As/Al0.2Ga0.8As/GaAs step quantum well are investigated theoretically based on the periodic boundary condition. A very large Stark shift occurs when the lowest subband electron remains confined to the small well while the higher subband electron confined to the big well. The optical nonlinearity in a step well due to resonant intersubband transition (ISBT) is analyzed using a density-matrix approach. The second-harmonic generation coefficient chi(2 omega)((2)) and nonlinear optical rectification chi(0)((2)) have also been investigated theoretically. The results show that the ISBT in a step well can generate very large second order optical nonlinearities, chi(0)((2)) and chi(2 omega)((2)) can be tuned by the electric field over a wide range.