High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites

Takabayashi, Sadao; Klein, William P.; Onodera, Craig; Rapp, Blake; Flores-Estrada, Juan; Lindau, Elias; Snowball, Lejmarc; Sam, Joseph Tyler; Padilla, Jennifer E.; Lee, Jeunghoon; Knowlton, William B.; Graugnard, Elton; Yurke, Bernard; Kuang, Wan; Hughes, Will

doi:10.1039/c4nr03069a

Cited by 29 publications

(44 citation statements)

References 52 publications

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“…We chose such short additional length because oligonucleotides attached to a gold nanoparticle can be pushed and squeezed upon mechanical restrictions reducing dramatically the hydrodynamic diameter of the oligonucleotide-GNP particles. [21,32] Overall, sizes Σ = 2·(r + s) of 9 nm and 14 nm were used . 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 …”

Section: B Model Detailsmentioning

confidence: 99%

“…Among the possible 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 9 causes stated above, our CFS analysis indicates that increasing the yield of the DNA ink formation is an important factor. Therefore, the use of cyclic disulfides such as lipoic acid derivatives [13] reported to increase binding of oligonucleotides to gold surfaces combined with increased DNA ink that can bind per each OGNP, [21] would provide improved yields to our DNA origami stamp method for gold nanoparticle alignment. Figure S8 shows examples of OGNP of each class obtained in CFS runs.…”

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confidence: 99%

“…[21] Moreover, yield analysis using the CFS runs ( Figure S9) showed that Yink yields over 90% will favor chains containing 8 OGNP for the 5 nm OGNP. On the other hand, the same high yields would favor chains containing 5-6 OGNP for 10 nm OGNP.…”

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DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

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The programmability [1] and self-assembly properties of DNA provides means of precise organization of matter at the nanoscale. [2] DNA origami allows the folding of DNA into twodimensional [3] and three-dimensional [4] structures, and has been used to organize biomolecules, [2b, e, 5] nanophotonic [2a, c, f, 6] and electronic [7] components with a resolution of 6 nm / pixel. [8] Two-dimensional DNA origami has been also used as a platform to organize other chemical [9] species that can then be placed on technologically relevant substrates. [2c, 10] Nevertheless, these approaches have only used the DNA nanostructure to hold the chemical species on the surface and, to the best of our knowledge, have never been utilized to immobilize nucleic acids patterns on surfaces with sub-10 nm resolution providing an enable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 2 platform for potential applications such as multiplexed biochemical assays. [11] to the creation of metasurfaces [12] with potentially reconfigurable features. Revised ManuscriptHerein we report on the use of a two-dimensional DNA origami as a template to covalently attach DNA with a pre-programmed pattern on a surface (see Scheme 1). The method utilizes the incorporation of modified staple strands in programmed positions of the DNA origami (DNA origami stamp), acting as DNA ink. Once the DNA origami is immobilized on the surface, the modified staples can react with the surface creating a defined DNA pattern (Stamping step). The pattern can then be exposed upon denaturation of the DNA origami stamp (Unmasking step), allowing the non-bound staples to be rinsed off of the surface. As a proof-of-principle of this methodology, we have created a linear pattern of thiolmodified DNA ink on gold surfaces. The formation of the linear pattern was revealed by the successful formation of bead-on-a-string-like structures (here named "chains" for simplicity) composed of gold nanoparticles conjugated with thiol-oligonucleotides (OGNP) that are hybridized to the DNA ink pattern (Development step). The linear pattern provided a direct evidence of the stamping process and was chosen as a simple geometry that can be statistically analysed in our experimental setup. Montecarlo Simulations have been used for better understanding of our statistical results and to determine key elements governing the process that can be used for future optimization of pattern information transfer with DNA origami stamp methodology. Furthermore, we have studied the development of more complex patterns using Montecarlo Simulations.We demonstrate that our approach can be employed to form DNA patterns with sub-10 nm resolution to flat gold surfaces, an unsolved goal to date. This methodology can thus be extended to other surfaces utilizing different covalent strategies. [10b, 13] M...

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Section: B Model Detailsmentioning

confidence: 99%

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DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

et al. 2017

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“…DNA nanotubes have greater structural rigidity than single DNA duplexes (39). This makes them suitable for such applications as the alignment of proteins in solution for nuclear magnetic resonance spectroscopy (40), the construction of molecular barcodes for calibration of super-resolution microscopy methods (41,42), or for scaffolding extended linear arrays of metallic nanoparticles (43)(44)(45), which is useful for the bottom-up construction of nanowires (46,47). In addition, nanotubes can organize nanoparticles into circular and helical arrays, which can be used to construct plasmonic nanostructures (48,49) with distinct optical resonances that depend on their chirality (12).…”

Section: Introductionmentioning

confidence: 99%

Design and Synthesis of Pleated DNA Origami Nanotubes with Adjustable Diameters

Berengut

Ruan

Kawamoto

et al. 2019

Preprint

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DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a simple computational approach that determines minimallystrained DNA staple crossover locations for arbitrary nanotube internal angles. We apply the method in the design and synthesis of radially symmetric DNA origami nanotubes with arbitrary diameters and DNA helix stoichiometries. These include regular nanotubes where the wall of the structure is composed of a single layer of DNA helices, as well as those with a thicker pleated wall structure that have a greater rigidity and allow for continuously adjustable diameters and distances between parallel helices. We also introduce a DNA origami staple strand routing that incorporates both antiparallel and parallel crossovers and demonstrate its application to further rigidify pleated DNA nanotubes.

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“…Structural DNA nanotechnology provides a powerful method for designing and realizing structures at the molecular level . The specificity of complementary Watson–Crick base pair hybridization allows functionalized elements, such as quantum dots, gold nanoparticles, and fluorophores to be arranged with nanoscale precision at specific locations on DNA templates. The versatility of this approach allows for the creation of complex multidimensional shapes where the (collective) activity of pendant molecules can be evaluated in pursuit of new functionalities.…”

Section: Introductionmentioning

confidence: 99%

Utilizing HomoFRET to Extend DNA‐Scaffolded Photonic Networks and Increase Light‐Harvesting Capability

Klein

Dı́az

Buckhout‐White

et al. 2017

Advanced Optical Materials

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hybridization allows functionalized elements, such as quantum dots, [3,4] gold nanoparticles, [5][6][7] and fluorophores [8,9] to be arranged with nanoscale precision at specific locations on DNA templates. The versatility of this approach allows for the creation of complex multidimensional shapes where the (collective) activity of pendant molecules can be evaluated in pursuit of new functionalities. Furthermore, commercial availability of synthetic DNA, along with a variety of open access design tools allow for the relatively rapid design and preparation of structural DNA templates. [10,11] Over the last decade, researchers have demonstrated a variety of DNA nanostructures that have potential for applications ranging from biosensors and biocomputing to energy harvesting. [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29] For energy harvesting based applications in particular, the designs look to mimic the functional properties of light harvesting complexes from bacteria and green plants, exploiting Förster resonance energy transfer (FRET) as the underlying mechanism that moves and directs excitonic energy. [30,31] In these excitonic networks, FRET is typically between two different fluorophores (hetero-FRET) with differing excited state levels and its one-way downhill nature is used to control the directionality. [32][33][34] In order to make such devices widely applicable, an overarching and continuous functional goal is to increase their ability to harvest excitonic energy and then transfer it over multiple steps both across extended portions of the spectra and physical space.In pursuit of these same goals, we have explored a variety of DNA-based architectures displaying different densities and combinations of fluorophore types. [4,35] A purely linear doublestranded (ds) DNA scaffold displaying single copies of seven sequential donor-acceptor dyes manifested poor end-to-end energy transfer efficiency (E ee ) due to an intermediary dye acting as a strong energy sink rather than a viable relay. [36] An effective way to overcome this issue was demonstrated based on the use of DNA dendrimers. [36] These utilized AF488, Cy3, Cy3.5, Cy5, and Cy5.5 dyes assembled into sequential four or five-dye FRET cascades based on dendrimeric structures with 2:1, 3:1, and even 4:1 donor:acceptor ratios based on branching ratio. Evaluating the performance across all these assemblies revealed that although the 3:1 dendrimer performed the best, DNA-based photonic wires that exploit Förster resonance energy transfer (FRET) between pendant fluorophores to direct and focus excitonic energyhave high research interest due to their potential applications in light harvesting, biocomputing, and biosensing. One important goal with these structures is to increase their ability to harvest energy and then transfer it over multiple steps both across extended portions of the spectra and physical space. Toward these goals, incorporating extended homogeneous or homo-FRET sections into three unique FRET cascade DNA dendrimer ar...

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High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites

Cited by 29 publications

References 52 publications

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

DNA‐Origami‐Driven Lithography for Patterning on Gold Surfaces with Sub‐10 nm Resolution

Design and Synthesis of Pleated DNA Origami Nanotubes with Adjustable Diameters

Utilizing HomoFRET to Extend DNA‐Scaffolded Photonic Networks and Increase Light‐Harvesting Capability

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