New Generation Computing

, Volume 33, Issue 3, pp 213–229

Cascading DNA Generation Reaction for Controlling DNA Nanomachines at a Physiological Temperature


DOI: 10.1007/s00354-015-0304-5

Cite this article as:
Komiya, K. & Yamamura, M. New Gener. Comput. (2015) 33: 213. doi:10.1007/s00354-015-0304-5


We developed a reaction system to generate multiple single-stranded DNA species at a physiological temperature for controlling the operation of DNA nanomachines. In this reaction system, cascading DNA generation is arbitrarily programmed by permutation and altering the combinations of template DNA sequences in a modular fashion. Because the dissociation of generated DNA strands from their templates is fully dependent on the strand displacement activity of DNA polymerase, generation and subsequent hybridization of DNA strands can be implemented in a one-pot reaction at the reaction temperature. We experimentally confirmed the generation and hybridization of DNA strands at a temperature remarkably lower than the melting temperature by monitoring the fluorescence change caused by the structural transition of molecular beacons as a simple DNA nanomachine operation. Then, we demonstrated the versatility and programmability of the cascading DNA generation up to three layers. By integrating the proposed DNA generation reaction with various types of DNA nanomachines, an intelligent molecular robotic system is expected to be achieved.


DNA Nanomachine DNA Hybridization Melting Temperature DNA Polymerase Molecular Robotic System 

Copyright information

© Ohmsha and Springer Japan 2015

Authors and Affiliations

  1. 1.Interdisciplinary Graduate School of Science and EngineeringTokyo Institute of TechnologyYokohamaJapan

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