Hairpin embedded DNA lattices grown on a mica substrate

Bashar, Saima; Lee, Chang-Won; Lee, Junwye; Kim, Byeonghoon H.; Gnapareddy, Bramaramba; Shin, Jihoon; Dugasani, Sreekantha Reddy; Park, Sungha

doi:10.1039/c3ra44320e

Cited by 5 publications

(5 citation statements)

References 24 publications

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“…This allows us to regulate DNA self‐assembly by tuning the DNA–surface interactions. It is related to other studies, such as blunt end stacking–driven assembly and surface assembly . However, this study showed that we could regulate DNA–DNA interactions by weak interaction (base stacking between one or two pairs of blunt ends) by DNA–surface interaction.…”

Section: Figurementioning

confidence: 55%

“…Both interactions contribute to DNA self‐assembly on the surface if the strengths of these two interactions are comparable. The effect of DNA–DNA interactions has been extensively studied, but the effect of DNA–surface interactions has barely been explored . In this report, we conducted a comprehensive study on the latter and found that DNA–surface interactions have a great effect on DNA self‐assembly on the surface.…”

Section: Figurementioning

confidence: 87%

“…Most of them are constructed in free solution, and very few studies have been devoted to assembly on solid surfaces. Recently, DNA assembly on surfaces has been studied because it offers many potential advantages . For example, DNA nanomotifs have reduced conformational freedom and higher structural rigidity, a very desired property for structural DNA nanotechnology .…”

Section: Figurementioning

confidence: 99%

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Regulating DNA Self‐assembly by DNA–Surface Interactions

Liu

Wang

et al. 2017

ChemBioChem

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DNA self-assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA-DNA interactions. When confined to surfaces, DNA-surface interactions become an additional, important factor to DNA self-assembly. However, the way in which DNA-surface interactions influence DNA self-assembly is not well studied. In this study, we showed that weak DNA-DNA interactions could be stabilized by DNA-surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds.

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Section: Figurementioning

confidence: 55%

Section: Figurementioning

confidence: 87%

Section: Figurementioning

confidence: 99%

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Regulating DNA Self‐assembly by DNA–Surface Interactions

Liu

Wang

et al. 2017

ChemBioChem

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“…Generally, DNA origami in solution starts breaking apart at about 50 °C and will completely denature at 70 °C [ 43 ]. However, during DNA origami assembly, annealing is done in the presence of excess staple strands, making it useful for growing well-formed nanostructures [ 44 , 45 , 46 ]. Pillers and Lieberman [ 31 ] studied thermal stability of DNA origami on the most common substrate, mica, using AFM and X-ray photoelectron spectroscopy to detect structural and chemical changes.…”

Section: Fabricationmentioning

confidence: 99%

Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization

et al. 2021

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Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.

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“…The advantage of DNA molecules is strengthened by their ability to be synthesised from given DNA sequences via automated processes and amplified via a polymerase chain reaction from microscopic to macroscopic quantities. Although DNA duplexes can be packed through multivalent cations and spermidines [4][5][6][7][8], the formation of artificially synthesised DNA nanostructures by complementary stickyend driven self-assembly has been recognised as one of the well-defined methods to construct various dimensional nanostructures [9][10][11][12][13][14][15][16][17][18][19][20][21]. Consequently, DNA nanotechnology might provide solutions to overcome the limitations of patterning sizes limited by the wavelength of light and nanomaterial alignment restricted by complicated geometries.…”

Section: Introductionmentioning

confidence: 99%

Binding feasibility and vibrational characteristics of single-strand spacer-added DNA and protein complexes

bashar¹,

Jo²,

Tandon³

et al. 2022

J. Phys. D: Appl. Phys.

Self Cite

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Two of the most important features in the field of nanotechnology are self-assembly with nanometre-scale precision, and the self-alignment of functionalised nanomaterials. Here, we discuss the binding feasibility of single-strand spacer-added DNA building blocks to biotin-streptavidin complexes. We use atomic force microscopy, photoluminescence spectroscopy, and dynamic simulation to study the topological, optical, and vibrational characteristics of DNA lattices. To construct the DNA lattices, we use two distinct DNA building blocks, i.e. a double-crossover tile with a biotin (DXB), and a double-crossover tile with a flexible single-strand spacer containing a biotin (DXSB). Biotinylated DXB and DXSB lattices grown on the substrate eventually attracted streptavidins (SA, a tetramer protein) and formed DXB + SA, and DXSB + SA lattices, respectively. Furthermore, we examine the feasibility of alignments of an individual DXB (DXSB) tile on SA-bound DXB (DXSB) lattices, and a SA-conjugated Au nanoparticle on DXB (DXSB) lattices. To use more than two binding sites of biotins on SA (to serve as a connector between biotinylated tiles), the introduction of flexible single-strand spacers in DX tiles helped to overcome geometrical hindrance. In addition, the photoluminescence spectra of DXB and DXSB lattices with SA–Au conjugates are analysed to understand the periodic bindings of Au nanoparticles on DXB (DXSB) lattices. We also conduct dynamics simulation of modal analysis and molecular dynamic simulation, which provide the vibrational characteristics and evidence of the importance of single-strand spacer-added DNA samples. Patterning of nanomaterials with specific functionalities with high precision using a simple method would be useful for the manufacture of high-density nanoelectronic devices and extreme-sensitivity biosensors.

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Hairpin embedded DNA lattices grown on a mica substrate

Cited by 5 publications

References 24 publications

Regulating DNA Self‐assembly by DNA–Surface Interactions

Regulating DNA Self‐assembly by DNA–Surface Interactions

Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization

Binding feasibility and vibrational characteristics of single-strand spacer-added DNA and protein complexes

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