Isothermal Hybridization Kinetics of DNA Assembly of Two-Dimensional DNA Origami

Song J, Zhang Z, Zhang S, Liu L, Li Q, Xie E, Gothelf KV, Besenbacher F, Dong M.

Small. 2013 Sep 9;9(17):2954-9. doi: 10.1002/smll.201202861. Epub 2013 Feb 22.

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.

Erratum in

  • Small. 2014 Feb 26;10(4):630.


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 DNAorigami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.

Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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