Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

Ijäs, Heini; Nummelin, Sami; Shen, Boxuan; Kostiainen, Mauri A.; Linko, Veikko

doi:10.3390/ijms19072114

Cited by 80 publications

(50 citation statements)

References 117 publications

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“…Like a "Swiss army knife" with many capabilities, DNA nanotechnology has the potential to create multivalent, dynamic and responsive gene delivery platforms capable of unprecedented control over targeting and delivery while integrating multiple distinct approaches using CPPs [134,135]. However, for optimization of this technology, robust and low-cost stabilization methods are critical for protecting DNA origami from low salt denaturation and enzymatic degradation in vivo.…”

Section: Dna Origamimentioning

confidence: 99%

Cell Penetrating Peptides, Novel Vectors for Gene Therapy

2020

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Cell penetrating peptides (CPPs), also known as protein transduction domains (PTDs), first identified ~25 years ago, are small, 6–30 amino acid long, synthetic, or naturally occurring peptides, able to carry variety of cargoes across the cellular membranes in an intact, functional form. Since their initial description and characterization, the field of cell penetrating peptides as vectors has exploded. The cargoes they can deliver range from other small peptides, full-length proteins, nucleic acids including RNA and DNA, liposomes, nanoparticles, and viral particles as well as radioisotopes and other fluorescent probes for imaging purposes. In this review, we will focus briefly on their history, classification system, and mechanism of transduction followed by a summary of the existing literature on use of CPPs as gene delivery vectors either in the form of modified viruses, plasmid DNA, small interfering RNA, oligonucleotides, full-length genes, DNA origami or peptide nucleic acids.

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Section: Dna Origamimentioning

confidence: 99%

Cell Penetrating Peptides, Novel Vectors for Gene Therapy

2020

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“…Structural DNA nanotechnology is developing fast into integrative fields of research with products of high complexity and functionality, with inspiring review articles published lately (Chidchob & Sleiman, ; Nummelin, Kommeri, Kostiainen, & Linko, ; Seeman & Sleiman, ). TLPs grown on origami templates may thus find their way into hierarchically organized smart hybrid materials (Hu & Niemeyer, ) and elaborate dynamic nano‐ and microstructures such as microrobots soon (Ijäs, Nummelin, Shen, Kostiainen, & Linko, ; Palagi & Fischer, ; J.‐T. Zhang et al, ).…”

Section: Bottom‐up Growth Of Lawns and Starsmentioning

confidence: 99%

From stars to stripes: RNA‐directed shaping of plant viral protein templates—structural synthetic virology for smart biohybrid nanostructures

Wege

Koch

2019

WIREs Nanomed Nanobiotechnol

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The self‐assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities—an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self‐organization of virus‐like particles. This offers great opportunities for their redesign into novel “green” carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV‐like particles (TLPs) may self‐assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'‐terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus‐deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to “cherrybombs” with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA‐based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft‐matter architectures for complex tasks. This article is categorized under: Biology‐Inspired Nanomaterials > Protein and Virus‐Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology‐Inspired Nanomaterials > Nucleic Acid‐Based Structures

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“…Connecting two thrombin-binding aptamers with a single-stranded DNA linker increased binding affinity up to 10-fold, when compared to individual aptamers [20]. Here, we used the DNA origami technique [21][22][23][24][25][26][27][28][29][30], which enables us to build dynamic Appl. Sci.…”

Section: Introductionmentioning

confidence: 99%

Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing

2019

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DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers—thrombin-binding aptamer (TBA) and HD22—in such a way that a thrombin molecule could be sandwiched by the aptamers to lock the metamolecule in a state of defined chirality. Our structure exhibited a Kd of 1.4 nM, which was an order of magnitude lower than those of the individual aptamers. The increased sensitivity arose from the avidity gained by the cooperative binding of the two aptamers, which was also reflected by a Hill coefficient of 1.3 ± 0.3. As we further exploited the strong plasmonic circular dichroism (CD) signals of the metamolecule, our method allowed one-step, high sensitivity optical detection of human thrombin proteins in solution.

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Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

Cited by 80 publications

References 117 publications

Cell Penetrating Peptides, Novel Vectors for Gene Therapy

Cell Penetrating Peptides, Novel Vectors for Gene Therapy

From stars to stripes: RNA‐directed shaping of plant viral protein templates—structural synthetic virology for smart biohybrid nanostructures

Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing

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