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.

Investigations of the origin of stereocontrol in syndiospecific Ziegler-Natta polymerizations

In order to expand our understanding of the mechanism of stereocontrol in syndiospecific α-olefin polymerization, a family of Cs-symmetric, ansa-group 3 metallocenes was targeted as polymerization catalysts. The syntheses of new ansa-yttrocene and scandocene derivatives that employ the doubly [SiMe₂]- bridged ligand array (1,2-SiMe₂)₂{C₅H-3,5-(CHMe₂)₂} (where R = t- butyl, tBuThp; where R = i-propyl, iPrThp) are described. The structures of tBuThpY(µ-Cl)₂K(THF)₂, tBuThpSc(µ-Cl)₂K(Et₂O)₂, tBuThpYCH(SiMe₃)₂, Y₂{µ₂-(tBuThp)₂}(µ₂-H)₂, and tBuThpSc(µ-CH₃)₂ have been examined by single crystal X-ray diffraction methods. Ansa-yttrocenes and scandocenes that incorporate the singly [CPh₂]-bridged ligand array (CPh₂)(C₅H₄)(C₁₃H₈)(where C₅H₄ = Cp, cyclopentadienyl; where C₁₃H₈ = Flu, fluourenyl) have also been prepared. Select meallocene alkyl complexes are active single component catalysts for homopolymerization of propylene and 1-pentene. The scandocene tetramethylaluminate complexes generate polymers with the highes molecular weights of the series. Under all conditions examined atactic polymer microstructures are observed, suggesting a chain-end mechanism for stereocontrol.

A series of ansa-tantalocenes have been prepared as models for Ziegler-Natta polymerization catalysts. A singly bridged ansa-tantalocene trimethyl complex, Me₂Si(η⁵-C₅H₄)₂TaMe₃, has been prepared and used for the synthesis of a tantalocene ethylene-methyl complex. Addition of propylene to this ethylene-methyl adduct results in olefin exchange to give a mixture of endo and exo propylene isomers. Doubly-silylene bridged ansa-tantalocene complexes have been prepared with the tBuThp ligand; a tantalocene trimethyl complex and a tantalocene methylidene-methyl complex have been synthesized and characterized by X-ray diffraction. Thermolysis of the methylidene-methyl complex affords the corresponding ethylene-hydride complex. Addition of either propylene or styrene to this ethylene-hydride compound results in olefin exchange. In both cases, only one product isomer is observed. Studies of olefin exchange with ansa-tantalocene olefin-hydride and olefin-methyl complexes have provided information about the important steric influences for olefin coordination in Ziegler-Natta polymerization.

Origin of Th/U variations in chondritic meteorites

Isotope dilution thorium and uranium analyses of the Harleton chondrite show a larger scatter than previously observed in equilibrated ordinary chondrites (EOC). The linear correlation of Th/U with 1/U in Harleton (and all EOC data) is produced by variation in the chlorapatite to merrillite mixing ratio. Apatite variations control the U concentrations. Phosphorus variations are compensated by inverse variations in U to preserve the Th/U vs. 1/U correlation. Because the Th/U variations reflect phosphate ampling, a weighted Th/U average should converge to an improved solar system Th/U. We obtain Th/U=3.53 (1_-mean=0.10), significantly lower and more precise than previous estimates.

To test whether apatite also produces Th/U variation in CI and CM chondrites, we performed P analyses on the solutions from leaching experiments of Orgueil and Murchison meteorites.

A linear Th/U vs. 1/U correlation in CI can be explained by redistribution of hexavalent U by aqueous fluids into carbonates and sulfates.

Unlike CI and EOC, whole rock Th/U variations in CMs are mostly due to Th variations. A Th/U vs. 1/U linear correlation suggested by previous data for CMs is not real. We distinguish 4 components responsible for the whole rock Th/U variations: (1) P and actinide-depleted matrix containing small amounts of U-rich carbonate/sulfate phases (similar to CIs); (2) CAIs and (3) chondrules are major reservoirs for actinides, (4) an easily leachable phase of high Th/U. likely carbonate produced by CAI alteration. Phosphates play a minor role as actinide and P carrier phases in CM chondrites.

Using our Th/U and minimum galactic ages from halo globular clusters, we calculate relative supernovae production rates for ²³²Th/²³⁸U and ²³⁵U/²³⁸U for different models of r-process nucleosynthesis. For uniform galactic production, the beginning of the r-process nucleosynthesis must be less than 13 Gyr. Exponentially decreasing production is also consistent with a 13 Gyr age, but very slow decay times are required (less than 35 Gyr), approaching the uniform production. The 15 Gyr Galaxy requires either a fast initial production growth (infall time constant less than 0.5 Gyr) followed by very low decrease (decay time constant greater than 100 Gyr), or the fastest possible decrease (≈8 Gyr) preceded by slow in fall (≈7.5 Gyr).

Time-Domain TeraHertz Spectroscopy and Observational Probes of Prebiotic Interstellar Gas and Ice Chemistry

Understanding the origin of life on Earth has long fascinated the minds of the global community, and has been a driving factor in interdisciplinary research for centuries. Beyond the pioneering work of Darwin, perhaps the most widely known study in the last century is that of Miller and Urey, who examined the possibility of the formation of prebiotic chemical precursors on the primordial Earth [1]. More recent studies have shown that amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth, are present in meteoritic samples, and that the molecules extracted from the meteorites display isotopic signatures indicative of an extraterrestrial origin [2]. The most recent major discovery in this area has been the detection of glycine (NH₂CH₂COOH), the simplest amino acid, in pristine cometary samples returned by the NASA STARDUST mission [3]. Indeed, the open questions left by these discoveries, both in the public and scientific communities, hold such fascination that NASA has designated the understanding of our "Cosmic Origins" as a key mission priority.

Despite these exciting discoveries, our understanding of the chemical and physical pathways to the formation of prebiotic molecules is woefully incomplete. This is largely because we do not yet fully understand how the interplay between grain-surface and sub-surface ice reactions and the gas-phase affects astrophysical chemical evolution, and our knowledge of chemical inventories in these regions is incomplete. The research presented here aims to directly address both these issues, so that future work to understand the formation of prebiotic molecules has a solid foundation from which to work.

From an observational standpoint, a dedicated campaign to identify hydroxylamine (NH₂OH), potentially a direct precursor to glycine, in the gas-phase was undertaken. No trace of NH₂OH was found. These observations motivated a refinement of the chemical models of glycine formation, and have largely ruled out a gas-phase route to the synthesis of the simplest amino acid in the ISM. A molecular mystery in the case of the carrier of a series of transitions was resolved using observational data toward a large number of sources, confirming the identity of this important carbon-chemistry intermediate B11244 as l-C₃H⁺ and identifying it in at least two new environments. Finally, the doubly-nitrogenated molecule carbodiimide HNCNH was identified in the ISM for the first time through maser emission features in the centimeter-wavelength regime.

In the laboratory, a TeraHertz Time-Domain Spectrometer was constructed to obtain the experimental spectra necessary to search for solid-phase species in the ISM in the THz region of the spectrum. These investigations have shown a striking dependence on large-scale, long-range (i.e. lattice) structure of the ices on the spectra they present in the THz. A database of molecular spectra has been started, and both the simplest and most abundant ice species, which have already been identified, as well as a number of more complex species, have been studied. The exquisite sensitivity of the THz spectra to both the structure and thermal history of these ices may lead to better probes of complex chemical and dynamical evolution in interstellar environments.

The origin of the transverse relaxation time in optically excited semiconductor quantum wells

The origin of the transverse relaxation time in optically excited semiconductor quantum wells is investigated based on the vector property of the interband transition matrix elements. The dephasing rate due to carrier-carrier (CC) scattering is found to be equal to half of the common momentum relaxation rate. The analytical expression of the polarization dephasing due to CC scattering in two-dimension is established and the dependence of the dephasing rate Gamma(cc) on the carrier density N is determined to be Gamma(cc) = constant (.) N-1/2, which is used to explain the experimental results and provides a promising physical picture. (C) 2004 Elsevier B.V. All rights reserved.

Origin of the double-peak structure in longitudinal momentum distributions for single ionization of an He atom in strong laser field

The single ionization of an He atom by intense linearly polarized laser field in the tunneling regime is studied by S- matrix theory. When only the first term of the expansion of the S matrix is considered and time, spatial distribution, and fluctuation of the laser pulse are taken into account, the obtained momentum distribution in the polarization direction of laser field is consistent with the semiclassical calculation, which only considers tunneling and the interaction between the free electron and external field. When the second term, which includes the interaction between the core and the free electron, is considered, the momentum distribution shows a complex multipeak structure with the central minimum and the positions of some peaks are independent of the intensity in some intensity regime, which is consistent with the recent experimental result. Based on our analysis, we found that the structures observed in the momentum distribution of an He atom are attributed to the " soft" collision of the tunneled electron with the core.

On the feeding of the larvae of Chironomidae during the planktonic period of life [Translation from: Nauch.Dokl.vyssh.Shk.Biol.Nauk 1 19-21, 1965]

It is known that the larvae of Chironomidae in the first stages of life after leaving the egg case, swim for a long time in a body of water. Positive reaction in light, the capability of directed swimming and passive floating in suspension allow the larvae to temporarily carry out a planktonic way of life. This study describes the behaviour of Chironomus dorsalis larvae after leaving the egg case. The feeding of chironomid larvae in the first stages of development was also described.

From organism to population: the role of life-history theory

The role of life-history theory in population and evolutionary analyses is outlined. In both cases general life histories can be analysed, but simpler life histories need fewer parameters for their description. The simplest case, of semelparous (breed-once-then-die) organisms, needs only three parameters: somatic growth rate, mortality rate and fecundity. This case is analysed in detail. If fecundity is fixed, population growth rate can be calculated direct from mortality rate and somatic growth rate, and isoclines on which population growth rate is constant can be drawn in a ”state space” with axes for mortality rate and somatic growth rate. In this space density-dependence is likely to result in a population trajectory from low density, when mortality rate is low and somatic growth rate is high and the population increases (positive population growth rate) to high density, after which the process reverses to return to low density. Possible effects of pollution on this system are discussed. The state-space approach allows direct population analysis of the twin effects of pollution and density on population growth rate. Evolutionary analysis uses related methods to identify likely evolutionary outcomes when an organism's genetic options are subject to trade-offs. The trade-off considered here is between somatic growth rate and mortality rate. Such a trade-off could arise because of an energy allocation trade-off if resources spent on personal defence (reducing mortality rate) are not available for somatic growth rate. The evolutionary implications of pollution acting on such a trade-off are outlined.

Microscopic Origin of Macroscopic Strength in Granular Media: A Numerical and Analytical Approach

Constitutive modeling in granular materials has historically been based on macroscopic experimental observations that, while being usually effective at predicting the bulk behavior of these type of materials, suffer important limitations when it comes to understanding the physics behind grain-to-grain interactions that induce the material to macroscopically behave in a given way when subjected to certain boundary conditions.

The advent of the discrete element method (DEM) in the late 1970s helped scientists and engineers to gain a deeper insight into some of the most fundamental mechanisms furnishing the grain scale. However, one of the most critical limitations of classical DEM schemes has been their inability to account for complex grain morphologies. Instead, simplified geometries such as discs, spheres, and polyhedra have typically been used. Fortunately, in the last fifteen years, there has been an increasing development of new computational as well as experimental techniques, such as non-uniform rational basis splines (NURBS) and 3D X-ray Computed Tomography (3DXRCT), which are contributing to create new tools that enable the inclusion of complex grain morphologies into DEM schemes.

Yet, as the scientific community is still developing these new tools, there is still a gap in thoroughly understanding the physical relations connecting grain and continuum scales as well as in the development of discrete techniques that can predict the emergent behavior of granular materials without resorting to phenomenology, but rather can directly unravel the micro-mechanical origin of macroscopic behavior.

In order to contribute towards closing the aforementioned gap, we have developed a micro-mechanical analysis of macroscopic peak strength, critical state, and residual strength in two-dimensional non-cohesive granular media, where typical continuum constitutive quantities such as frictional strength and dilation angle are explicitly related to their corresponding grain-scale counterparts (e.g., inter-particle contact forces, fabric, particle displacements, and velocities), providing an across-the-scale basis for better understanding and modeling granular media.

In the same way, we utilize a new DEM scheme (LS-DEM) that takes advantage of a mathematical technique called level set (LS) to enable the inclusion of real grain shapes into a classical discrete element method. After calibrating LS-DEM with respect to real experimental results, we exploit part of its potential to study the dependency of critical state (CS) parameters such as the critical state line (CSL) slope, CSL intercept, and CS friction angle on the grain's morphology, i.e., sphericity, roundness, and regularity.

Finally, we introduce a first computational algorithm to ``clone'' the grain morphologies of a sample of real digital grains. This cloning algorithm allows us to generate an arbitrary number of cloned grains that satisfy the same morphological features (e.g., roundness and aspect ratio) displayed by their real parents and can be included into a DEM simulation of a given mechanical phenomenon. In turn, this will help with the development of discrete techniques that can directly predict the engineering scale behavior of granular media without resorting to phenomenology.

Origin of Chinese ancient glasses;study on the earliest Chinese ancient glasses

The earliest Chinese ancient glasses before the West Han Dynasty (200 BC) from different regions are studied. The glass samples were unearthed from Hunan, Hubei, Yunnan, Sichuan, Guizhou, Guangdong and Xinjiang of China. The chemical composition of these glasses samples is analyzed by proton induced X-ray emission (PIXE) technique, energy dispersive X-ray fluorescence (EDXRF) method and inductively coupled plasma atomic emission spectrometry (ICP-AES). It is shown that the glass chemical compositions belong to barium-lead silicate BaO-PbO-SiO2, potash soda lime silicate K2O (Na2O)-CaO-SiO2 (K2O/Na2O > 1), soda potash lime silicate Na2O (K2O)-CaO-SiO2 (K2O/Na2O < 1) and potash silicate K2O-SiO2 glass systems, respectively. The origins of the earliest Chinese ancient glasses are discussed from the archaeological and historical points of view. These four types of Chinese ancient glasses were all made in Chinese territory using local raw materials. The glass preparation technology was related to the Chinese ancient bronze metallurgy and proto-porcelain glaze technology. The glass technology relationship between the East and the West is analyzed at the same time.

The origin of the super-resolution via a nonlinear thin film

In laser applications, resolutions beyond the diffraction limit can be obtained with a thin film of strong optical nonlinear effect. The optical index of the silicon thin film is modified with the incident laser beam as a function of the local field intensity n(r) similar to E-2(r). For ultrathin films of thickness d << lambda the transmitted light through the film forms a profile of annular rings. Therefore, the device can be related to the realization of super-resolution with annular pupils. Theoretical analysis shows that the focused light spot appears significantly reduced in comparison with the diffraction limit that is determined by the laser wavelength and the numerical aperture of the converging lens. Analysis on the additional optical transfer function due to the thin film confirms that the resolving power is improved in the high spatial frequency region. (C) 2007 Published by Elsevier B.V.

Comparison of life history parameters for landed and discarded fish captured off the southeastern United States

Commercial fisheries that are managed with minimum size limits protect small fish of all ages and may affect size-selective mortality by the differential removal of fast growing fish. This differential removal may decrease the average size at age, maturation, or sexual transition of the exploited population. When fishery-independent data are not available, a comparison of life history parameters of landed with those of discarded fish (by regulation) will indicate if differential mortality is occurring with the capture of young but large fish (fast growing phenotypes). Indications of this differential size-selective mortality would include the following: the discarded portion of the target fish would have similar age ranges but smaller sizes at age, maturation, and sexual transition as that of landed fish. We examined three species with minimum size limits but different exploitation histories. The known heavily exploited species (Rhomboplites aurorubens [vermilion snapper] and Pagrus pagrus [red porgy]) show signs of this differential mortality. Their landed catch includes many young, large fish, whereas discarded fish had a similar age range and mean ages but smaller sizes at age than the landed fish. The unknown exploited species, Mycteroperca phenax (scamp), showed no signs of differential mortality due to size-selective fishing. Landed catch consisted of old, large fish and discarded scamp had little overlap in age ranges, had significantly different mean ages, and only small differences in size at age when compared to comparable data for landed fish.

The Origin of the Florida Sponge Fishery

Sponges were used domestically by Key West, Fla., pioneers soon after the town was settled in 1822 (Collins, 1887). Fortunately, aroung 1852, it was discovered that Florida sponges were able to compete with imported sponges from the Mediterranean, and they soon became commercially successful (Moore, 1910). These Florida-caught sponges were shipped to markets in New York and sold for domestic cleaning and personal hygiene, as upholstery stuffing and packing material, and for cleaning military cannons.