Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates

Surwade, Sumedh P.; Zhou, Feng; Li, Z.; Powell, A. Blair; O’Donnell, Christina; Liu, Hengzhou

doi:10.1039/c5cc08183a

Cited by 26 publications

(22 citation statements)

References 50 publications

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“…DNA origami nanostructures are also increasingly employed in various materials science applications. Many studies have used DNA origami nanostructures as templates or lithography masks in order to transfer their shapes into other biological [ 22 , [91] , [92] , [93] ], organic [ [94] , [95] , [96] , [97] ], and especially inorganic materials [ 21 , 23 , 29 , 30 , [98] , [99] , [100] , [101] ]. Even if this requires conditions that deviate from the usual solution conditions, the shapes of the DNA origami templates are often transferred in a single processing step, so that their structural stability is usually of little concern.…”

Section: Materials Science Applicationsmentioning

confidence: 99%

Structural stability of DNA origami nanostructures under application-specific conditions

Ramakrishnan

Ijäs

Linko

et al. 2018

Computational and Structural Biotechnology Journal

152

124

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With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis. Since many of those applications rely on structurally intact, well-definedDNA origami shapes, the issue of DNA origami stability under numerous application-relevant environmental conditions has received increasing interest in the past few years. In this mini-review we discuss the structural stability, denaturation, and degradation of DNA origami nanostructures under different conditions relevant to the fields of biophysics and biochemistry, biomedicine, and materials science, and the methods to improve their stability for desired applications.

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Section: Materials Science Applicationsmentioning

confidence: 99%

Structural stability of DNA origami nanostructures under application-specific conditions

Ramakrishnan

Ijäs

Linko

et al. 2018

Computational and Structural Biotechnology Journal

152

124

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“…Since the first demonstration by Rothemund in 2006 [2], DNA origami nanostructures have found their way into many different fields of fundamental and applied research [3]. For instance, DNA origami nanostructures are currently employed as drug delivery vehicles [4,5,6,7,8], sensors [9,10,11,12], templates for the fabrication of nanoelectronic [13,14,15,16] and plasmonic devices [17,18,19,20,21], substrates for single-molecule studies [22,23,24,25,26,27], and masks in molecular lithography [28,29,30,31,32]. While all these applications crucially rely on an intact DNA origami shape, many of them subject the employed DNA origami nanostructures to rather harsh treatments.…”

Section: Introductionmentioning

confidence: 99%

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

Kielar

Yang

et al. 2019

Molecules

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DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at −20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.

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“…Just ten years after their introduction, DNA origami nanostructures are widely used in various fields of applied and fundamental research. Nowadays, DNA origami act as masks in molecular lithography, templates for nanoelectronic and plasmonic device fabrication, as delivery vehicles in molecular medicine, and substrates for single‐molecule experiments . Many of these applications rely on an intact and well‐defined shape as well as tailored mechanical properties of the DNA origami.…”

mentioning

confidence: 99%

Cation‐Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride

Ramakrishnan

Krainer

Grundmeier

et al. 2017

Small

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The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na and Mg concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes.

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Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates

Cited by 26 publications

References 50 publications

Structural stability of DNA origami nanostructures under application-specific conditions

Structural stability of DNA origami nanostructures under application-specific conditions

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

Cation‐Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride

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