DNA Tile Based Self‐Assembly: Building Complex Nanoarchitectures

Lin, Chenxiang; Liu, Yan; Rinker, Sherri

doi:10.1002/cphc.200600260

Cited by 369 publications

(267 citation statements)

References 70 publications

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“…We started to build the 3D model from building the tile by joining A-form RNA duplexes with T-junction loop and 5-nt loop that generated 90°turn. T-junction loop was adapted from a DNA T-junction [19][20][21] and generated in computer software Win COOT to ensure the T-shape. To manually connect the 6-nt loop with the duplex (indicated as P a in Fig.…”

Section: Methodsmentioning

confidence: 99%

“…In nanoengineering, DNA has been well explored for nanoconstruction and a range of well-behaved DNA building blocks (tiles) have been developed 17,18 . One single DNA tile can self-oligomerize/ polymerize into nanocages, one-dimensional nanotubes, twodimensional (2D) arrays and three-dimensional (3D) crystals 19 . In contrast, no RNA tile has been developed to have enough structural rigidity to homopolymerize/oligomerize into a defined large architecture.…”

mentioning

confidence: 99%

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De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

Liu

Jiang

et al. 2015

Nat Commun

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Rational, de novo design of RNA nanostructures can potentially integrate a wide array of structural and functional diversities. Such nanostructures have great promises in biomedical applications. Despite impressive progress in this field, all RNA building blocks (or tiles) reported so far are not geometrically well defined. They are generally flexible and can only assemble into a mixture of complexes with different sizes. To achieve defined structures, multiple tiles with different sequences are needed. In this study, we design an RNA tile that can homo-oligomerize into a uniform RNA nanostructure. The designed RNA nanostructure is characterized by gel electrophoresis, atomic force microscopy and cryogenic electron microscopy imaging. We believe that development along this line would help RNA nanotechnology to reach the structural control that is currently associated with DNA nanotechnology.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

Liu

Jiang

et al. 2015

Nat Commun

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“…8 However, the DNA junction (a 4-arm DNA junction) amplified there had a relatively simple structure. Therefore, the following important questions remained open: [1] can RCA replicate DNA nano-objects with more complex secondary structures; and [2] what would be the replication efficiency if it can? In this study, we set out to address these two questions by using RCA to replicate a paranemic crossover (PX) DNA molecule.…”

Section: Introductionmentioning

confidence: 99%

Rolling Circle Enzymatic Replication of a Complex Multi-Crossover DNA Nanostructure

et al. 2007

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Nature has evolved replicable biological molecules, such as DNA, as genetic information carriers. The replication process is tightly controlled by complicated cellular machinery. It is interesting to ask if artificial DNA nano-objects with a complex secondary structure can be replicated in the same way as simple DNA double helices. Here we demonstrate that paranemic crossover DNA, a structurally complicated multi-crossover DNA molecule, can be replicated successfully using Rolling Circle Amplification (RCA). The amplification efficiency is moderate with high fidelity, confirmed by native PAGE, thermal transition study and Ferguson analysis. The structural details of the DNA structure after the full replication circle are verified by hydroxyl radical autofootprinting. We conclude that RCA can serve as a reliable method to replicate complex DNA structures. We also discuss the possibility of using viruses and bacteria to clone artificial DNA nano-objects. The findings that single stranded paranemic crossover DNA molecules can be replicated by DNA polymerase will not only be useful in nanotechnology, but may have implications for the possible existence of such complicated DNA structures in nature.

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“…In a recent study, "DNA origami" for fabricating two-dimensional nanostructures has been developed by Rothemund and allows the assembly of long single-stranded DNA and several oligonucleotides. 4 In addition, various shapes of DNA nanostructures, such as tiles, [5][6][7] tubes, 8 and six-point stars 9 have been developed by research groups. Moreover, by employing biotin-conjugated DNA and streptavidin, nucleic acid supercoiling has been proposed by Niemeyer and coworkers as a technique for the ionic switching of DNA-nanoparticle networks.…”

Section: The Fabrication Of Biomolecular Devices Using Dna and Proteinsmentioning

confidence: 99%

MEMS/NEMS-based Devices for Bio-measurements

Yanagida

2017

Electrochemistry

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Recently, the development of fabrication technology has simplified the construction of micro/nano electricalmechanical systems (MEMS/NEMS). For example, bottom-up techniques allowing the deposition of atoms and molecules to fabricate nanostructures have been studied. Molecular self-assembly using biomolecules has become an important process for the fabrication of nanostructures through bottom-up techniques. Of the various biomolecules, DNA has several advantages such as ease of synthesis, and well-developed cut-and-paste techniques that are suitable for nanostructure fabrication. Also, analytical methods that enable detection of the activity of living cells and biomolecules are critical for biomedical sensing applications because these substrates are the basis of life. MEMS/NEMS technologies enable the micro/nanometer-scale construction of many types of devices and thus hold great potential for biotechnology and biomedical sensing applications. Consequently, numerous studies have been performed using cell-based micro-devices based on MEMS/NEMS technologies. BioMEMS/NEMS devices will become powerful tools for the measurement of biological and biomedical functions.

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DNA Tile Based Self‐Assembly: Building Complex Nanoarchitectures

Cited by 369 publications

References 70 publications

De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

Rolling Circle Enzymatic Replication of a Complex Multi-Crossover DNA Nanostructure

MEMS/NEMS-based Devices for Bio-measurements

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