Poster abstracts

Poster number 8 submitted by Quincy Bizjak

Kinetic analysis of the folding and polymerization of DNA origami structures

Quincy Bizjak (Chemical and Biomolecular Engineering), Anjelica Kucinic (Chemical and Biomolecular Engineering), Wolfgang Pfeifer (Mechanical and Aerospace Engineering), Carlos E. Castro (Mechanical and Aerospace Engineering)

Abstract:
DNA origami describes the process of folding a long, single strand of DNA, called the scaffold strand, using the addition of shorter strands of DNA, called staples. The staples bind to discontinuous portions of the scaffold that have complimentary sequences to create a more complex shape for a variety of applications. These final structures can be used in medicine such as drug and gene delivery, manufacturing, and robotics on the nanoscale. (1) With the rapid growth of the DNA nanotechnology field, it is important to shorten the amount of time needed for these structures to fold. To do this, the assembly process, commonly spanning up to several, days needs to be optimized, ideally allowing successful fabrication within a few hours. Polymerization describes the process of attaching multiple structures together to form long chains or more complex shapes and is necessary for many applications of DNA origami. (2, 3) To perform a kinetic analysis, structures will be polymerized at different time points and analyzed using agarose gel electrophoresis. Comparison of band intensities from agarose gel electrophoresis and images from atomic force microscopy will give information about the rate of the polymerization process.

References:
(1)Dey, S., Fan, C., Gothelf, K.V. et al. DNA origami. Nat Rev Methods Primers 1, 13 (2021). https://doi.org/10.1038/s43586-020-00009-8

(2)Pfeifer W, Saccà B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. Chembiochem. 2016 Jun 16;17(12):1063-80. doi: 10.1002/cbic.201600034. Epub 2016 May 17. PMID: 27186937.

(3)Marras, A.E. Hierarchical assembly of DNA origami nanostructures. MRS Communications 12, 543–551 (2022). https://doi.org/10.1557/s43579-022-00248-8

Keywords: DNA Origami, Polymerization, Kinetics