DNA and Origami

DNA and Origami, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

DNA and Origami

Curator: Larry H. Bernstein, MD, FCAP



Practical DNA

The promise of DNA origami shows signs of coming to fruition a decade after its debut.

15 March 2016   PDF

Science seeks to understand the mechanisms of nature, to develop tools of investigation and to make useful and sometimes revolutionary things with which to build our future. And every now and again, a piece of science comes along that seems like a work of art.

All of this was exemplified by a research paper published in Nature ten years ago that, literally, produced smiles (see Nature 440, 297–302; 2006). Using an astoundingly simple and general method to assemble strands of DNA into arbitrary shapes, the research generated ‘smileys’ that graced the cover of Nature and announced the arrival of DNA origami to the world.

The robustness of this method changed the game for DNA nanotechnology, which has since developed at an astonishing pace. It is a beautiful demonstration of how science can progress.

The concept behind DNA origami was laid down in the early 1980s by crystallographer Nadrian Seeman, who realized that the ability of DNA molecules to carry and transfer information according to strict base-pairing rules could be used to rationally assemble structures with precisely controlled nanoscale features.

This unprecedented level of programmability makes DNA a unique building material. Nanodesigners have embraced the biomolecule to fabricate intricate tiled patterns, boxes with lids that can be opened and arrays of precisely located binding elements that can incorporate proteins, dyes and other functional materials into regular lattices.

Pivotal to the success of DNA as a nanoscale building material have been automated methods to synthesize short DNA molecules of any sequence. A detailed understanding of how base-pairing translates into the formation of DNA double helices has also been crucial. Such helices control the shapes into which DNA molecules with given sequences will fold.

DNA origami provides the missing ingredient: a versatile yet straightforward assembly method. Computer-aided design programs determine how DNA scaffolds can be folded to realize desired structures, as well as which short DNA strands, or staples, are needed to hold the structures in shape.

Individual structures can also be assembled into more complex patterns, and sites that bind to functional materials can be introduced at any position.

The many eye-catching structures that have been built have pleased those of us with an appreciation of beauty. But even the most creative science will ultimately face the question: what is the point?

DNA nanotechnology has long searched for relevance. It is unrivalled in its ability to build complex structures with near-atomic precision, but the results tend to be labile, soft and so small that it is a challenge to put them to practical use.

Yet applications that address basic problems in science have emerged. DNA structures can serve as tools for determining the structures of proteins or as templates for assembling electronic components and basic devices. Responsive DNA structures can target diseased cells, and artificial membrane channels formed from DNA can act as single-molecule sensors.

Real-world applications might become feasible through recent developments — for example, improvements to the folding process that reduce assembly time and boost yield. Initial steps have also been taken to efficiently pair DNA nanostructures with technologically relevant substrates.

Many challenges remain, and DNA nanotechnology is far from maturity. But a growing number of scientists are entering the field to make more than just art. Watch this space.
Nature 531, 276 (17 March 2016)   http://dx.doi.org:/10.1038/531276a


Editor’s Summary   16 March 2006

DNA origami

DNA is a popular building block for nanostructures as it combines self-assembly with programmability and a plethora of chemical techniques for its manipulation. There is an extensive literature on DNA nanomaterials, but a procedure described this week breaks many of the fabrication rules established in the field. Paradoxically, although it ignores sequence design, strand purity and strand concentration ratios, the new method yields DNA nanostructures that are larger and more complex than previously possible. The one-pot method uses a few hundred short DNA strands to ‘staple’ a very long strand into two-dimensional structures that adopt any desired shape, like the ‘nanoface’ on the cover. Individual staples can be made into nanometre-scale pixels that create surface patterns on a given 100-nm shape (like the Americas map and snowflakes), or to combine shapes into larger structures (the hexagon of triangles).

NEWS AND VIEWSNanostructures: The manifold faces of DNA

When it comes to making shapes out of DNA, the material is there, and its properties are understood. What was missing was a convincing, universal design scheme to allow our capabilities to unfold to the full.

As civilization has developed over the past 10,000 years, humankind has learned how to build larger and larger structures; over the past two decades, we have begun to learn how to build smaller and smaller structures. On page 297 of this issue1, Paul Rothemund presents a material step forward in this second arena: he describes a stunningly simple and versatile approach to the fabrication, by self-assembly, of two-dimensional DNA nanostructures of arbitrary shape.

Lloyd M. Smith   http://dx.doi.org:/10.1038/440283a   Full Text | PDF (749K)

‘Bottom-up fabrication’, which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by ‘top-down’ methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide ‘staple strands’ to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

Figure 1   Design of DNA origami.
Full size figure and legend (127K)

Figure 2   DNA origami shapes.
Full size figure and legend (81K)

Figure 3     Patterning and combining DNA origami.

Supplementary Notes 1–11
Notes on the design process; helix bending and the inter-helix gap; models and sequences; experimental methods; control experiments; patterning with dumbbell hairpins; the combination of shapes into larger structures; secondary structure of the scaffold and staples; the robustness of the scaffolded approach; the cost of the scaffold versus staples; and additiona references.

Full designs for all structures. Staple sequences are drawn out explicitly where they occur in the design. Because the designs are very large and the fonts are very small, this file will not print legibly. Instead of printing this file, open it in a PDF viewer and use the zoom feature to inspect the designs.    Download PDF file (188KB)


Designed DNA molecules: principles and applications of molecular nanotechnology

Anne Condon     Nature Reviews Genetics 7, 565-575 (July 2006) | http://dx.doi.org:/10.1038/nrg1892

Long admired for its informational role in the cell, DNA is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered DNA sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid DNA structures that serve as scaffolds for the organization of matter at the molecular scale, and can build simple DNA-computing devices, diagnostic machines and DNA motors. The integration of biological and engineering advances offers great potential for therapeutic and diagnostic applications, and for nanoscale electronic engineering.

Single-molecule chemical reactions on DNA origami

Niels V. Voigt1,2, Thomas Tørring1,2, Alexandru Rotaru1,2, Mikkel F. Jacobsen1,2, Jens B. Ravnsbæk1,2, Ramesh Subramani1,3, Wael Mamdouh1,3, Jørgen Kjems1,4, Andriy Mokhir5, Flemming Besenbacher1,3 & Kurt Vesterager Gothelf1,2
Nature Nanotechnology 5, 200 – 203 (2010)
     Published online: 28 February 2010 | doi:10.1038/nnano.2010.5

DNA nanotechnology1, 2 and particularly DNA origami3, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures4, 5, 6, 7, 8, 9, 10. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged11, 12,13. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami

Albert M. Hung1,2, Christine M. Micheel2,3, Luisa D. Bozano2, Lucas W. Osterbur2,4, Greg M. Wallraff2 & Jennifer N. Cha1,2 
Nature Nanotechnology 5, 121 – 126 (2010) Published online: 20 December 2009 | http://dx.doi.org:/10.1038/nnano.2009.450

The development of nanoscale electronic and photonic devices will require a combination of the high throughput of lithographic patterning and the high resolution and chemical precision afforded by self-assembly1, 2, 3, 4. However, the incorporation of nanomaterials with dimensions of less than 10 nm into functional devices has been hindered by the disparity between their size and the 100 nm feature sizes that can be routinely generated by lithography. Biomolecules offer a bridge between the two size regimes, with sub-10 nm dimensions, synthetic flexibility and a capability for self-recognition. Here, we report the directed assembly of 5-nm gold particles into large-area, spatially ordered, two-dimensional arrays through the site-selective deposition of mesoscopic DNA origami5 onto lithographically patterned substrates6 and the precise binding of gold nanocrystals to each DNA structure. We show organization with registry both within an individual DNA template and between components on neighbouring DNA origami, expanding the generality of this method towards many types of patterns and sizes.

DNA Origami Could Help Build Faster, Cheaper Computer Chips

American Chemical Society  http://www.scientificcomputing.com/news/2016/03/dna-origami-could-help-build-faster-cheaper-computer-chips?et_cid=5181802&et_rid=535648082

SAN DIEGO — Electronics manufacturers constantly hunt for ways to make faster, cheaper computer chips, often by cutting production costs or by shrinking component sizes. Now, researchers report that DNA, the genetic material of life, might help accomplish this goal when it is formed into specific shapes through a process reminiscent of the ancient art of paper folding.

The researchers presented their work at the 251st National Meeting & Exposition of the American Chemical Society (ACS).

Prototypes for cheaper computer chips are being built with metal-containing DNA origami structures. Courtesy of Zoie Young, Kenny Lee and Adam Woolley


Prototypes for cheaper computer chips are being built with metal-containing DNA origami structures. Courtesy of Zoie Young, Kenny Lee and Adam Woolley

“We would like to use DNA’s very small size, base-pairing capabilities and ability to self-assemble, and direct it to make nanoscale structures that could be used for electronics,” Adam T. Woolley, Ph.D., says. He explains that the smallest features on chips currently produced by electronics manufacturers are 14 nanometers wide. That’s more than 10 times larger than the diameter of single-stranded DNA, meaning that this genetic material could form the basis for smaller-scale chips.

“The problem, however, is that DNA does not conduct electricity very well,” he says. “So, we use the DNA as a scaffold and then assemble other materials on the DNA to form electronics.”

To design computer chips similar in function to those that Silicon Valley churns out, Woolley, in collaboration with Robert C. Davis, Ph.D., and John N. Harb, Ph.D., at Brigham Young University, is building on other groups’ prior work on DNA origami and DNA nanofabrication.

The most familiar form of DNA is a double helix, which consists of two single strands of DNA. Complementary bases on each strand pair up to connect the two strands, much like rungs on a twisted ladder. But to create a DNA origami structure, researchers begin with a long single strand of DNA. The strand is flexible and floppy, somewhat like a shoelace. Scientists then mix it with many other short strands of DNA — known as “staples” — that use base pairing to pull together and crosslink multiple, specific segments of the long strand to form a desired shape.

However, Woolley’s team isn’t content with merely replicating the flat shapes typically used in traditional two-dimensional circuits. “With two dimensions, you are limited in the density of components you can place on a chip,” Woolley explains. “If you can access the third dimension, you can pack in a lot more components.”

Kenneth Lee, an undergraduate who works with Woolley, has built a 3-D, tube-shaped DNA origami structure that sticks up like a smokestack from substrates, such as silicon, that will form the bottom layer of their chip. Lee has been experimenting with attaching additional short strands of DNA to fasten other components such as nano-sized gold particles at specific sites on the inside of the tube. The researchers’ ultimate goal is to place such tubes, and other DNA origami structures, at particular sites on the substrate. The team would also link the structures’ gold nanoparticles with semiconductor nanowires to form a circuit. In essence, the DNA structures serve as girders on which to build an integrated circuit.

Lee is currently testing the characteristics of the tubular DNA. He plans to attach additional components inside the tube, with the eventual aim of forming a semiconductor.

Woolley notes that a conventional chip fabrication facility costs more than $1 billion, in part because the equipment necessary to achieve the minuscule dimensions of chip components is expensive and because the multi-step manufacturing process requires hundreds of instruments. In contrast, a facility that harnesses DNA’s knack for self-assembly would likely entail much lower start-up funding, he states. “Nature works on a large scale, and it is really good at assembling things reliably and efficiently,” he says. “If that could be applied in making circuits for computers, there’s potential for huge cost savings.”


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