title: Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami.
abstract: The Watson-Crick base-pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA-based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room-temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple-scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.
authors: Centre for DNA Nanotechnology (CDNA), at Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark, Phone: +45-87156729, Fax: +45-87154041; School of Physical Science and Technology, Lanzhou University, Lanzhou 730000, PR China.
authors: Jie
authors: J
authors: Song
authors: Zhao
authors: Z
authors: Zhang
authors: Shuai
authors: S
authors: Zhang
authors: Lei
authors: L
authors: Liu
authors: Qiang
authors: Q
authors: Li
authors: Erqing
authors: E
authors: Xie
authors: Kurt Vesterager
authors: KV
authors: Gothelf
authors: Flemming
authors: F
authors: Besenbacher
authors: Mingdong
authors: M
authors: Dong
mesh_terms: D004247:DNA / Q000737:chemistry*; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D013696:Temperature
chemical_list: D004247:DNA
keywords: DNA hybridization; DNA origami; atomic force microscopy; hybridization kinetics; thermal control