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.

Part I. Influence of membrane morphology on ion-exchange and charge propagation in composite polyelectrolyte electrode coatings. Part II. Dynamic surface tension measurements of polarization relaxation at mercury pool electrodes by the method of Wilhelmy.

Part I. Novel composite polyelectrolyte materials were developed that exhibit desirable charge propagation and ion-retention properties. The morphology of electrode coatings cast from these materials was shown to be more important for its electrochemical behavior than its chemical composition.

Part II. The Wilhelmy plate technique for measuring dynamic surface tension was extended to electrified liquid-liquid interphases. The dynamical response of the aqueous NaF-mercury electrified interphase was examined by concomitant measurement of surface tension, current, and applied electrostatic potential. Observations of the surface tension response to linear sweep voltammetry and to step function perturbations in the applied electrostatic potential (e.g., chronotensiometry) provided strong evidence that relaxation processes proceed for time-periods that are at least an order of magnitude longer than the time periods necessary to establish diffusion equilibrium. The dynamical response of the surface tension is analyzed within the context of non-equilibrium thermodynamics and a kinetic model that requires three simultaneous first order processes.

Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

The impact of physical processes on algal growth

Mixing and transport processes in surface waters strongly influence the structure of aquatic ecosystems. The impact of mixing on algal growth is species-dependent, affecting the competition among species and acting as a selective factor for the composition of the biocoenose. Were it not for the ever-changing ”aquatic weather”, the composition of pelagic ecosystems would be relatively simple. Probably just a few optimally adapted algal species would survive in a given water-body. In contrast to terrestrial ecosystems, in which the spatial heterogeneity is primarily responsible for the abundance of niches, in aquatic systems (especially in the pelagic zone) the niches are provided by the temporal structure of physical processes. The latter are discussed in terms of the relative sizes of physical versus biological time-scales. The relevant time-scales of mixing and transport cover the range between seconds and years. Correspondingly, their influence on growth of algae is based on different mechanisms: rapid changes are relevant for the fast biological processes such as nutrient uptake and photosynthesis, and the slower changes are relevant for the less dynamic processes such as growth, respiration, mineralization, and settling of algal cells. Mixing time-scales are combined with a dynamic model of photosynthesis to demonstrate their influence on algal growth.

Climate forcing by changing solar radiation

By how much does changing radiation from the Sun influence Earth's climate compared with other natural and anthropogenic processes? Answering this question is necessary for making policy regarding anthropogenic global change, which must be detected against natural climate variability. Current knowledge of the amplitudes and time scales of solar radiative output variability available from contemporary solar monitoring and historical reconstructions can help specify climate forcing by changing radiation over multiple time scales.

Graphene-passivated nickel as an oxidation-resistant electrode for spintronics.

We report on graphene-passivated ferromagnetic electrodes (GPFE) for spin devices. GPFE are shown to act as spin-polarized oxidation-resistant electrodes. The direct coating of nickel with few layer graphene through a readily scalable chemical vapor deposition (CVD) process allows the preservation of an unoxidized nickel surface upon air exposure. Fabrication and measurement of complete reference tunneling spin valve structures demonstrate that the GPFE is maintained as a spin polarizer and also that the presence of the graphene coating leads to a specific sign reversal of the magneto-resistance. Hence, this work highlights a novel oxidation-resistant spin source which further unlocks low cost wet chemistry processes for spintronics devices.

Thylakoid terminal oxidases are essential for the cyanobacterium Synechocystis sp. PCC 6803 to survive rapidly changing light intensities.

Cyanobacteria perform photosynthesis and respiration in the thylakoid membrane, suggesting that the two processes are interlinked. However, the role of the respiratory electron transfer chain under natural environmental conditions has not been established. Through targeted gene disruption, mutants of Synechocystis sp. PCC 6803 were generated that lacked combinations of the three terminal oxidases: the thylakoid membrane-localized cytochrome c oxidase (COX) and quinol oxidase (Cyd) and the cytoplasmic membrane-localized alternative respiratory terminal oxidase. All strains demonstrated similar growth under continuous moderate or high light or 12-h moderate-light/dark square-wave cycles. However, under 12-h high-light/dark square-wave cycles, the COX/Cyd mutant displayed impaired growth and was completely photobleached after approximately 2 d. In contrast, use of sinusoidal light/dark cycles to simulate natural diurnal conditions resulted in little photobleaching, although growth was slower. Under high-light/dark square-wave cycles, the COX/Cyd mutant suffered a significant loss of photosynthetic efficiency during dark periods, a greater level of oxidative stress, and reduced glycogen degradation compared with the wild type. The mutant was susceptible to photoinhibition under pulsing but not constant light. These findings confirm a role for thylakoid-localized terminal oxidases in efficient dark respiration, reduction of oxidative stress, and accommodation of sudden light changes, demonstrating the strong selective pressure to maintain linked photosynthetic and respiratory electron chains within the thylakoid membrane. To our knowledge, this study is the first to report a phenotypic difference in growth between terminal oxidase mutants and wild-type cells and highlights the need to examine mutant phenotypes under a range of conditions.

Magnetic control of bioelectrocatalytic processes based on assembled iron oxide particles

A facile magnetic control system was designed in bioelectrocatalytic process based on functionalized iron oxide particles. The iron oxide particles were modified with glucose oxidase, and ferrocene dicarboxylic acid was used as electron transfer mediator. Functionalized iron oxide particles can assemble along the direction of applied magnetic field, and the directional dependence of the assembled iron oxide particles can be utilized for device purposes. We report here how such functionalized magnetic particles are used to modulate the bioelectrocatalytic signal by changing the orientation of the applied magnetic field. (C) 2008 Elsevier B.V. All rights reserved.

Simultaneous electrochemical determination of dopamine, uric acid and ascorbic acid using palladium nanoparticle-loaded carbon nanofibers modified electrode

Palladium nanoparticle-loaded carbon nanofibers (Pd/CNFs) were prepared by electrospinning and subsequent thermal treatment processes. Pd/CNFs modified carbon paste electrode (Pd/CNF-CPE) displayed excellent electrochemical catalytic activities towards dopamine (DA), uric acid (UA) and ascorbic acid (AA). The oxidation overpotentials of DA, UA and AA were decreased significantly compared with those obtained at the bare CPE. Differential pulse voltammetry was used for the simultaneous determination of DA, UA and AA in their ternary mixture.

The structural composite effect of Au-WO3-Al interconnecting electrode on performance of each unit in stacked OLEDs

In this article, we report the effects of the thickness of metal and oxide layers of the Al/WO3/Au interconnecting structure on the electrical and optical characteristics of the and bottom units of the two-unit stacked organic-light-emitting-devices (OLEDs). It is found that light emission performance of the upper unit is sensitive to the transmittance of semitransparent Al/WO3/Au structure, which can be improved by changing the thickness of each layer of the Al/WO3/Au structure. It is important to note that the introduction WO3 between Al and Au significantly enhances the current efficiency of both the upper and bottom units with respect to that of the corresponding Al/Au structure without WO3. In addition, the emission spectra of both the upper and bottom units are narrower than that of the control device due to microcavity effect. Our results indicate that the All WO3/Au interconnecting structure is a good candidate for fabricating independently controllable high efficiency stacked OLEDs.

The enhancement effect of Eu3+ on electro-oxidation of ethanol at Pt electrode

It is reported for the first time that the slow electrochemical kinetics process for the electro-oxidation of ethanol can be promoted by changing the electrochemical environment. The electro-oxidation of ethanol at a Pt electrode in the presence of Eu3+ cations was studied and an enhancement effect was exhibited. Cyclic voltammetry experiment results showed that the peak current density for the electro-oxidation of ethanol was increased in the presence of EU3+ in the ethanol solution. A preliminary discussion of the mechanism of the enhancement effect is given. This is based on a CO stripping experiment, which shows that either the onset potential or the peak potential of CO oxidation is shifted negatively after adding Eu3+ to the solution.

pH-dependent conformational changes of ferricytochrome c induced by electrode surface microstructure

pH-dependent processes of bovine heart ferricytochrome c have been investigated by electronic absorption and circular dichroism (CD) spectra at functionalized single-wall carbon 'nanotubes (SWNTs) modified glass carbon electrode (SWNTs/ GCE) using a long optical path thin layer cell. These methods enabled the pH-dependent conformational changes arising from the heme structure change to be monitored. The spectra obtained at functionalized SWNTs/GCE reflect electrode surface microstructure-dependent changes for pH-induced protein conformation, pK(a) of alkaline transition and structural microenvironment of the ferricytochrome c heme. pH-dependent conformational distribution curves of ferricytochrome c obtained by analysis of in situ CD spectra using singular value decomposition least square (SVDLS) method show that the functionalized SWNTs can retain native conformational stability of ferricytochrome c during alkaline transition.

Electrooxidation of COad intermediated from methanol oxidation on polycrystalline Pt electrode

The poisonous intermediate of methanol oxidation on a Pt electrode was validated to be COad by electrochemical method. An approximate treatment to bimolecular elementary reactions on an electrode was advanced and then was applied to the stripping normal pulse voltammetry (NPV) for complex multistep multielectron transfer processes on plane electrodes to study the kinetics of completely irreversible process Of COad oxidation to CO2. The kinetic parameters for this process, such as standard rate constant (0) and anodic transfer coefficient (alpha) for this irreversible heterogeneous electron-transfer process at electrode/solution interface and apparent diffusion coefficient (D-app) for charge-transfer process within the monolayer of COad on electrode surface, were obtained with stripping NPV method. The effect of the approximate treatment on the kinetic parameters was also analyzed.

Electrochemical detection of DNA immobilized on gold colloid particles modified self-assembled monolayer electrode with silver nanoparticle label

The target DNA was immobilized successfully on gold colloid particles associated with a cysteamine monolayer on gold electrode surface. Self-assembly of colloidal An onto a cysteamine modified gold electrode can enlarge the electrode surface area and enhance greatly the amount of immobilized single stranded DNA (ssDNA). The electrontransfer processes of [Fe(CN)(6)](4)-/[Fe(CN)(6)](3-) on the gold surface were blocked due to the procedures of the target DNA immobilization, which was investigated by impedance spectroscopy. Then single stranded target DNA immobilized on the gold electrode hybridized with the silver nanoparticle-oligonucleotide DNA probe, followed by the release of the silver metal atoms anchored on the hybrids by oxidative metal dissolution, and the indirect determination of the released solubilized Ag-1 ions by anodic stripping voltammetry (ASV) at a carbon fiber microelectrode. The results show that this method has good correlation for DNA detection in the range of 10-800 pmol/1 and allows the detection level as low as 5 pmol/1 of the target oligonucleotides.

Synthesis, characterization and fabrication on a glassy carbon electrode of a tetra-iron substituted sandwich-type pentadecatungstodiarsenate heteropolyanion

A novel sandwich-type compound, Na-12[Fe-4(H2O)(2)(As2W15O56)2].41H(2)O, has been synthesized. The compound was well-characterized by means of IR, UV-vis, W-183 NMR and elemental analyses. The compound crystallizes in the triclinic, P (1) over bar symmetry group. The structure of the compound is similar to that of Na-16[M-4(H2O)(2)(As2W15O56)(2)].nH(2)O (M = Cu, Zn, Co, Ni, Mn, Cd), and consists of an oxo-aqua tetranuclear iron core, [(Fe4O14)-O-III(H2O)(2)], sandwiched by two trivacant alpha-Wells-Dawson structural moieties, alpha-[As2W15O56]. Redoxelectrochemistry of the compound has been studied in buffer solutions at pH = 4.7 using polarography and cyclic voltammetry ( CV). The compound exhibited four one-electron couples associated with the Fe(III) center followed by three four-electron redox processes attributed to the tungsten-oxo framework. The compound-containing monolayer and multilayer films have been fabricated on a 4-aminobenzoic acid modified glassy carbon electrode surface by alternating deposition with a quaternized poly(4-vinylpyridine) partially complexed with [Os(bpy)(2)Cl](2+/-). CV, X-ray photoelectron spectroscopy (XPS), UV-vis spectroscopy and atomic force microscopy (AFM) have been used to characterize the multilayer films.