Chemical ligation of an entire DNA Origami nanostructure

Abstract MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

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The Art of Designing DNA Nanostructures with CAD Software

Molecules ◽

10.3390/molecules26082287 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2287

Author(s):

Martin Glaser ◽

Sourav Deb ◽

Florian Seier ◽

Amay Agrawal ◽

Tim Liedl ◽

...

Keyword(s):

Human Error ◽

Dna Nanotechnology ◽

Holliday Junctions ◽

Dna Origami ◽

Dna Nanostructures ◽

Dna Structures ◽

Current State ◽

Software Packages ◽

Wide Range ◽

Time Required

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.

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Determinants of ligand-functionalized DNA nanostructure-cell interactions

10.1101/2021.02.24.432702 ◽

2021 ◽

Author(s):

Glenn A.O. Cremers ◽

Bas J.H.M. Rosier ◽

Ab Meijs ◽

Nicholas B. Tito ◽

Sander M.J. van Duijnhoven ◽

...

Keyword(s):

Three Dimensional ◽

Dna Nanotechnology ◽

Absolute Number ◽

Design Parameters ◽

Dna Nanostructures ◽

Surface Receptors ◽

Protein Ligands ◽

Dna Nanostructure ◽

Functionalized Nanomaterials ◽

Ligand Orientation

AbstractSynthesis of ligand-functionalized nanomaterials with control over size, shape and ligand orientation, facilitates the design of tailored nanomedicines for therapeutic purposes. DNA nanotechnology has emerged as a powerful tool to rationally construct two- and three-dimensional nanostructures, enabling site-specific incorporation of protein ligands with control over stoichiometry and orientation. To efficiently target cell surface receptors, exploration of the parameters that modulate cellular accessibility of these nanostructures is essential. In this study we systematically investigate tunable design parameters of antibody-functionalized DNA nanostructures binding to therapeutically relevant receptors. We show that, although the native affinity of antibody-functionalized DNA nanostructures remains unaltered, the absolute number of bound surface receptors is lower compared to soluble antibodies and is mainly governed by nanostructure size and DNA handle location. The obtained results provide key insights in the ability of ligand-functionalized DNA nanostructures to bind surface receptors and yields design rules for optimal cellular targeting.

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DNA-Based Self-Assembly of Gold Nanostructures

Journal of Biomedical and Allied Research ◽

10.37191/mapsci-2582-4937-2(1)-014 ◽

2020 ◽

Author(s):

Song J

Keyword(s):

Gold Nanoparticles ◽

Chemical Stability ◽

Self Assembly ◽

Three Dimensional ◽

Dna Nanotechnology ◽

Dna Origami ◽

Gold Nanostructures ◽

Two Dimensional ◽

Specific Targeting ◽

Targeting Ability

Plasmonic assemblies of gold nanoparticles (AuNPs) triggered by DNA exhibited excellent biocompatibility and specific-targeting ability. Moreover, the integration of AuNPs and DNA allows the DNA scaffolds exhibit greater chemical stability and optical plasmonic properties. In this mini review, we summarized the development of DNA nanotechnology, especially DNA framework and DNA origami that were employed to fabricate two-dimensional and three-dimensional (3D) Au nanoassembled nanostructures.

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Adenita: interactive 3D modelling and visualization of DNA nanostructures

Nucleic Acids Research ◽

10.1093/nar/gkaa593 ◽

2020 ◽

Vol 48 (15) ◽

pp. 8269-8275 ◽

Cited By ~ 3

Author(s):

Elisa de Llano ◽

Haichao Miao ◽

Yasaman Ahmadi ◽

Amanda J Wilson ◽

Morgan Beeby ◽

...

Keyword(s):

Dna Nanotechnology ◽

Software Tool ◽

Building Blocks ◽

Dna Origami ◽

Dna Nanostructures ◽

User Interactions ◽

Dna Nanostructure ◽

Dna Tiles ◽

The Creation ◽

Interactive 3D

Abstract DNA nanotechnology is a rapidly advancing field, which increasingly attracts interest in many different disciplines, such as medicine, biotechnology, physics and biocomputing. The increasing complexity of novel applications requires significant computational support for the design, modelling and analysis of DNA nanostructures. However, current in silico design tools have not been developed in view of these new applications and their requirements. Here, we present Adenita, a novel software tool for the modelling of DNA nanostructures in a user-friendly environment. A data model supporting different DNA nanostructure concepts (multilayer DNA origami, wireframe DNA origami, DNA tiles etc.) has been developed allowing the creation of new and the import of existing DNA nanostructures. In addition, the nanostructures can be modified and analysed on-the-fly using an intuitive toolset. The possibility to combine and re-use existing nanostructures as building blocks for the creation of new superstructures, the integration of alternative molecules (e.g. proteins, aptamers) during the design process, and the export option for oxDNA simulations are outstanding features of Adenita, which spearheads a new generation of DNA nanostructure modelling software. We showcase Adenita by re-using a large nanorod to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

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Choice of fluorophore affects dynamic DNA nanostructures

10.1101/2020.12.12.422444 ◽

2020 ◽

Author(s):

Kevin Jahnke ◽

Helmut Grubmüller ◽

Maxim Igaev ◽

Kerstin Göpfrich

Keyword(s):

Energy Landscape ◽

Dna Nanotechnology ◽

Reaction Diffusion ◽

Md Simulations ◽

Dna Origami ◽

Dna Nanostructures ◽

Diffusion Modeling ◽

Ph Responsive ◽

Dna Nanostructure ◽

Potential Impact

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modeling, we demonstrate for twelve different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation - without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

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Minimizing Cholesterol-Induced Aggregation of Membrane-Interacting DNA Origami Nanostructures

Membranes ◽

10.3390/membranes11120950 ◽

2021 ◽

Vol 11 (12) ◽

pp. 950

Author(s):

Jasleen Kaur Daljit Singh ◽

Minh Tri Luu ◽

Jonathan F. Berengut ◽

Ali Abbas ◽

Shelley F. J. Wickham ◽

...

Keyword(s):

Dna Nanotechnology ◽

Dna Origami ◽

Second Step ◽

Dna Nanostructures ◽

Spacer Length ◽

Modified Dna ◽

Functional Membrane ◽

Cholesterol Control ◽

2D And 3D ◽

Induced Aggregation

DNA nanotechnology provides methods for building custom membrane-interacting nanostructures with diverse functions, such as shaping membranes, tethering defined numbers of membrane proteins, and transmembrane nanopores. The modification of DNA nanostructures with hydrophobic groups, such as cholesterol, is required to facilitate membrane interactions. However, cholesterol-induced aggregation of DNA origami nanostructures remains a challenge. Aggregation can result in reduced assembly yield, defective structures, and the inhibition of membrane interaction. Here, we quantify the assembly yield of two cholesterol-modified DNA origami nanostructures: a 2D DNA origami tile (DOT) and a 3D DNA origami barrel (DOB), by gel electrophoresis. We found that the DOT assembly yield (relative to the no cholesterol control) could be maximised by reducing the number of cholesterols from 6 to 1 (2 ± 0.2% to 100 ± 2%), optimising the separation between adjacent cholesterols (64 ± 26% to 78 ± 30%), decreasing spacer length (38 ± 20% to 95 ± 5%), and using protective ssDNA 10T overhangs (38 ± 20% to 87 ± 6%). Two-step folding protocols for the DOB, where cholesterol strands are added in a second step, did not improve the yield. Detergent improved the yield of distal cholesterol configurations (26 ± 22% to 92 ± 12%), but samples re-aggregated after detergent removal (74 ± 3%). Finally, we confirmed functional membrane binding of the cholesterol-modified nanostructures. These findings provide fundamental guidelines to reducing the cholesterol-induced aggregation of membrane-interacting 2D and 3D DNA origami nanostructures, improving the yield of well-formed structures to facilitate future applications in nanomedicine and biophysics.

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Multiform DNA origami arrays using minimal logic control

Nanoscale ◽

10.1039/d0nr00783h ◽

2020 ◽

Vol 12 (28) ◽

pp. 15066-15071 ◽

Cited By ~ 1

Author(s):

Congzhou Chen ◽

Jin Xu ◽

Xiaolong Shi

Keyword(s):

Dna Nanotechnology ◽

Dna Origami ◽

Dna Nanostructures ◽

Minimal Logic ◽

Logic Control ◽

Self Assembled

Self-assembled DNA nanostructures significantly contribute to DNA nanotechnology.

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Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

Current Topics in Medicinal Chemistry ◽

10.2174/1568026622666220112143401 ◽

2022 ◽

Vol 22 ◽

Author(s):

Raghu Pradeep Narayanan ◽

Leeza Abraham

Keyword(s):

Dna Nanotechnology ◽

Building Blocks ◽

Holliday Junctions ◽

Dna Origami ◽

Building Structures ◽

Dna Nanostructures ◽

3 Dimensional ◽

Scientific World ◽

2D And 3D ◽

Structural Dna Nanotechnology

Abstreact: DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the ‘tile’ based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

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DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells

Nanoscale ◽

10.1039/d0nr02361b ◽

2020 ◽

Vol 12 (27) ◽

pp. 14818-14824 ◽

Cited By ~ 1

Author(s):

Tatsuoki Maezawa ◽

Shozo Ohtsuki ◽

Kumi Hidaka ◽

Hiroshi Sugiyama ◽

Masayuki Endo ◽

...

Keyword(s):

Molecular Weight ◽

Immune Cells ◽

Three Dimensional ◽

Dna Origami ◽

Structural Flexibility ◽

Dna Nanostructures ◽

Density Dependent ◽

Dna Density

Using DNA nanostructures with almost identical molecular weight and structural flexibility, this work clearly showed that compactly packaged DNA nanostructures with high DNA density are suitable for the delivery to immune cells.

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