1,023 research outputs found

    Man-made molecular machines: membrane bound

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    Photo- and Redox-Driven Artificial Molecular Motors

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    Directed motion at the nanoscale is a central attribute of life, and chemically driven motor proteins are nature's choice to accomplish it. Motivated and inspired by such bionanodevices, in the past few decades chemists have developed artificial prototypes of molecular motors, namely, multicomponent synthetic species that exhibit directionally controlled, stimuli-induced movements of their parts. In this context, photonic and redox stimuli represent highly appealing modes of activation, particularly from a technological viewpoint. Here we describe the evolution of the field of photo- and redox-driven artificial molecular motors, and we provide a comprehensive review of the work published in the past 5 years. After an analysis of the general principles that govern controlled and directed movement at the molecular scale, we describe the fundamental photochemical and redox processes that can enable its realization. The main classes of light- and redox-driven molecular motors are illustrated, with a particular focus on recent designs, and a thorough description of the functions performed by these kinds of devices according to literature reports is presented. Limitations, challenges, and future perspectives of the field are critically discussed

    A modular DNA signal translator for the controlled release of a protein by an aptamer

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    Owing to the intimate linkage of sequence and structure in nucleic acids, DNA is an extremely attractive molecule for the development of molecular devices, in particular when a combination of information processing and chemomechanical tasks is desired. Many of the previously demonstrated devices are driven by hybridization between DNA ‘effector’ strands and specific recognition sequences on the device. For applications it is of great interest to link several of such molecular devices together within artificial reaction cascades. Often it will not be possible to choose DNA sequences freely, e.g. when functional nucleic acids such as aptamers are used. In such cases translation of an arbitrary ‘input’ sequence into a desired effector sequence may be required. Here we demonstrate a molecular ‘translator’ for information encoded in DNA and show how it can be used to control the release of a protein by an aptamer using an arbitrarily chosen DNA input strand. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences

    Engineering a multi-functional DNA origami nanorod for the control of nanoscale processes

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    Processes that occur at the nanoscale are the foundational building blocks of our world. As such, there is considerable interest in ways to study and manipulate matter at this scale, with applications in biomedicine and other fields. DNA origami has emerged over the past decade as a promising technology for nanofabrication, offering the capacity for precise and tunable nanoscale synthesis while maintaining the ease and scale of bottom-up self-assembly. The goal of this work is to develop novel ways in which DNA origami can be used to manipulate nanoscale processes. To this end, I developed a single DNA origami nanorod which is used in two distinct studies, highlighting the multifunctionality of this structure. I first investigated the effect of iron oxide nanoparticle clustering on MRI contrast generation by organizing particles in precise patterns on the nanorod. I found that small changes in the number of attached iron oxide nanoparticles lead to significant enhancement in T2 relaxivity, while inter-particle spacing has a minimal effect. In the second part of thesis, I developed the first DNA origami molecular motor, which converts chemical energy into mechanical activity and demonstrates autonomous directed motion over micron distances. By leveraging the unique addressability of DNA origami, I found that these motors predominately exhibit a rolling motion and that this behavior can be tuned via small alterations to the nanorod. Combined, this work demonstrates two novel applications for DNA origami nanostructures. We expect this work will serve as an initial platform for further studies and open up a range of new possibilities for the use of DNA origami as MRI contrast agents and molecular motors.Ph.D

    Finite state machines implementation using DNA Techniques

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    Abstract A finite-state machine (FSM) is an abstract mathematical model of computation used to design both computer programs and sequential logic circuits. Considered as an abstract model of computation, the finite state machine is weak; it has less computational power than some other models of computation such as the Turing machine. This paper overview the finite-state automata based on Deoxyribonucleic Acid (DNA). Such automata uses massive parallel processing offered by molecular approach for computation and exhibits a number of advantages over traditional electronic implementations

    DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size

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    We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions

    Advances in colloidal manipulation and transport via hydrodynamic interactions

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    In this review article, we highlight many recent advances in the field of micromanipulation of colloidal particles using hydrodynamic interactions (HIs), namely solvent mediated long-range interactions. At the micrsocale, the hydrodynamic laws are time reversible and the flow becomes laminar, features that allow precise manipulation and control of colloidal matter. We focus on different strategies where externally operated microstructures generate local flow fields that induce the advection and motion of the surrounding components. In addition, we review cases where the induced flow gives rise to hydrodynamic bound states that may synchronize during the process, a phenomenon essential in different systems such as those that exhibit self-assembly and swarming

    Biophysics of DNA based Nanosystems Probed by Optical Nanoscopy

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    A dynamic DNA nanosystem exploits the programmable structure and energy landscape of DNA self-assembly to encode designed processes in a fuctuating molecular environment. One type of such a dynamic system, DNA walker, is reminiscent of biological motor proteins that convert chemical energy into mechanical translocation. Typical DNA walker travels tens of nanometers at a speed orders of magnitude slower than motor proteins. Two major challenges limited the development of functional DNA walkers. First, there are no suitable characterization methods that o˙er adequate spatial and temporal resolution to extract walker kinetics. Second, no guidelines have been established for the design and development of DNA walkers with specifed properties. In this work, an enzymatic DNA walker system that integrate oligonucleotides with nanomaterials is designed. This approach takes advantage of novel optical properties of nanomaterials and sub-di˙raction imaging techniques to study the kinetics and biophysical nature of synthetic DNA walkers. Design principles are extracted from walker kinetics for constructing functional walkers that can rival motor proteins. Multiple schemes are explored to regulate the walker motility so that various behaviors can be encoded into the system. This work demonstrates novel methods to design and construct molecular systems with programmed functions, which will pave the road for creating synthetic systems with encoded behaviors from the bottom up

    The Effect of Defects and Surface Modification on Biomolecular Assembly and Transport

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    Nanoscale transport using the kinesin-microtubule (MT) biomolecular system has been successfully used in a wide range of nanotechnological applications including self-assembly, nanofluidic transport, and biosensing. Most of these applications use the ‘gliding motility geometry’, in which surface-adhered kinesin motors attach and propel MT filaments across the surface, a process driven by ATP hydrolysis. It has been demonstrated that active assembly facilitated by these biomolecular motors results in complex, non-equilibrium nanostructures currently unattainable through conventional self-assembly methods. In particular, MTs functionalized with biotin assemble into rings and spools upon introduction of streptavidin and/or streptavidin-coated nanoparticles. Upon closer examination of these structures using fluorescence and electron microscopy, the structures revealed a level of irregularity including kinked and coiled domains, as well as in- and out- of -plane loops. In this work, we describe the effects of large scale “defective” segments (i.e. non-biotinylated MTs) on active assembly of nanocomposite spools. We demonstrate the preferential removal of the defective portions from spools during assembly to overcome structurally induced strain in regions that lack biotin-streptavidin bonds. Additionally, we show how the level of defective MTs affect the morphology and physical properties of the resulting nanostructures.Further, we explore alternative nanostructures for controlling transport using the kinesin-MT biomolecular system. Guiding MT transport has been achieved using lithographically patterning physical and chemical features, which have been shown to limit the MT trajectories, causing MTs to escape the barriers and lead to stalling or complete loss of MTs. Here, we demonstrate reliable guiding and transport of MTs on three different chemically modified, and structurally varying surfaces using 1) self-assembled monolayers (SAMs) with varying functional groups, 2) Fetal-bovine serum (FBS) coated SAMs to generate protein patterns, and 3) silicification of the FBS coated SAMs to preserve the surface. Overall, the work presented in this dissertation provides crucial insights for future development of dynamic and adaptable hybrid nanostructures, as well as provides biocompatible patterns to modulate MT motility with the goal of advancing self-regulating, multi-functional materials
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