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.


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.

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.

Using computer simulations to model bacterial microcompartment assembly

Bacterial microcompartments are protein shells found in bacteria that surround enzymes and other chemicals required for certain biological reactions.  For example, the carboxysome is a type of microcompartment that enables bacteria to convert the products of photosynthesis into sugars (thus taking carbon out of the atmosphere).  During the formation of a microcompartment, the outer protein shell assembles around hundreds of enzymes and chemicals required for the reaction.  Because the intermediates in this assembly process are small and short-lived, it is hard to study in detail using experiments. It is therefore useful to develop computational models that can help explain how proteins collect the necessary cargo, and then assemble into an ordered shell with the cargo on the inside.  The videos in this post show some examples of computer simulations of a model for bacterial microcompartment assembly, with each video corresponding to a different set of parameters that control the strengths of interactions among the proteins and cargo.

The study is described in the research article “Many-molecule encapsulation by an icosahedral shell” by Jason Perlmutter, Farzaneh Mohajerani, and Michael Hagan in eLife (eLife 2016;10.7554/eLife.14078).

Video 1: Multistep assembly of a microcompartment encapsulating hundreds of molecules (I) video1
Video 2: Multistep assembly of a microcompartment encapsulating hundreds of molecules (II)  video2
Video 3: Assembly of a microcompartment and encapsulation of hundreds of diffuse cargo molecules  video3

Lipids hit a “sweet spot” to direct cellular membrane remodeling.

Lipid membrane reshaping is critical to many common cellular processes, including cargo trafficking, cell motility, and organelle biogenesis. The Rodal lab studies how dynamic membrane remodeling is achieved by the active interplay between lipids and proteins. Recent results, published in Cell Reports, demonstrate that for the membrane remodeling protein Nervous Wreck (Nwk), intramolecular autoregulation and membrane charge work together in surprising ways to restrict remodeling to a limited range of lipid compositions.

F-BAR (Fes/Cip4 homology Bin/Amphiphysin/Rvs) domain family proteins are important mediators of membrane remodeling events. The F-BAR domain forms a crescent-shaped α-helical dimer that interacts with and deforms negatively charged membrane phospholipids by assembling into higher-order scaffolds. In this paper, Kelley et al. have shown that the neuronal F-BAR protein Nwk is autoregulated by its C-terminal SH3 domains, which interact directly with the F-BAR domain to inhibit membrane binding. Until now, the dogma in the field has been that increasing concentrations of negatively charged lipids would increase Nwk membrane binding, and thus would induce membrane deformation.

Surprisingly, Kelley et al. found that autoregulation does not mediate this kind of simple “on-off” switch for membrane remodeling. Instead, increasing the concentration of negatively charged lipids increases membrane binding, but inhibits F-BAR membrane deforming activities (see below). Using a combination of in vitro assays and single particle electron microscopy, they found that the Nwk F-BAR domain efficiently assembles into higher-order structures and deforms membranes only within “sweet spot” of negative membrane charge, and that autoregulation elevates this range. The implication of this work is that autoregulation could either reduce membrane binding or promote higher-order assembly, depending on local cellular membrane composition. This study suggests a significant role for the regulation of membrane composition in remodeling.

Brandeis authors on the study included Molecular and Cell Biology graduate students Charlotte Kelley and Shiyu Wang, staff member Tania Eskin, and undergraduate Emily Messelaar ’13 from the Rodal lab; postdoctoral fellow Kangkang Song, Associate Professor of Biology Daniela Nicastro (currently at UT Southwestern), and Associate Professor of Physics Michael Hagan.

Kelley CF, Messelaar EM, Eskin TL, Wang S, Song K, Vishnia K, Becalska AN, Shupliakov O, Hagan MF, Danino D, Sokolova OS, Nicastro D, Rodal AA. Membrane Charge Directs the Outcome of F-BAR Domain Lipid Binding and Autoregulation. Cell reports. 2015;13(11):2597-609.

Simulations Say Viral Genome Lengths are Optimal for Capsid Assembly

Viruses are infectious agents made up of proteins and a genome made of DNA or RNA. Upon infecting a host cell, viruses hijack the cell’s gene expression machinery and force it to produce copies of the viral genome and proteins, which then assemble into new viruses that can eventually infect other host cells. Because assembly is an essential step in the viral life cycle, understanding how this process occurs could significantly advance the fight against viral diseases.

In many viral families, a protein shell called a capsid forms around the viral genome during the assembly process. Capsids can also assemble around nucleic acids in solution, indicating that a host cell is not required for their formation. Since capsid proteins are positively charged, and nucleic acids are negatively charged, electrostatic interactions between the two are thought to be important in capsid assembly. Current questions of interest are how structural features of the viral genome affect assembly, and why the negative charge on viral genomes is actually far greater than the positive charge on capsids. These questions are difficult to address experimentally because most of the intermediates that form during virus assembly are too short-lived to be imaged.


Snapshots from a computer simulation in which model capsid subunits (blue) assemble around a linear, negatively charged polymer (red). Positive charges on the capsid proteins are shown in yellow.

In a new paper in eLife, Brandeis postdoc Jason Perlmutter, Physics grad student Cong Qiao, and Associate Professor Michael Hagan have used state of the art computational methods and advances in graphical processing units (on our High Performance Computing cluster) to produce the most realistic model of capsid assembly to date. They showed that the stability of the complex formed between the nucleic acid and the capsid depends on the length of the viral genome. Yield was highest for genomes within a certain range of lengths, and capsids that assembled around longer or shorter genomes tended to be malformed.

Perlmutter et al. also explored how structural features of the virus — including base-pairing between viral nucleic acids, and the size and charge of the capsid — determine the optimal length of the viral genome. When they included structural data from real viruses in their simulations and predicted the optimal lengths for the viral genome, the results were very similar to those seen in existing viruses. This indicates that the structure of the viral genome has been optimized to promote packaging into capsids. Understanding this relationship between structure and packaging will make it easier to develop antiviral agents that thwart or misdirect virus assembly, and could aid the redesign of viruses for use in gene therapy and drug delivery.

Perlmutter JD, Qiao C, Hagan MF. Viral genome structures are optimal for capsid assembly. eLife 2013;2:e00632

More science

We’ve all been busy this spring writing grants and teaching courses and doing research and graduating(!), so lots of publications snuck by that we didn’t comment on. Here’s a few I think that might be interesting to our readers.

  • From Chris Miller‘s lab, bacterial antiporters do act as “virtual proton efflux pumps”:
  • nsrv2Are ninja stars responsible for controlling actin disassembly? Seems like the Goode lab might think so.
    • Chaudhry F, Breitsprecher D, Little K, Sharov G, Sokolova O, Goode BL. Srv2/cyclase-associated protein forms hexameric shurikens that directly catalyze actin filament severing by cofilin. Mol Biol Cell. 2013;24(1):31-41.
  • What do you get from statistical mechanics of self-propelled particles? The Hagan and Baskaran groups team up to find out.
  • From John Lisman and Ole Jensen (PhD ’98), thoughts about what the theta and gamma rhythms in the brain encode
  • From Mike Marr‘s lab, studeies using genome-wide nascent sequencing to understand how transcrption bursting is controlled in eukaryotic cells
  • From the Lau and Sengupta labs, RNAi pathways contribute to long term plasticity in worms that have gone through the Dauer stage
    • Hall SE, Chirn GW, Lau NC, Sengupta P. RNAi pathways contribute to developmental history-dependent phenotypic plasticity in C. elegans. RNA. 2013;19(3):306-19.
  • Can nanofibers selectively disrupt cancer cell types? Early results from Bing Xu‘s group.
    • Kuang Y, Xu B. Disruption of the Dynamics of Microtubules and Selective Inhibition of Glioblastoma Cells by Nanofibers of Small Hydrophobic Molecules. Angew Chem Int Ed Engl. 2013.

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