DNA-based robots could form a massive part of the medicine of the future and a new tool could design incredibly complex nanomachines in a matter of minutes rather than days.
This “airplane,” made of strands of DNA, is 1000 times smaller than the width of a human hair. Image Credit: The Ohio State University.
The future of drug and medicine delivery is very much linked to the creation of nanomachines as is the detection of hazardous pathogens within our bodies. The nanomachine revolution is now so sophisticated that scientists can use DNA to create nanodevices that can be employed in not just medicines, but also in fields as diverse as nanomanufacturing, synthetic biology, biosensing, and biophysics.
One challenge that exists between current research and the widespread application of DNA-based nanomachines is the fact that current creation methods hinge on geometric design, making functional properties such as force-response or actuation behavior difficult to build in.
These properties may have just become more achievable thanks to research emerging from Ohio State University.
A team of researchers hailing from the institute and led by former engineering doctoral student Chao-Min Huang have unveiled a new tool which they say can design complex DNA robots in a matter of minutes. The development is a significant improvement on current platforms which can take days to create a design.
The team’s mechanism has been labeled MagicDNA and is discussed in a paper published in the latest edition of the journal Nature Materials¹.
“There is getting to be more and more commercial interest in DNA nanotechnology,” says Carlos Castro a professor of mechanical and aerospace engineering at Ohio State, and one of the study’s co-authors.
I think in the next five to 10 years we will start seeing commercial applications of DNA nanodevices and we are optimistic that this software can help drive that.
Carlos Castro, Ohio State University
MagicDNA Points the Way to Complex DNA Devices
The team’s MagicDNA software gives researchers a method of taking strands for DNA and uniting them in complex structures. It combines computer-aided engineering based on coarse-grained molecular dynamics with a versatile computer-aided design approach that combines top-down automation with a bottom-up focus on the control of geometry.
The framework allows the quick construction of large assemblies with multiple components. Even though the system is fully automated it allows designers to finely control properties of the DNA such as its geometry, mechanical structure, and dynamical action.
These designs can include moving elements like rotors and hinges, parts that allow the nano-machines to perform a wide range of jobs.
“Previously, we could build devices with up to about six individual components and connect them with joints and hinges and try to make them execute complex motions,” says Hai-Jun Su, professor of mechanical and aerospace engineering at Ohio State and one of the paper’s co-authors. “With this software, it is not hard to make robots or other devices with upwards of 20 components that are much easier to control.”
One of the advantages of the team’s system is that it allows scientists to design a nanomachine in full 3D throughout the creation process. Current methods only allow the design to be started in 2D which then must be mapped onto a 3D model.
This means that these designs could not be too complex. MagicDNA opens the doorway to this complexity, and added complexity means wider applicability.
Allowing for Bottom-Up and Top-Down Design in Record Time
Cutting out the middle-man of mapping a 2D design onto a 3D structure speeds the nanomachine design process up significantly. The team believes that their system could make the difference between getting a new design to where it is needed in minutes rather than days.
“Researchers have been doing this for a number of years with slower tools with tedious manual steps,” says Castro. “But now, nanodevices that may have taken us several days to design before now take us just a few minutes.”
In addition to this, the MagicDNA system allows designers to select how they build their nanomachines.
Users can work from the bottom-up — taking individual DNA strands and organizing them into a specific structure. Alternatively, the system also allows users to take a top-down approach which means they can first decide on their device’s geometrical shape and then automate the process that brings DNA together to form it.
The MagicDNA system also lets scientists run simulations of how their DNA-based nanomachines will operate in the real world. This is a massive bonus when dealing with devices of increasing complexity.
“As you make these structures more complex, it is difficult to predict exactly what they are going to look like and how they are going to behave,” Castro adds.“It is critical to be able to simulate how our devices will actually operate. Otherwise, we waste a lot of time.”
Demonstrating the Usefulness of the MagicDNA System
To demonstrate the system’s abilities, co-author Anjelica Kucinic, a doctoral student in chemical and biomolecular engineering at Ohio State, created a range of designs and characterized them.
These designs included robot arms with claw parts that could grasp and pick up items, and a structure resembling an airplane — albeit measuring just less than one-thousandth of a human hair.
The complexity of these nanomachines means they could perform multiple tasks. That means that a DNA robot that delivers a drug could also hang around the body looking for harmful pathogens and responding to their presence by releasing further doses.
“But a more complex device may not only detect that something bad is happening but can also react by releasing a drug or capturing the pathogen,” says Castro.“We want to be able to design robots that respond in a particular way to a stimulus or move in a certain way.”
For the foreseeable future, the software will be utilized at Universities and in research labs, but the team envisions bigger prospects for MagicDNA.
Speaking about the system, Su concludes: “It is a huge step in our ability to design nanodevices that can perform the complex actions that we want them to do.”
References and Further Reading
¹ Huang. C-M., Kucinic. A., Johnson. J. A., et al, , ‘Integrated computer-aided engineering and design for DNA assemblies,’ Nature Materials, [https://doi.org/10.1038/s41563-021-00978-5]