Designing synthetic DNA nanoparticles that assemble into tubules

How does nature assemble nanoscale structures? Unlike the typical top-down methods for manufacturing, biological systems manufacture functional nanomaterials from the bottom up using a process called self-assembly. In self-assembly, individual ‘building blocks’ are encoded with instructions about how to interact with one another. As a result, ordered structures spontaneously form from a soup of building blocks through thermal fluctuations alone. Famous examples of self-assembling structures in nature include viral capsids, which protect the genetic material and orchestrate viral infections, and microtubules, which form part of the highway systems used for intracellular transportation. However, until recently, manufacturing similarly complex nanostructures from synthetic materials was out of reach because there were no methods for synthesizing building blocks with the kinds of complex geometries and interactions common to biological molecules.

Assembled Tubules Under TEM

In collaboration with the Dietz Lab at the Technical University of Munich and the Grason Group at the University of Massachusetts Amherst, a team of scientists from the Rogers Lab, Hagan Group,  and Fraden Lab in the Department of Physics at Brandeis developed a class of nanoscale particles that can overcome this hurdle. They designed and synthesized triangular building blocks using a technique known as DNA origami, in which the single-stranded DNA genome from a bacteriophage is ‘folded’ into a user-prescribed 3D shape using a cocktail of short DNA oligonucleotides. The triangular particles that they designed bind to other triangles through specific edge-edge interactions with bond angles that can be independently tuned to make a surface with programmable curvature.

Daichi Hayakawa, a Ph.D. student in the Rogers Lab, tuned the triangle design so that the particles would spontaneously assemble into a tubule with a programmed width and chirality. Interestingly, the assembled tubules were highly polymorphic. In other words, the width and chirality varied from tubule to tubule. Working together with the Hagan Group in Physics, the team rationalized this observation by considering the ‘softness’ of the edge interaction, which allows thermal fluctuations to steer assembly away from the target geometry. To constrain this polymorphism, the research team came up with an alternative method. By using more than one distinct triangle type to assemble a single tubule geometry, they found that they could eliminate some of these off-target structures, thereby making tubule assembly more specific.

In summary, this work highlights two avenues for increasing the fidelity of self-closing structures self-assembled from simple building blocks: control of the curvature through precise geometrical design and addressable complexity through increasing the number of unique species in the assembly mixture. Not only will this result be useful for constructing self-closing nanostructures through self-assembly, but it may also help us understand the role of symmetry and complexity in other self-closing structures found in nature.

Publication:

Geometrically programmed self-limited assembly of tubules using DNA origami colloids. Daichi Hayakawa, Thomas E. Videbaek, Douglas M. Hall and W. Benjamin Rogers.  Proc Natl Acad Sci USA. 2022 Oct 25;119(43):e2207902119.

SciFest XI to be held on Thursday, 8/11/22

Save the Date for SciFest!

SciFest, the Division of Science’s annual celebration of undergraduate research, is a poster session featuring work done by undergraduates in Brandeis laboratories each summer. This is a capstone event for the undergraduate researchers where they can present the results of their research to peers, grad students, and faculty.

Join us for the SciFest XI which will be held on Thursday, August 11, 2022 in the Shapiro Science Center.

Divisional Prize Instructors design & teach new classes

The University Prize Instructorships have been a great opportunity for our graduate students to gain experience designing and teaching their own class, and a great opportunity for our undergraduates to engage in learning new areas with a great instructor. When the UPIs were put on hiatus during the pandemic, the Division of Science stepped in to keep this opportunity going for our community. We are really excited for the new courses that will be taught by Xin Yao Lin and Narges Iraji in the Spring 2022 semester- “Science versus Science Fiction” by Narges Iraji, and “Technology Use and Well-Being: Multidisciplinary Perspectives”.

Xin Yao Lin

Xin Yao LinI am very honored and delighted to receive the Divisional Prize Instructorship. I am currently a 5th-year psychology PhD student and I will be teaching a psychology course entitled “PSYC 55B: Technology Use and Well-Being: Multidisciplinary Perspectives” in the spring of 2022. The increase in technology use is changing how we connect, feel, and act. We are relying on technology more than ever, but whether the increased usage of technology is beneficial or detrimental to well-being has been controversial. Drawing on perspectives from psychology, neuroscience, computer-human interaction, and public health, this course explores the positive and negative impact of technology usage on our well-being across the lifespan. We will examine technology use in computer-mediated communication (e.g., smartphone, social media, internet, social apps), mHealth and telehealth, gaming, and other technology trends (e.g., Artificial intelligence, robots, virtual reality), and will explore how these technologies influence social life, adult development and aging, and health/health behavior (e.g., physical activity, diet, sleep).

I am very thankful for this opportunity provided by the Division of Science, and for my mentors and peers who have provided feedback and supported me along the way. I look forward to teaching this course and engaging students with how technology influences our social life, how we develop and age, and our health/health behavior.

Narges Iraji

Narges IrajiThe course Science and Science Fiction, designed for students with little to no science or math background, encourages conversations around science within the context of culture. Reading the works of science fiction by a diverse group of authors and discussing the science and imagination in them illuminates the inseparability of science from its human nature. I hope that this approach not only bridges the materials taught in class and the outside world but also sparks a curiosity that goes beyond the classroom.

Our inner urge to observe, decode patterns, and predict has existed well past the modern times and so has our passing of knowledge to the future in the form of storytelling. The combination of imagination and science is nothing new but the access to both, who can imagine and who can be a scientist, has changed throughout history. During the course, the students will read, discuss, and write about science fiction stories that inspire questions and problems which call for mathematical modeling. After becoming more familiar with some well-known mathematical models in areas such as population modeling and epidemiology, the students start working on a final project. They will formulate a question related to what they are passionate or curious about and pursue the answer using the tools that they have gained from the course. The goal is not to solve the problem, but to gain some insight into the steps required in doing so.

Teaching a University Prize Instructorship course has been a dream of mine since I heard about this opportunity in my first or second year. I am grateful for this, and thankful to all those who are helping me along the way. Numerous challenges follow developing a course, and while being one of the greatest projects that I have taken on, it has tested my patience a few times. I hope that after serving as a University Prize Instructorship instructor, I can help other graduate students who are interested in this opportunity by sharing some resources, such as information on inviting speakers or reserving classrooms with computers. My experience as a graduate student in physics and my research in the field of mathematical biology have truly led me to a new perspective. I now look around and find questions in all that I observe knowing someone else might have already started working on the answer. The course, Science and Science Fiction, encapsulates one of my attempts to pass this curiosity about the universe and life forward.

New Undergraduate Engineering Science Program Approved

Technology is central to our society. Universities play a key role as innovation hubs in new technology development, by linking knowledge creation, workforce development and commerce. After a multi-year planning process with Brandeis stakeholders and Engineering education experts, the Brandeis Faculty and Board of Trustees has approved the creation of a distinctively Brandeisian undergraduate Engineering Science program, designed for ABET accreditation. Unlike other models in which Engineers are siloed in their own department or school, this interdepartmental program is designed to  maximize horizontal integration across and beyond the Sciences.  All hands are now on deck to make this program a reality.  Institutional Advancement is working closely with faculty to raise the funds necessary to meet our ambitious goals.

Science Engineering LogoTo build up this program, we will  capitalize on the existing synergy between the life and physical sciences, while enhancing core research areas with an emphasis on translating basic research to technological applications.  Our goal is to integrate the engineering curriculum with the social justice mission that is integral to Brandeis. We envision providing opportunities for our students and faculty to deeply engage in science, design, and problem-solving while participating in a curriculum and culture that grapples with issues of social justice, business ethics and sustainability. The curriculum will be designed with these aspirations by engaging faculty from all of arts and sciences, IBS and Heller.  Ultimately, we hope that this new program will give our students the tools to intervene in the world and challenge them to build a better one.

We welcome input from our friends and alums as we begin to engage in the task of building up this exciting new program.

Summer Research Program back to (nearly) normal in 2021

SciFest 2019With increasing vaccination rates and declining positive Covid test rates, the Division of Science is looking forward to a vibrant, in-person summer undergraduate research program kicking off right after Memorial Day. 

The Division of Science summer program pairs first-hand research, community building, and guidance from Brandeis graduate students and postdoctoral fellows to provide undergraduate students a high-quality research experience. Past summer undergraduates have gone on to make substantial contributions (even as first authors!) to peer-reviewed research publications in fields such as materials chemistry (Shi et al., “Sunlight-activated phase change materials for controlled heat storage and triggered release”), molecular biology (Lamper et al., “A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress”) and neuroscience (He et al., “Rapid adaptation to Elevated Extracellular Potassium in the Pyloric Circuit of the Crab, Cancer borealis).

For Summer 2021, we are excited to announce that 58 Brandeis undergraduate researchers will be supported through the Division of Science programs and funding sources including NSF, NIH, and generous Brandeis alumni and foundation donors.

Additionally, the MRSEC Research Experience for Undergraduates (REU) program will support 6 undergraduate students from Hampton University for a 10-week, hands-on research program that runs in parallel with the MRSEC Summer Materials Undergraduate Research Fellowship. REU participants are mentored by MRSEC graduate students and postdoctoral fellows and contribute to materials science research efforts on Brandeis’s campus.

We will conclude the summer with SciFest, our annual summer poster session showcasing undergraduate research in the sciences, on August 5. Check the SciFest website for updates about the time and details for the session. 

Congratulations to all fellowship recipients! 

Learning from how viruses assemble

Capsid image from paper

credit: eLife

Michael Hagan, Professor of Physics, is quoted extensively in the Chemical & Engineering News article, Lessons learned from watching viruses assemble. The paper discusses how scientists are studying the ability for viruses to self-assemble. During a viral infection, infected cells manufacture the genetic material and other components of the virus. These components then self-assemble, or build themselves into complex shapes, to form new viruses capable of infecting additional cells.

Many viruses contain their genetic material within a protective shell known as a capsid. Michael Hagan is one of the scientists studying how these capsids are formed by modeling the conditions and chemical properties that allow viruses to build themselves. Once understood, researchers hope this will help in drug design and delivery.

Article: Lessons learned from watching viruses assemble, Laura Howes, Chemical & Engineering News-C&EN,  December 15, 2020.

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