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Self-assembly pathways of DNA origami

Friday, November 20, 2015
4:00 PM - 5:00 PM
Location: Moore B280
Fritz Dannenberg, Graduate Student, Computer Science, Oxford University

Seminar abstract:

Despite the frequent application of DNA origami, quantitative understanding of the origami self-assembly process remains elusive. The yield of well-formed origami is known to be sensitive to the crossover placements, and layered structures in particular may require adjustments in order to optimize the yield. Frequent prototyping could be avoided, in principle, if the assembly process and kinetics were fully understood. To this end, we introduce an unique origami tile that self-assembles into several distinct shapes. We develop a thermodynamic model of the self-assembly process and apply our model to the polymorphic tile. The model indicates that the early formation of stable bonds between distant sites strongly correlates with the eventual shape of the tile. It also indicates that the reversible nature of hybridization helps to avoid kinetic traps. We find that that small changes to the design significantly affect the folding pathway and the observed distribution of shapes, allowing us to effectively steer the self-assembly pathway. The model and experiment show that the self-assembly is cooperative, and sensitive to the domain and crossover design.

Dunn, Dannenberg et al.  Nature, 525, 82–86 (2015)

Dannenberg et al. J. Chem. Phys, 143, 165102 (2015)


Speaker bio:

Frits Dannenberg is/was a graduate student with Marta Kwiatkowska in Computer Science at Oxford University.   He has worked on synthesis and verification of stochastic systems, as well as — in collaboration with Andrew Turberfield's group and Tom Ouldridge — developed biophysical models that provide new insights into DNA nanotechnology.

Host:  Erik Winfree.  Please contact me (winfree@caltech.edu) if you would like to meet with Frits during his visit, which includes Nov 20, Nov 23, and Nov 24.

For more information, please phone 626 395 4843/626 395 5707 or email lucinda@caltech.edu

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