The Art of Designing DNA Nanostructures with CAD Software

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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Hybrid Nanoassemblies from Viruses and DNA Nanostructures

Nanomaterials ◽

10.3390/nano11061413 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1413

Author(s):

Sofia Ojasalo ◽

Petteri Piskunen ◽

Boxuan Shen ◽

Mauri A. Kostiainen ◽

Veikko Linko

Keyword(s):

Cell Activation ◽

Immune Cell ◽

Dna Nanotechnology ◽

Biological Properties ◽

Dna Nanostructures ◽

Dna Structures ◽

Nanoscale Structures ◽

Immune Cell Activation ◽

Wide Range ◽

Structural Dna Nanotechnology

Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as “structured” genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.

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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 nanotechnology approaches for microRNA detection and diagnosis

Nucleic Acids Research ◽

10.1093/nar/gkz580 ◽

2019 ◽

Vol 47 (20) ◽

pp. 10489-10505 ◽

Cited By ~ 14

Author(s):

Arun Richard Chandrasekaran ◽

Jibin Abraham Punnoose ◽

Lifeng Zhou ◽

Paromita Dey ◽

Bijan K Dey ◽

...

Keyword(s):

Dna Nanotechnology ◽

Dna Origami ◽

Great Promise ◽

Dna Nanostructures ◽

New Class ◽

Advantages And Disadvantages ◽

Critical Comparison ◽

Microrna Detection ◽

Disease Diagnostics ◽

Detection And Diagnosis

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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Visualization Design for Human-Collective Teams

Proceedings of the Human Factors and Ergonomics Society Annual Meeting ◽

10.1177/1071181319631028 ◽

2019 ◽

Vol 63 (1) ◽

pp. 417-421

Author(s):

Karina A. Roundtree ◽

Jason R. Cody ◽

Jennifer Leaf ◽

H. Onan Demirel ◽

Julie A. Adams

Keyword(s):

Human Error ◽

Information Overload ◽

Sequential Decision ◽

Infrastructure Monitoring ◽

Current State ◽

Wide Range ◽

High Workload ◽

The Individual ◽

Future Outcomes ◽

Robotic Collectives

Robotic collectives (i.e., colonies and swarms) are applicable to a wide range of applications, including environmental monitoring, search and rescue, as well as infrastructure monitoring. The presented evaluation focuses on how two visualization designs impact human-collective team performance during a best-of- n sequential decision making task with colonies of 200 agents. Traditional visualizations present all the individual robots that encompass the entirety of the collective, which may cause the human operator to suffer from information overload which hinders understanding the collective’s current state, the reasoning behind actions, and associated predictive future outcomes. Interface designs that abstract the individual collective member details and present the collective’s state are needed to alleviate high workload and mitigate human error. The evaluation determined that an abstract visualization of the collective’s state produced better overall performance than the visualization that showed all the individual agents.

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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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Regulation of 2D DNA Nanostructures by the Coupling of Tile Curvatures and Arm Twists

10.26434/chemrxiv.14755005.v2 ◽

2021 ◽

Author(s):

Chuan Jiang ◽

Biao Lu ◽

Wei Zhang ◽

Yoel P. Ohayon ◽

Caihong Ni ◽

...

Keyword(s):

Transverse Section ◽

Regular Polygon ◽

Holliday Junctions ◽

Dna Origami ◽

Dna Nanostructures ◽

Base Pairs ◽

Left Handed ◽

Different Types ◽

Sticky End ◽

Structural Descriptions

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only a theoretical approach of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists were missing. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E<sub>p/q</sub> designs (bLW tile cores joined together by inter-tile arms of an even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E<sub>p/q</sub> tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of the integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

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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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Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures

Molecules ◽

10.3390/molecules25215099 ◽

2020 ◽

Vol 25 (21) ◽

pp. 5099

Author(s):

Saminathan Ramakrishnan ◽

Sivaraman Subramaniam ◽

Charlotte Kielar ◽

Guido Grundmeier ◽

A. Francis Stewart ◽

...

Keyword(s):

Room Temperature ◽

Genetic Recombination ◽

Protein Complexes ◽

Dna Nanotechnology ◽

Holliday Junctions ◽

Dna Nanostructures ◽

Fundamental Building Block ◽

In Vitro Investigation ◽

Functional Dna

Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions.

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