A virus-based single-enzyme nanoreactor

Comellas-Aragonès, Marta; Engelkamp, Hans; Claessen, Victor I.; Sommerdijk, Nico A. J. M.; Rowan, Alan E.; Christianen, Peter C. M.; Maan, J. C.; Verduin, B.J.M.; Cornelissen, Jeroen J. L. M.; Nolte, Roeland J. M.

doi:10.1038/nnano.2007.299

Cited by 409 publications

(344 citation statements)

References 34 publications

(33 reference statements)

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“…It has been used to demonstrate that DNA conformational flexibility could be exploited to assemble nanostructures that are otherwise difficult to prepare. DNA nanocages have attracted significant research efforts (9-14, 16, 30) not only because they are interesting structures, but also because they could potentially serve as encapsulation agents (31,32), nanoreactors (33), and organizational scaffolds (34,35).…”

Section: Resultsmentioning

confidence: 99%

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Zhang¹,

He³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

247

244

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Molecular self-assembly is a promising approach to the preparation of nanostructures. DNA, in particular, shows great potential to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range of nanostructures. It is generally believed that rigidities of DNA nanomotifs (tiles) are essential for programmable self-assembly of well defined nanostructures. Recently, we have shown that adequate conformational flexibility could be exploited for assembling 3D objects, including tetrahedra, dodecahedra, and buckyballs, out of DNA three-point star motifs. In the current study, we have integrated tensegrity principle into this concept to assemble well defined, complex nanostructures in both 2D and 3D. A symmetric five-pointstar motif (tile) has been designed to assemble into icosahedra or large nanocages depending on the concentration and flexibility of the DNA tiles. In both cases, the DNA tiles exhibit significant flexibilities and undergo substantial conformational changes, either symmetrically bending out of the plane or asymmetrically bending in the plane. In contrast to the complicated natures of the assembled structures, the approach presented here is simple and only requires three different component DNA strands. These results demonstrate that conformational flexibility could be explored to generate complex DNA nanostructures. The basic concept might be further extended to other biomacromolecular systems, such as RNA and proteins.icosahedron ͉ three-dimensional ͉ polyhedron ͉ cryo-EM ͉ molecular cages M olecular self-assembly provides a bottom-up approach to the preparation of nanostructures (1-3). DNA, in particular, shows great potential to be a superb molecular system (4). In the last 20 years, DNA has been explored as building blocks for nanoconstructions, including preparation of periodic and aperiodic 2D nanopatterns (5-8) and 3D polyhedra (9-14). Most of the branched DNA structures are intrinsically flexible and are not suitable building blocks for construction of well defined geometric structures. How to overcome the conformational flexibility of branched DNA structures is a major challenge in structural DNA nanotechnology. In the last decade, a series of rigid structural motifs have been successfully engineered that lead to the rapid evolution of structural DNA nanotechnology (4). However, with more experience and knowledge, it is possible to controllably introduce the conformational flexibility to prepare complex DNA nanostructures (15). In our recent study of 3D self-assembly of DNA three-point-star tiles (16), we found that DNA tetrahedra could be readily assembled, and the tetrahedra are well behaved during sample characterizations. In contrast, DNA dodecahedra and buckyballs have significantly lower assembly yields and are prone to deformation. This phenomenon can be explained by the geometrical differences of these structures. Tetrahedra consist of triangular faces, but others do not. According to tensegrity principle, triangular faces will lead to rigid s...

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Section: Resultsmentioning

confidence: 99%

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Zhang¹,

He³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

247

244

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“…Even in nano-reactors, it is still a major challenge to cleave chemical bonds by design and the performance of nano-catalysts strongly depends on their dimension and geometry. 3 The Scanning Tunneling Microscope (STM) is an ideal tool for the manipulation and characterization of chemical bonds in the nano-cavity that is formed by the STM tip and substrate and contains a single molecule. [4][5][6][7][8] The geometry and size of STM nanocavities can be precisely tuned by changing the substrate topography and the tip-substrate distance.…”

mentioning

confidence: 99%

Trapping and Characterization of a Single Hydrogen Molecule in a Continuously Tunable Nanocavity

Wang

et al. 2015

J. Phys. Chem. Lett.

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“…Even with their simple composition, viruses have evolved to attain the capability to enter a cell and utilize the host to replicate their genomes, re-assemble, and disseminate their progeny. Over the past century, these processes have been extensively studied to achieve better control of viral diseases, especially in plants; moreover, at present, attempts are being made in nanotechnology and biotechnology to engineer viruses for diagnostic/ therapeutic applications, [13][14][15][16][17] nanomaterial synthesis, 18,19 protein recombination, 20,21 energy harvesting, 22,23 and even the fabrication of electronic components. 24,25 These new approaches to virus engineering involve eliminating the viral disease-causing characteristics or, more accurately, incorporating only the inherent circulatory and targeting capabilities of viruses into the design of applications.…”

Section: Introductionmentioning

confidence: 99%

Bioinspired optical antennas: gold plant viruses

et al. 2015

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The ability to capture the chemical signatures of biomolecules (i.e., electron-transfer dynamics) in living cells will provide an entirely new perspective on biology and medicine. This can be accomplished using nanoscale optical antennas that can collect, resonate and focus light from outside the cell and emit molecular spectra. Here, we describe biologically inspired nanoscale optical antennas that utilize the unique topologies of plant viruses (and thus, are called gold plant viruses) for molecular fingerprint detection. Our electromagnetic calculations for these gold viruses indicate that capsid morphologies permit high amplification of optical scattering energy compared to a smooth nanosphere. From experimental measurements of various gold viruses based on four different plant viruses, we observe highly enhanced optical cross-sections and the modulation of the resonance wavelength depending on the viral morphology. Additionally, in label-free molecular imaging, we successfully obtain higher sensitivity (by a factor of up to 10 6 ) than can be achieved using similar-sized nanospheres. By virtue of the inherent functionalities of capsids and the plasmonic characteristics of the gold layer, a gold virus-based antenna will enable cellular targeting, imaging and drug delivery. Keywords: molecular sensor; nanophotonics; optical antenna; optical spectroscopy; plant virus; plasmonics; plasmonic resonant energy transfer (PRET); surface enhanced Raman scattering (SERS) INTRODUCTIONIn current nanotechnology, the development of nanoscale optical antennas that are capable of receiving and transmitting light in unique light-electron interactions called 'surface plasmons' 1 is of considerable interest because of the potential applications of such antennas in molecular detection, 2-4 multiple harmonic generation, 5,6 plasmonic photovoltaics, 7 optoelectronics, 8 negative-index materials 9 and more. In particular, the use of an optical antenna as a molecular sensor permits the dynamic detection of chemical signatures in a non-invasive and label-free manner. Moreover, the detection sensitivity can reach the single-molecule level. 3,10 These powerful characteristics distinguish the optical antenna as a potential method for unraveling the inherent complexity of biological systems (i.e., cells), which is a difficult task using current techniques.To be suitable for use as a biomolecular sensor in cellular systems, an optical antenna should not interfere with cellular components and should be efficiently accessible (or mobile) to subcellular regions. These characteristics can be achieved by exploiting the nanoscale size and chemical stability of non-fixed, biochemical-moiety-containing nanoparticles. In this context, gold nanospheres have been successfully demonstrated to be capable of actively targeting subcellular regions and carrying imaging agents and drugs. 11,12 However, the smooth surfaces of chemically synthesized gold nanoparticles do not impart these nanoparticles with ideal functionality for molecular fingerprint detect...

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A virus-based single-enzyme nanoreactor

Cited by 409 publications

References 34 publications

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

Trapping and Characterization of a Single Hydrogen Molecule in a Continuously Tunable Nanocavity

Bioinspired optical antennas: gold plant viruses

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