Programmable motion of DNA origami mechanisms Marras, Alexander E.; Zhou, Lifeng; Su, Hai-Jun ...
Proceedings of the National Academy of Sciences - PNAS,
01/2015, Letnik:
112, Številka:
3
Journal Article
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DNA origami enables the precise fabrication of nanoscale geometries. We demonstrate an approach to engineer complex and reversible motion of nanoscale DNA origami machine elements. We first design, ...fabricate, and characterize the mechanical behavior of flexible DNA origami rotational and linear joints that integrate stiff double-stranded DNA components and flexible single-stranded DNA components to constrain motion along a single degree of freedom and demonstrate the ability to tune the flexibility and range of motion. Multiple joints with simple 1D motion were then integrated into higher order mechanisms. One mechanism is a crank–slider that couples rotational and linear motion, and the other is a Bennett linkage that moves between a compacted bundle and an expanded frame configuration with a constrained 3D motion path. Finally, we demonstrate distributed actuation of the linkage using DNA input strands to achieve reversible conformational changes of the entire structure on ∼minute timescales. Our results demonstrate programmable motion of 2D and 3D DNA origami mechanisms constructed following a macroscopic machine design approach.
Biosensors play increasingly important roles in many fields, from clinical diagnosis to environmental monitoring, and there is a growing need for cheap and simple analytical devices. DNA ...nanotechnology provides methods for the creation of sophisticated biosensors, however many of the developed DNA-based sensors are limited by cumbersome and time-consuming readouts involving advanced experimental techniques. Here we describe design, construction, and characterization of an optical DNA origami nanobiosensor device exploiting arrays of precisely positioned organic fluorophores. Two arrays of donor and acceptor fluorophores make up a multifluorophore Förster resonance energy-transfer pair that results in a high-output signal for microscopic detection of single devices. Arrangement of fluorophores into arrays increases the signal-to-noise ratio, allowing detection of signal output from singular biosensors using a conventional fluorescence microscopy setup. Single device analysis enables detection of target DNA sequences in concentrations down to 100 pM in <45 min. We expect that the presented nanobiosensor can function as a general platform for incorporating sensor modules for a variety of targets and that the strong signal amplification properties may allow detection in portable microscope systems to be used for biosensor applications in the field.
Nucleic acids can be used as building blocks for highly regular and complex structures at the nanoscale due to their inherent self-assembly and programmability resulting from intra- and ...inter-molecular interactions. Three-way junctions (TWJs) structure is recognized as the smallest type of junction in nucleic acids. To form TWJ nanostructures, three DNA or RNA strands with complementary segments at each end are hybridized and form a Y-shaped structure. TWJ skeletons, having three independent arms, provide multifunctional sites for beneficial amplification, recognition, and signaling purposes in specific biomolecular nanoarchitecture. In this study, we represent the superiority aspects on the achievements of the biosensors with the cooperation of DNA/RNA TWJ nanoskeletons for monitoring different targets. Moreover, some discussions are declared to achieve a perspective for developing promising TWJ-based aptasensors in the future. This in-depth study can open a constructive way for commercializing and miniaturizing TWJ-tuned aptasensors as user-friendly lab-on-chip sensing devices.
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•Nano-biotechnology has emerged as a promising route in biosensing engineering by representing the diverse DNA/RNA skeletons as smart recognition elements.•DNA/RNA skeletons based on three-way junction (TWJ) structures provide multifunctional sites for beneficial amplification, recognition, and signaling purposes.•Biosensors based on TWJ structures are ease-of-use, real-time, cost-effective, and label-free non-enzymatic sensing tools for the diagnosis of diverse targets.•We represent the superiority aspects on the achievements of biosensors with the cooperation of TWJ nano-skeletons.
A functional cancer theranostic nanoplatform is developed, specifically tailored toward the optoacoustic modality by combining gold nanorods with DNA nanostructures (D–AuNR). DNA origami is used as ...an efficient delivery vehicle owing to its prominent tumor‐targeting property. The D–AuNR hybrids display an enhanced tumor diagnostic sensitivity by improved optoacoustic imaging and excellent photothermal therapeutic properties in vivo.
ABSTRACT
Microtubules are dynamic cytoskeletal filaments that can generate forces when polymerizing and depolymerizing. Proteins that follow growing or shortening microtubule ends and couple forces ...to cargo movement are important for a wide range of cellular processes. Quantifying these forces and the composition of protein complexes at dynamic microtubule ends is challenging and requires sophisticated instrumentation. Here, we present an experimental approach to estimate microtubule-generated forces through the extension of a fluorescent spring-shaped DNA origami molecule. Optical readout of the spring extension enables recording of force production simultaneously with single-molecule fluorescence of proteins getting recruited to the site of force generation. DNA nanosprings enable multiplexing of force measurements and only require a fluorescence microscope and basic laboratory equipment. We validate the performance of DNA nanosprings against results obtained using optical trapping. Finally, we demonstrate the use of the nanospring to study proteins that couple microtubule growth and shortening to force generation.
Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have ...been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.
DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained ...challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.
The spatial configuration and optical properties of non‐photoresponsive DNA‐origami‐based plasmonic assemblies can be controlled with light using a photoresponsive medium. Upon exposure to visible light, the medium's pH decreases, inducing the formation of DNA triplex links in the plasmonic assemblies, leading to their spatial reconfiguration, which can be reversed by turning the light off.
Blood Glucose Monitoring
In article number 2208820, Qiao Jiang, Baoquan Ding, Yan Wu, Ran Liu, and co‐workers describe a fluorescence‐amplified origami microneedle (FAOM) device for quantitatively ...monitoring blood glucose. Through collaboratively integrating the advantages of fluorescence imaging, DNA origami, and the microneedle patch, the FAOM device can monitor blood glucose in real‐time in a trivially painful, highly sensitive and accurate manner, thus improving test tolerance and patient compliance.
DNA nanotechnology enables the synthesis of nanometer‐sized objects that can be site‐specifically functionalized with a large variety of materials. For these reasons, DNA‐based devices such as DNA ...origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)–polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost‐effective, and robust route to protect DNA‐based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded.
Polymeric protection: DNA origami nanostructures generally need higher ionic strengths than those of common cell culture buffers to maintain their integrity and are quickly degraded by nucleases. They can, however, be protected from these processes through the formation of polyplex micelles with poly(ethylene glycol)‐b‐polylysine.
Delivery of biomolecules to plants relies on Agrobacterium infection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional ...biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene in Nicotiana benthamiana leaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
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