Programmable icosahedral shell system for virus trapping

Sigl, Christian; Willner, Elena M.; Engelen, Wouter; Kretzmann, Jessica A.; Sachenbacher, Ken; Liedl, Anna; Kolbe, Fenna; Wilsch, Florian; Aghvami, S. Ali; Protzer, Ulrike; Hagan, Michael F.; Fraden, Seth; Dietz, Hendrik

doi:10.1038/s41563-021-01020-4

Cited by 148 publications

(201 citation statements)

References 48 publications

Supporting

Mentioning

177

Contrasting

Unclassified

Order By: Relevance

“… 1 Nowadays, quite large and complex higher-order DNA origami structures (“superstructures”) are being used for nanometer-precise positioning of structures over micrometer scales, 12 , 13 molecular “tubing” systems for linear transport of cargo, 14 or the encapsulation of cargo that itself is tens of nanometers in diameter. 15 …”

Section: Introductionmentioning

confidence: 99%

Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes

et al. 2021

View full text Add to dashboard Cite

Nanotechnology often exploits DNA origami nanostructures assembled into even larger superstructures up to micrometer sizes with nanometer shape precision. However, large-scale assembly of such structures is very time-consuming. Here, we investigated the efficiency of superstructure assembly on surfaces using indirect cross-linking through low-complexity connector strands binding staple strand extensions, instead of connector strands binding to scaffold loops. Using single-molecule imaging techniques, including fluorescence microscopy and atomic force microscopy, we show that low sequence complexity connector strands allow formation of DNA origami superstructures on lipid membranes, with an order-of-magnitude enhancement in the assembly speed of superstructures. A number of effects, including suppression of DNA hairpin formation, high local effective binding site concentration, and multivalency are proposed to contribute to the acceleration. Thus, the use of low-complexity sequences for DNA origami higher-order assembly offers a very simple but efficient way of improving throughput in DNA origami design.

show abstract

Section: Introductionmentioning

confidence: 99%

Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes

et al. 2021

View full text Add to dashboard Cite

show abstract

“…To demonstrate the broad experimental applicability of the JIS supply strategy with a concrete example, we discuss in detail in SI Appendix , section 5 how the JIS strategy could efficiently be used to assemble artificial T = 1 capsids. Artificial capsids have important potential technological and medical applications ( 35 – 37 ) and the simulations show that the JIS strategy might indeed be a feasible and efficient way to assemble these structures.…”

Section: Time Complexity Analysismentioning

confidence: 99%

The time complexity of self-assembly

Gartner

Graf

Frey

2022

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Time efficiency of self-assembly is crucial for many biological processes. Moreover, with the advances of nanotechnology, time efficiency in artificial self-assembly becomes ever more important. While structural determinants and the final assembly yield are increasingly well understood, kinetic aspects concerning the time efficiency, however, remain much more elusive. In computer science, the concept of time complexity is used to characterize the efficiency of an algorithm and describes how the algorithm’s runtime depends on the size of the input data. Here we characterize the time complexity of nonequilibrium self-assembly processes by exploring how the time required to realize a certain, substantial yield of a given target structure scales with its size. We identify distinct classes of assembly scenarios, i.e., “algorithms” to accomplish this task, and show that they exhibit drastically different degrees of complexity. Our analysis enables us to identify optimal control strategies for nonequilibrium self-assembly processes. Furthermore, we suggest an efficient irreversible scheme for the artificial self-assembly of nanostructures, which complements the state-of-the-art approach using reversible binding reactions and requires no fine-tuning of binding energies.

show abstract

“…In this issue of Nature Materials, Christian Sigl and colleagues report a programmable icosahedral 'canvas'-platform for the design and synthesis of DNA origami triangular tiles that self-assemble into icosahedral shells. These structures can work as 'catcher-like' decoys to tightly trap entire virions through multivalent interactions for effective virus inhibition 3 .…”

Section: Dna Nanostructures Nanocages For Virus Inhibitionmentioning

confidence: 99%