Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization. Issue 23 (4th May 2018)

• Record Type: Journal Article
• Authors: Liber, Miran; Tomov, Toma E.; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C.; Nir, Eyal
• Is Part Of: Small. Volume 14:Issue 23(2018)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2018-05-04
• Subjects: alternating laser excitation -- DNA nanotechnology -- DNA origami -- origami tiling -- single molecule fluorescence; Nanotechnology -- Periodicals; Nanoparticles -- Periodicals; Microtechnology -- Periodicals; 620.5
• DOI: 10.1002/smll.201800218
• Languages: English
• ISSNs: 1613-6810

Abstract

Abstract: Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single‐molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self‐dimerization of the origami monomers, likely via blunt‐end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. Abstract : DNA origami dimerization yield is typically not very high. Single molecule fluorescence, atomic force microscopy and gel electrophoresis show that the low yield cannot be explained by thermodynamic instability or origami structural imperfections and reveal that self‐dimerization of the origami monomers, caused by the presence of bridging strands, are the main reason for the low dimerization yield.