Rare form: novel structures built from DNA emerge

July 20, 2015

DNA, the molecular foundation of life, has new tricks up its sleeve. The four bases from which it is composed snap together like jigsaw pieces and can be artificially manipulated to construct endlessly varied forms in two and three dimensions.

The technique, known as DNA origami, promises to bring futuristic microelectronics and biomedical innovations to market. scaffold-folding paths for different DNA shapes The images show the scaffold-folding paths for A) star shape B) 2-D Penrose tiling C) eight-fold quasicrystalline 2-D pattern D) waving grid. E) circle array. F) fishnet pattern G) flower and bird design The completed nanostructures are seen in the accompanying atomic force microscopy images. Photo by: The Biodesign Institute at Arizona State University - See more at: https://biodesign.asu.edu/news/rare-form-novel-structures-bui Download Full Image

Hao Yan, a researcher at Arizona State University’s Biodesign Institute, has worked for many years to refine the technique. His aim is to compose new sets of design rules, vastly expanding the range of nanoscale architectures generated by the method. In new research, a variety of innovative nanoforms are described, each displaying unprecedented design control.

Yan is the Milton D. Glick Distinguished Chair of Chemistry and Biochemistry and directs Biodesign’s Center for Molecular Design and Biomimetics.

In the current study, complex nanoforms displaying arbitrary wireframe architectures have been created, using a new set of design rules.

“Earlier design methods used strategies including parallel arrangement of DNA helices to approximate arbitrary shapes, but precise fine-tuning of DNA wireframe architectures that connect vertices in 3D space has required a new approach,” Yan says.

Yan has long been fascinated with Nature’s seemingly boundless capacity for design innovation. The new study describes wireframe structures of high complexity and programmability, fabricated through the precise control of branching and curvature, using novel organizational principles for the designs. (Wireframes are skeletal three-dimensional models represented purely through lines and vertices.)

The resulting nanoforms include symmetrical lattice arrays, quasicrystalline structures, curvilinear arrays, and a simple wire art sketch in the 100-nm scale, as well as 3-D objects including a snub cube with 60 edges and 24 vertices and a reconfigurable Archimedean solid that can be controlled to make the unfolding and refolding transitions between 3-D and 2-D.

The research appears in the advanced online edition of the journal Nature Nanotechnology.

In previous investigations, the Yan group created subtle architectural forms at an astonishingly minute scale, some measuring only tens of nanometers across – roughly the diameter of a virus particle. These nano-objects include spheres, spirals, flasks, Möbius forms, and even an autonomous spider-like robot capable of following a prepared DNA track.

The technique of DNA origami capitalizes on the simple base-pairing properties of DNA, a molecule built from the four nucleotides Adenine (A), Thymine (T) Cytosine (C) and (Guanine). The rules of the game are simple: A’s always pair with T’s and C’s with G’s. Using this abbreviated vocabulary, the myriad body plans of all living organisms are constructed; though duplicating even Nature’s simpler designs has required great ingenuity.

The basic idea of DNA origami is to use a length of single-stranded DNA as a scaffold for the desired shape. Base-pairing of complementary nucleotides causes the form to fold and self-assemble. The process is guided by the addition of shorter “staple strands,” which act to help fold the scaffold and to hold the resulting structure together. Various imaging technologies are used to observe the tiny structures, including fluorescence-, electron- and atomic force microscopy.

Although DNA origami originally produced nanoarchitectures of purely aesthetic interest, refinements of the technique have opened the door to a range of exciting applications including molecular cages for the encapsulation of molecules, enzyme immobilization and catalysis, chemical and biological sensing tools, drug delivery mechanisms, and molecular computing devices.

The technique described in the new study takes this approach a step further, allowing researchers to overcome local symmetry restrictions, creating wireframe architectures with higher order arbitrariness and complexity. Here, each line segment and vertex is individually designed and controlled. The number of arms emanating from each vertex may be varied from 2 to 10 and the precise angles between adjacent arms can be modified.

In the current study, the method was first applied to symmetrical, regularly repeating polygonal designs, including hexagonal, square and triangular tiling geometries. Such common designs are known as tessellation patterns. A clever strategy involving a series of bridges and loops was used to properly route the scaffold strand, allowing it to pass through the entire structure, touching all lines of the wireframe once and only once. Staple strands were then applied to complete the designs.

In subsequent stages, the researchers created more complex wireframe structures, without the local translational symmetry found in the tessellation patterns. Three such patterns were made, including a star shape, a five-fold Penrose tile and an eight-fold quasicrystalline pattern. (Quasicrystals are structures that are highly ordered but non-periodic. Such patterns can continuously fill available space, but are not translationally symmetric.)

Loop structures inserted into staple strands and unpaired nucleotides at the vertex points of the scaffold strands were also used, allowing researchers to perform precision modifications to the angles of junction arms.

The new design rules were next tested with the assembly of increasingly complex nanostructures, involving vertices ranging from two to 10 arms, with many different angles and curvatures involved, including a complex pattern of birds and flowers.

The accuracy of the design was subsequently confirmed by AFM imaging, proving that the method could successfully yield highly sophisticated wireframe DNA nanostructures. The method was then adapted to produce a number of 3-D structures as well, including a cuboctahedron, and another Archimedian solid known as a snub cube – a structure with 60 edges, 24 vertices and 38 faces, including six squares and 32 equilateral triangles.

The authors stress that the new design innovations described can be used to compose and construct any imaginable wireframe nanostructure – a significant advancement for the burgeoning field. On the horizon, nanoscale structures may one day be marshaled to hunt cancer cells in the body or act as robot assembly lines for the design of new drugs.

Richard Harth

Science writer, Biodesign Institute at ASU


Resilient cities: Changing the way we think about urban infrastructure

July 21, 2015

In the early morning of Sept. 8, 2014, rain began to fall across the Phoenix metro area. It showed no signs of stopping during the morning commute, and soon lakes were forming on streets and freeways. Drivers scrambled from their cars as floodwaters overtook their vehicles.

When the skies cleared that afternoon, nearly half of Phoenix’s annual rainfall had been dumped on the city in a matter of hours. Infrastructure built to handle rainwater and runoff – such as retention basins, storm sewers and washes – was overwhelmed. As a result, cars and homes were flooded and two people lost their lives. Flooded Tempe neighborhood Parts of the Phoenix metro area, such as this Tempe neighborhood, experienced flooding as a result of the Sept. 8, 2014, deluge. Photo by: Diane Boudreau Download Full Image

The chances of such a rain event occurring in Phoenix during a given year are only 0.2 percent. This is also known as a 500-year flood event because it is expected to be so rare as to occur only once during that period. Just a few weeks after the Sept. 8 rain, another storm soaked the city, a storm that only had a 1 percent chance of occurring (also known as a 100-year flood event).

As extreme weather events like these occur more frequently, global climate change may demand that we recalibrate our definition of “rare.”

In addition to urban flooding, global climate change is predicted to bring increased coastal flooding, like that associated with Hurricane Katrina and Superstorm Sandy, as well as extreme heat.

Historically, infrastructure to mitigate flooding and extreme heat has been designed to be fail-safe, meaning that it is designed to be fail-proof. But recently we have seen that fail-safe can be a dangerous illusion.

“The failing in these extreme weather events was that people built and trained themselves to think that events of this magnitude will never happen,” said Charles Redman, founding director and professor in the School of Sustainability at Arizona State University. “It happens now, and we can expect them to happen more frequently in the future!”

Reimagining infrastructure

Three ASU researchers from different disciplines have joined together to lead a team of 50 researchers from 15 institutions to face these challenges and to change the way we think about urban infrastructure.

Collectively they are leading the Urban Resilience to Extreme Weather-Related Events Sustainability Research Network (UREx SRN). The National Science Foundation has awarded the network $12 million over five years through its Sustainability Research Networks program, which focuses on urban sustainability. The international UREx SRN includes researchers and partner organizations across nine cities in North and South America.

“Extreme events present a great challenge to global sustainability, and urban areas are particularly vulnerable to these events, often due to their location, interdependent infrastructure and people concentration,” said Georgia Kosmopoulou, program director in economics at the National Science Foundation.

“This SRN team will develop, through a novel, more holistic approach, methods and tools to assess how infrastructure can become more resilient, providing ecosystem services, in an effort to improve social well-being. They will exploit new technologies promoting flexibility and adaptability in infrastructure that benefit urban populations. The geographical breadth of the proposal is an advantage; cities that represent alternative cultural backgrounds can offer new ideas about socio-ecological-technological infrastructure.”

Despite working in different fields, the ASU researchers leading the UREx SRN each saw a need to improve our current approach to infrastructure.

Project director Redman, an anthropologist, saw that infrastructure does not always serve populations equally. He gives the example of retention basins, used to collect storm water, which are developed into parks in some neighborhoods.

“When you drive around, the retention basins that have soccer fields in them are in the better neighborhoods. Yet it rains the same in other neighborhoods,” he said.

Project co-director Nancy Grimm is an ecologist and professor in the ASU School of Life Sciences. To her, infrastructure that incorporates elements of the natural environment into its design may be more effective in the long run.

“We're interested in letting a little bit more of nature back into the city,” Grimm said. “We can actually benefit quite a lot from using some of the characteristics of natural systems and incorporating those into our designs.”

She points to coastal wetlands and sand dunes as examples of natural infrastructure protecting urban areas from storms and flooding. Cities should be working with, instead of against, their natural ecosystem setting.

Project co-director Mikhail Chester is an engineer and assistant professor in the ASU School of Sustainable Engineering and the Built Environment. He had a lightbulb moment while driving with Grimm through north Phoenix.

“Nancy said to me, ‘How do engineers use landscape design to minimize indoor heat exposure?’ I thought about it and realized that engineers don’t think about that; landscape architects do. We realized there’s an opportunity to rethink how disciplines can come together to design infrastructure to be more resilient to extreme events,” he said.

What is UREx SRN? from ASU Research on Vimeo.

When fail-safe fails

Sewage-contaminated storm water that floods the streets and pollutes drinking water sources sounds like a problem of the developing world. But it’s actually happening in 300 cities across the U.S. because of combined sewer overflow systems where rainwater runoff and sewage is collected in the same pipes.

These systems usually deliver sewage to a sewage treatment plant, but during times of heavy rainfall the pipe capacity is exceeded and excess water is discharged without treatment directly to nearby streams and other bodies of water. Sometimes it overflows into the streets. (Phoenix has a divided overflow system and does not face this issue).

“This is not a third-world problem alone,” Redman said. “Nice icons of sustainability, like Portland, which we’re studying, have combined sewer outlets. They do get floods on their streets, and sometimes they are made up of sewage as well as rainfall. It’s an under-the-rug kind of issue that people in charge don’t talk about.”

“We’re here to say that everything is not OK,” Chester said. “We need to find a way to build a new approach to an old problem.”

The team members’ holistic approach to urban infrastructure is novel. They will evaluate the social, ecological and technical systems (SETS) related to infrastructure. This includes recognizing the values of all stakeholders, from city decision makers to the citizens who will use infrastructure; understanding the natural environment; and evaluating available technology. The result will be a suite of tools supporting the assessment and implementation of urban infrastructure that is resilient, safe-to-fail and tailored to a particular city.

“Fail-safe is built on a risk-management principle. It’s all about how often does it happen, how potentially bad is it, who does it affect. Those are the parameters you work with and you work with acceptable levels of those parameters. It leads you to build things that are bigger and heavier,” Redman said.

“Safe-to-fail has to be built on less certainty, but it also has to be built on restructuring the dynamics of the system – and that’s where SETS comes in. We think we need to really understand these dynamics better than people currently do.”

One example of fail-safe vs. safe-to-fail is the comparison of a greenbelt in Scottsdale and the Los Angeles River channel.

In Scottsdale, the Indian Bend Wash Greenbelt winds through the city in a swath of green and dappled shade. A bike path and green space along the wash improve social well-being for residents in the area. Trees and plants along the wash provide numerous ecosystem services such as creating habitat for animals, maintaining cooler air temperatures and producing oxygen. After it rains, the wash fills with storm water drained from the surrounding roads and neighborhoods. Because the wash is designed to be safe-to-fail, floodwaters do occasionally wash out the bike path and create a river – but repairs are easily made.

Alternatively, the Los Angeles River channel is designed to be fail-safe. Devastating flooding of the LA River in the 1800s resulted in a call for its taming. In the 1930s the river was converted – through feats of engineering and hundreds of hours of manual labor – from natural and meandering to cement and controlled.

While directing the river through a built channel has helped control flooding, it has removed the multifunctionality and ecosystem services that a river typically provides. In addition, the entire system could be paralyzed if one part of the structure sustains significant damage, such as from an earthquake. As a result, the City of Los Angeles has recently begun planning for transforming parts of the river to recapture parts of the lost ecosystem.

Building resilience

Creating safe-to-fail scenarios requires consideration of SETS and the current and future needs of a city. UREx SRN teams co-led by one engineer, one social scientist and one environmental scientist will be based in each partner city. This will ensure that an interdisciplinary approach will be represented across the network and will in turn produce a rich understanding of infrastructure needs and impacts across cities and cultures.

“There is a lot of opportunity to think about who is vulnerable to climate change and where they live in the city; to tailor redevelopment of infrastructure to protect the people who are the most vulnerable,” said Chester, adding that infrastructure design should be appropriate to each location and no single solution applies to all cities.

Teams in Puerto Rico, Mexico and Chile will capture Latin American attitudes in order to understand the cultural value placed on environmental amenities and financial efficiency. Our U.S. cities will look increasingly like Latin American cities, said Redman, who observes that people of Latino ethnicity make up an increasing proportion of the population in U.S. cities.

He adds: “By bringing this all together I think we may be able to really talk to people who build the future. From the first day of designing something like highways and power grids we’re going to talk about how Earth’s systems work and how human institutions react. And we’re going to build for that.

“We’re going to build infrastructure to be more resilient and equitable and not just more efficient.”

Kelsey Wharton

Science Writer, Knowledge Enterprise Development