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.

Magnetospheric access of solar particles and the configuration of the distant geomagnetic field

The access of 1.2-40 MeV protons and 0.4-1.0 MeV electrons from interplanetary space to the polar cap regions has been investigated with an experiment on board a low altitude, polar orbiting satellite (OG0-4).

A total of 333 quiet time observations of the electron polar cap boundary give a mapping of the boundary between open and closed geomagnetic field lines which is an order of magnitude more comprehensive than previously available.

Persistent features (north/south asymmetries) in the polar cap proton flux, which are established as normal during solar proton events, are shown to be associated with different flux levels on open geomagnetic field lines than on closed field lines. The pole in which these persistent features are observed is strongly correlated to the sector structure of the interplanetary magnetic field and uncorrelated to the north/south component of this field. The features were observed in the north (south) pole during a negative (positive) sector 91% of the time, while the solar field had a southward component only 54% of the time. In addition, changes in the north/south component have no observable effect on the persistent features.

Observations of events associated with co-rotating regions of enhanced proton flux in interplanetary space are used to establish the characteristics of the 1.2 - 40 MeV proton access windows: the access window for low polar latitudes is near the earth, that for one high polar latitude region is ~250 R_⊕ behind the earth, while that for the other high polar latitude region is ~1750 R_⊕ behind the earth. All of the access windows are of approximately the same extent (~120 R_⊕). The following phenomena contribute to persistent polar cap features: limited interplanetary regions of enhanced flux propagating past the earth, radial gradients in the interplanetary flux, and anisotropies in the interplanetary flux.

These results are compared to the particle access predictions of the distant geomagnetic tail configurations proposed by Michel and Dessler, Dungey, and Frank. The data are consistent with neither the model of Michel and Dessler nor that of Dungey. The model of Frank can yield a consistent access window configuration provided the following constraints are satisfied: the merging rate for open field lines at one polar neutral point must be ~5 times that at the other polar neutral point, related to the solar magnetic field configuration in a consistent fashion, the migration time for open field lines to move across the polar cap region must be the same in both poles, and the open field line merging rate at one of the polar neutral points must be at least as large as that required for almost all the open field lines to have merged in 0 (one hour). The possibility of satisfying these constraints is investigated in some detail.

The role played by interplanetary anisotropies in the observation of persistent polar cap features is discussed. Special emphasis is given to the problem of non-adiabatic particle entry through regions where the magnetic field is changing direction. The degree to which such particle entry can be assumed to be nearly adiabatic is related to the particle rigidity, the angle through which the field turns, and the rate at which the field changes direction; this relationship is established for the case of polar cap observations.

The complex angular momentum theory of the production of three particles in collisions of two strongly interacting particles at high energy

The problem of the continuation to complex values of the angular momentum of the partial wave amplitude is examined for the simplest production process, that of two particles → three particles. The presence of so-called "anomalous singularities" complicates the procedure followed relative to that used for quasi two-body scattering amplitudes. The anomalous singularities are shown to lead to exchange degenerate amplitudes with possible poles in much the same way as "normal" singularities lead to the usual signatured amplitudes. The resulting exchange-degenerate trajectories would also be expected to occur in two-body amplitudes.

The representation of the production amplitude in terms of the singularities of the partial wave amplitude is then developed and applied to the high energy region, with attention being paid to the emergence of "double Regge" terms. Certain new results are obtained for the behavior of the amplitude at zero momentum transfer, and some predictions of polarization and minima in momentum transfer distributions are made. A calculation of the polarization of the ρ^o meson in the reaction π ^- p → π ^- ρ^op at high energy with small momentum transfer to the proton is compared with data taken at 25 Gev by W. D. Walker and collaborators. The result is favorable, although limited by the statistics of the available data.

I. Non-linear effects in a self-consistent calculation of SU_3 symmetry breaking in strong interaction coupling constants. II. Direct-channel reggeization of strong interaction scattering amplitudes

The thesis is divided into two parts. Part I generalizes a self-consistent calculation of residue shifts from SU₃ symmetry, originally performed by Dashen, Dothan, Frautschi, and Sharp, to include the effects of non-linear terms. Residue factorizability is used to transform an overdetermined set of equations into a variational problem, which is designed to take advantage of the redundancy of the mathematical system. The solution of this problem automatically satisfies the requirement of factorizability and comes close to satisfying all the original equations.

Part II investigates some consequences of direct channel Regge poles and treats the problem of relating Reggeized partial wave expansions made in different reaction channels. An analytic method is introduced which can be used to determine the crossed-channel discontinuity for a large class of direct-channel Regge representations, and this method is applied to some specific representations.

It is demonstrated that the multi-sheeted analytic structure of the Regge trajectory function can be used to resolve apparent difficulties arising from infinitely rising Regge trajectories. Also discussed are the implications of large collections of "daughter trajectories."

Two things are of particular interest: first, the threshold behavior in direct and crossed channels; second, the potentialities of Reggeized representations for us in self-consistent calculations. A new representation is introduced which surpasses previous formulations in these two areas, automatically satisfying direct-channel threshold constraints while being capable of reproducing a reasonable crossed channel discontinuity. A scalar model is investigated for low energies, and a relation is obtained between the mass of the lowest bound state and the slope of the Regge trajectory.

Elimination of parity doublets in Regge amplitudes

In Part I, the common belief that fermions lying on linear trajectories must have opposite-parity partners is shown to be false. Reggeization of a sequence of positive-parity fermion resonance is carried out in the Van Hove model. As a consequence of the absence of negative-parity states, the partial-wave amplitudes must have a fixed cut in the J plane. This fixed cut, in conjunction with the moving Regge pole, provides a new parametrization for fermion-exchange reactions, which is in qualitative agreement with the data.

In Part II, the spin structure of three particle vertices is determined from the quark model. Using these SU(6)_W vertices in the Van Hove model, we derive a Reggeized scattering amplitude. In addition to Regge poles there are necessarily fixed Regge cuts in both fermion and boson exchange amplitudes. These fixed cuts are similar to those found in Part I, and may be viewed as a consequence of the absence of parity doubled quarks. The magnitudes of the pole and cut terms in an entire class of SU(6) related reactions are determined by their magnitudes in a single reaction. As an example we explain the observed presence or absence of wrong-signature nonsense dips in a class of reactions involving vector meson exchange.