International team develops novel DNA nano-engine

October 19, 2023

An international team of scientists has recently developed a novel type of nano-engine made of DNA. It is driven by a clever mechanism and can perform pulsing movements. The researchers are now planning to fit it with a coupling and install it as a drive in complex nanomachines. Their results were published today in the journal Nature Nanotechnology.

Petr Šulc, an assistant professor at Arizona State University's School of Molecular Sciences and the Biodesign Center for Molecular Design and Biomimetics, has collaborated with Professor Michael Famulok (project lead) from the University of Bonn, Germany, and Professor Nils Walter from the University of Michigan on this project. Petr Sulc sitting at a desk. Petr Šulc is an assistant professor at Arizona State University's School of Molecular Sciences and the Biodesign Center for Molecular Design and Biomimetics. Courtesy photo Download Full Image

Šulc has used his group’s computer modeling tools to gain insights into the design and operation of this leaf-spring nano-engine. The structure is comprised of almost 14,000 nucleotides, which form the basic structural units of DNA.

“Being able to simulate motion in such a large nanostructure would be impossible without oxDNA, the computer model that our group uses for design and design of DNA nanostructures,” explains Šulc. “It is the first time that a chemically powered DNA nanotechnology motor has been successfully engineered. We are very excited that our research methods could help with studying it, and are looking forward to building even more complex nanodevices in the future.”

This novel type of engine is similar to a hand grip strength trainer that strengthens your grip when used regularly. However, the motor is around 1 million times smaller. Two handles are connected by a spring in a V-shaped structure.

In a hand grip strength trainer, you squeeze the handles together against the resistance of the spring. Once you release your grip, the spring pushes the handles back to their original position. “Our motor uses a very similar principle,” says Famulok, from the Life and Medical Sciences Institute (LIMES) at the University of Bonn. “But the handles are not pressed together but rather pulled together.”

A schematic design of leaf-spring engine operation

A schematic design of leaf-spring engine operation. Courtesy image

The researchers have repurposed a mechanism without which there would be no plants or animals on Earth. Every cell is equipped with a sort of library. It contains the blueprints for all types of proteins that each cell needs to perform its function. If the cell wants to produce a certain type of protein, it orders a copy from the respective blueprint. This transcript is produced by the enzymes called RNA polymerases.

RNA polymerases drive the pulsing movements

The original blueprint consists of long strands of DNA. The RNA polymerases move along these strands and copy the stored information letter by letter.

“We took an RNA polymerase and attached it to one of the handles in our nanomachine,” explains Famulok. “In close proximity, we also strained a DNA strand between the two handles. The polymerase grabs on to this strand to copy it. It pulls itself along the strand and the nontranscribed section becomes increasingly smaller. This pulls the second handle bit by bit towards the first one, compressing the spring at the same time.”

The DNA strand between the handles contains a particular sequence of letters shortly before its end. This so-called termination sequence signals to the polymerase that it should let go of the DNA. The spring can then relax again and moves the handles apart. This brings the start sequence of the strand close to the polymerase, and the molecular copier can start a new transcription process. The cycle then repeats.

“In this way, our nanomotor performs a pulsing action,” explains Mathias Centola, who is part of the research group headed by Famulok and who carried out a large proportion of the experiments.

Leaf-spring nano engine as simulated in oxDNA model

Leaf-spring nano-engine as simulated in oxDNA model. Courtesy image

An alphabet soup serves as fuel

This motor also needs energy just like any other type of motor. It is provided by the “alphabet soup” from which the polymerase produces the transcripts. Every one of these letters (in technical terminology, nucleotides) has a small tail consisting of three phosphate groups — a triphosphate. In order to attach a new letter to an existing sentence, the polymerase has to remove two of these phosphate groups. This releases energy that it can use for linking the letters together. “Our motor thus uses nucleotide triphosphates as fuel,” says Famulok. “It can only continue to run when a sufficient number of them are available.”

The researchers were able to demonstrate that the motor can be easily combined with other structures. This should make it possible for it to, for example, wander across a surface — similar to an inchworm that pulls itself along a branch in its own characteristic style. “We are also planning to produce a type of clutch that will allow us to only utilize the power of the motor at certain times and otherwise leave it to idle,” explains Famulok. In the long term, the motor could become the heart of a complex nanomachine. “However, there is still a lot of work to be done before we reach this stage.”

Šulc's lab is highly interdisciplinary and applies broadly the methods of statistical physics and computational modeling to problems in chemistry, biology and nanotechnology. The group develops new multiscale models to study interactions between biomolecules, particularly in the context of design and simulations of DNA and RNA nanostructures and devices.

“Just as complex machines in our everyday use — planes, cars and chips in electronics — require sophisticated computer-aided design tools to make sure they perform a desired function, there is a pressing need to have access to such methods in the molecular sciences,” says Šulc.

Professor Tijana Rajh, director of the School of Molecular Sciences, said, “Petr Šulc and his group are doing extremely innovative molecular science, using the methods of computational chemistry and physics to study DNA and RNA molecules in the context of biology as well as nanotechnology. Our younger faculty members in the School of Molecular Sciences have an extraordinary record of achievement, and Professor Šulc is an exemplar in this regard."

Advances in bionanotechnology to continue

DNA and RNA are the basic molecules of life. They fulfill many functions, including information storage and information transfer in living cells. They also have promising applications in the field of nanotechnology, where designed DNA and RNA strands are used to assemble nanoscale structures and devices. As Šulc explains, “It is a little bit like playing with Lego blocks except that each Lego block is only a few nanometers (a millionth of a millimeter) in size, and instead of putting each block into the place where it should go, you put them inside a box and shake it randomly until only the desired structure comes out.

“The promising applications of this field include diagnostics, therapeutics, molecular robotics and building of new materials. My lab has developed the software to design these blocks, and we work closely with experimental groups at ASU as well as other universities in the U.S. and Europe. It is exciting seeing our methods used to design and characterize nanostructures of increasing complexity, as the field progresses and we achieve new advanced designs and successfully operate them at nanoscale."

Jenny Green

Clinical associate professor, School of Molecular Sciences


ASU awarded $10M to advance future-generation wireless networks

ASU Professor Yanchao Zhang will lead a new DOD-funded Center of Excellence to advance wireless communications

October 19, 2023

The U.S. Department of Defense has awarded Arizona State University $10 million to establish a Center of Excellence in Future Generation Wireless TechnologyThe Center of Excellence in FutureG will be directed by ASU Professor Yanchao Zhang with support from six accomplished co-principal investigators at Arizona State University and The Ohio State University: Daniel Bliss; Chaitali Chakrabarti; Antonia Papandreou-Suppappola in the School of Electrical, Computer and Energy Engineering; Robert LiKamWa in the School of Electrical, Computer and Energy Engineering and the School of Arts, Media and Engineering; Guoliang Xue in the School of Computing and Augmented Intelligence; and Ness B. Shroff at The Ohio State University. (Center of Excellence in FutureG), which seeks to advance wireless communications technology to bolster national security.

The center was awarded through the Historically Black Colleges and Universities and Minority-Serving Institutions Research and Education Program and is administered by the Army Research Laboratory. Group of researchers talking in a lab setting. Yanchao Zhang (standing), a Fulton Schools professor of electrical engineering, discusses hardware and software solutions to ensure wireless network capacity with electrical engineering graduate students. Photo by Erika Gronek/ASU Download Full Image

Yanchao Zhang, a professor of electrical engineering in the Ira A. Fulton Schools of Engineering at ASU, will lead the initiative over the next five years. Fulton Schools researchers will collaborate with researchers at The Ohio State University to drive technological advancements to address a wide spectrum of network challenges and opportunities, including signal processing technologies, distributed control and machine learning algorithms, and innovative security mechanisms.

The Center of Excellence in FutureG is strategically positioned to enhance ASU’s research and educational capabilities while positioning the university as a critical contributor to preserving the military’s technological edge in future-generation wireless, or FutureG, technology.

Pushing communications technology to new heights

FutureG networks, such as 6G and beyond, are designed to seamlessly incorporate artificial intelligence and machine learning into integrated sensing, communication and computation.

FutureG networks are distinct from existing networks like 5G due to various advances, including global coverage, faster data rates, lower delays, high-precision positioning, improved network reliability, greater energy efficiency and better security.

The Center of Excellence in FutureG seeks to gain tactical advantages for the U.S. military by using FutureG networks. The center’s team will develop fundamental hardware and software solutions to ensure extraordinary network capacity, establish scalable network control, foster intelligent and resilient network management, and fortify security and reliability. Researchers in the center also aim to develop energy-efficient system-on-a-chip technology and pioneer augmented and virtual reality applications in the FutureG realm.

Zhang says ASU’s selection as the lead institution for the new center can likely be credited to the university’s established reputation for leadership in networking technologies. He based the premise for the center on his ongoing work in the Cyber and Network Security Group, which conducts fundamental and experimental research on security and privacy issues in computer and networked systems.

“Each technical thrust within the center is guided by an eminent expert with a remarkable track record in their respective area of specialization,” says Zhang, a faculty member in the School of Electrical, Computer and Energy Engineering, part of the Fulton Schools. “Our diverse range of complementary expertise empowers us to collaboratively address the challenges presented by FutureG networks. I believe this collective strength is a key factor behind our selection by the DOD.”

The group’s focus on wireless networks and systems, artificial intelligence and machine learning has led to several research projects supported by federal research agencies.

“The FutureG Center of Excellence is a prime demonstration of ASU’s commitment to advancing wireless communications technology and recruiting and building the workforce needed to deploy it globally,” says Stephen Phillips, professor and director of the School of Electrical, Computer and Energy Engineering.

Zhang’s contributions to wireless and mobile security technology have earned him the status of fellow of the Institute of Electrical and Electronics Engineers and key leadership roles in the research community. He has chaired four workshops for the National Science Foundation and U.S. Army Research Office and collaborated with both organizations to identify critical research challenges and shape their research agendas in cybersecurity and privacy within networked systems.

An asset for the ASU community

Zhang says that beyond technological advances, the ASU community stands to benefit greatly as the home of the Center of Excellence in FutureG. He says hosting the center will further distinguish the research initiatives already being led by ASU.

“Our center’s team aspires to establish ASU as a premier leader and invaluable contributor in upholding the DOD’s technological superiority in FutureG technology, both during the project’s five-year duration and beyond,” Zhang says.

He is particularly proud of the opportunities the center will offer engineering students, especially those from communities often underrepresented in engineering and technology fields.

Kyle Squires, ASU vice provost for engineering, computing and technology and dean of the Fulton Schools, praises the center for exemplifying the Fulton Schools’ values.

“Being awarded this new center of excellence reflects the DOD’s confidence in ASU’s established leadership in areas vital to future-generation wireless technologies,” Squires said. “Not only will this center contribute advances to help support an efficient and reliable communications infrastructure, it’s fulfilling one of the university’s core missions to offer learning opportunities to a broader community through purposeful, impactful research.”

Named a Hispanic-Serving Institute, or HSI, in 2022, ASU is committed to serving a diverse community. The Center of Excellence in FutureG at ASU is one of four centers across the U.S. being established to help increase the number of graduates in STEM fields, including those from underrepresented minorities. 

“Establishing the centers at minority-serving institutions also strengthens the STEM pipeline by improving the skill sets of future scientists and engineers, preparing them for careers that will help advance the department’s research enterprise,” said DOD HBCU/MI Program and Outreach Director Evelyn Kent in an Oct. 17 press release.

Hannah Weisman

Science writer, Ira A. Fulton Schools of Engineering, Marketing and Communications