Zinc‐Finger Proteins for Site‐Specific Protein Positioning on DNA‐Origami Structures

Nakata, Eiji; Liew, Fong Fong; Uwatoko, Chisana; Kiyonaka, Shigeki; Mori, Yasuo; Katsuda, Yousuke; Endo, Masayuki; Sugiyama, Hiroshi; Morii, Takashi

doi:10.1002/anie.201108199

Cited by 125 publications

(93 citation statements)

References 50 publications

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“…36 The use of strong domain interactions (Zinc-finger for example) is another approach for site-specific protein-oligo coupling and can be achieved by tethering one binding domain to a protein, and the other binding domain to an oligonucleotide. 37–38 The versatility of DNA nanostructures has also been used to improve the binding affinity between molecules. The assembly of a multi-valent ligand complex was achieved by combining several individual ligands on a DNA nanostructure, where the distance between ligands was carefully controlled.…”

Section: Dna-directed Self-assemblymentioning

confidence: 99%

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

2012

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Conspectus Living systems have evolved a variety of nanostructures to control the molecular interactions that mediate many functions including the recognition of targets by receptors, the binding of enzymes to substrates, and the regulation of enzymatic activity. Mimicking these structures outside of the cell requires methods that offer nanoscale control over the organization of individual network components. Advances in DNA nanotechnology have enabled the design and fabrication of sophisticated one-, two- and three-dimensional (1D, 2D and 3D) nanostructures that utilize spontaneous and sequence specific DNA hybridization. Compared to other self-assembling biopolymers, DNA nanostructures offer predictable and programmable interactions, and surface features to which other nanoparticles and bio-molecules can be precisely positioned. The ability to control the spatial arrangement of the components while constructing highly-organized networks will lead to various applications of these systems. For example, DNA nanoarrays with surface displays of molecular probes can sense noncovalent hybridization interactions with DNA, RNA, and proteins and covalent chemical reactions. DNA nanostructures can also align external molecules into well-defined arrays, which may improve the resolution of many structural determination methods, such as X-ray diffraction, cryo-EM, NMR, and super-resolution fluorescence. Moreover, by constraining target entities to specific conformations, self-assembled DNA nanostructures can serve as molecular rulers to evaluate conformation-dependent activities. This Account describes the most recent advances in the DNA nanostructure directed assembly of biomolecular networks and explores the possibility of applying this technology to other fields of study. Recently, several reports have demonstrated the DNA nanostructure directed assembly of spatially-interactive biomolecular networks. For example, researchers have constructed synthetic multi-enzyme cascades by organizing the position of the components using DNA nanoscaffolds in vitro, or by utilizing RNA matrices in vivo. These structures display enhanced efficiency compared to the corresponding unstructured enzyme mixtures. Such systems are designed to mimic cellular function, where substrate diffusion between enzymes is facilitated and reactions are catalyzed with high efficiency and specificity. In addition, researchers have assembled multiple choromophores into arrays using a DNA nanoscaffold that optimizes the relative distance between the dyes and their spatial organization. The resulting artificial light harvesting system exhibits efficient cascading energy transfers. Finally, DNA nanostructures have been used as assembly templates to construct nanodevices that execute rationally-designed behaviors, including cargo loading, transportation and route control.

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Section: Dna-directed Self-assemblymentioning

confidence: 99%

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

2012

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“…[51] Additionally, other labs have used DNA templates and zinc finger protein fusion to engineer metabolic pathways. [52] A major setback to the use of oligomer scaffolds to alter cellular pathways is the requirement that the protein of interest be genetically tagged, thus not allowing for the reorganization of endogenous signaling pathways. In summary, the precision of base pairing, the diversity of oligonucleotide nanostructures and the ease of design has made DNA and RNA templates a helpful tool in scaffolding reactions from the molecular scale up to the organization of complex metabolic pathways, regardless of the obstacles associated with biocompatibility.…”

Section: Dna/rna Templated Reactionsmentioning

confidence: 99%

Effective Molarity Redux: Proximity as a Guiding Force in Chemistry and Biology

Hobert

Doerner

Walker

et al. 2013

Israel Journal of Chemistry

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The cell interior is a complex and demanding environment. An incredible variety of molecules jockey to identify the correct position–the specific interactions that promote biology that are hidden among countless unproductive options. Ensuring that the business of the cell is successful requires sophisticated mechanisms to impose temporal and spatial specificity–both on transient interactions and their eventual outcomes. Two strategies employed to regulate macromolecular interactions in a cellular context are co-localization and compartmentalization. Macromolecular interactions can be promoted and specified by localizing the partners within the same subcellular compartment, or by holding them in proximity through covalent or non-covalent interactions with proteins, lipids, or DNA– themes that are familiar to any biologist. The net result of these strategies is an increase in effective molarity: the local concentration of a reactive molecule near its reaction partners. We will focus on this general mechanism, employed by Nature and adapted in the lab, which allows delicate control in complex environments: the power of proximity to accelerate, guide, or otherwise influence the reactivity of signaling proteins and the information that they encode.

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“…[10] A previous study showed site-specific positioning of ZnFs on DNA origami. [11] We used a ZnF, called QNK-QNK-RHR, showing a nanomolar affinity for dsDNA.…”

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confidence: 99%

Size‐Controlled Construction of Magnetic Nanoparticle Clusters Using DNA‐Binding Zinc Finger Protein

et al. 2014

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Nanoparticle clusters (NPCs) have attracted significant interest owing to their unique characteristics arising from their collective individual properties. Nonetheless, the construction of NPCs in a structurally well-defined and size-controllable manner remains a challenge. Here we demonstrate a strategy to construct size-controlled NPCs using the DNA-binding zinc finger (ZnF) protein. Biotinylated ZnF was conjugated to DNA templates with different lengths, followed by incubation with neutravidin-conjugated nanoparticles. The sequence specificity of ZnF and programmable DNA templates enabled a size-controlled construction of NPCs, resulting in a homogeneous size distribution. We demonstrated the utility of magnetic NPCs by showing a three-fold increase in the spin-spin relaxivity in MRI compared with Feridex. Furthermore, folate-conjugated magnetic NPCs exhibited a specific targeting ability for HeLa cells. The present approach can be applicable to other nanoparticles, finding wide applications in many areas such as disease diagnosis, imaging, and delivery of drugs and genes.

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Zinc‐Finger Proteins for Site‐Specific Protein Positioning on DNA‐Origami Structures

Cited by 125 publications

References 50 publications

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

Spatially-Interactive Biomolecular Networks Organized by Nucleic Acid Nanostructures

Effective Molarity Redux: Proximity as a Guiding Force in Chemistry and Biology

Size‐Controlled Construction of Magnetic Nanoparticle Clusters Using DNA‐Binding Zinc Finger Protein

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