Logic Gate Operation by DNA Translocation through Biological Nanopores

Hiroki Yasuga; Ryuji Kawano; Masahiro Takinoue; Yutaro Tsuji; Toshihisa Osaki; Koki Kamiya; Norihisa Miki; Shoji Takeuchi

doi:10.1371/journal.pone.0149667

Logic Gate Operation by DNA Translocation through Biological Nanopores

PLoS One. 2016 Feb 18;11(2):e0149667. doi: 10.1371/journal.pone.0149667. eCollection 2016.

Authors

Hiroki Yasuga^{1

2}, Ryuji Kawano^{1

3}, Masahiro Takinoue⁴, Yutaro Tsuji^{1

2}, Toshihisa Osaki^{1

5}, Koki Kamiya¹, Norihisa Miki^{1

2}, Shoji Takeuchi^{1

5}

Affiliations

¹ Artificial Cell Membrane Systems Group, Kanagawa Academy of Science and Technology, Kawasaki, Japan.
² Department of Mechanical Engineering, Keio University, Yokohama, Japan.
³ Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
⁴ Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan.
⁵ Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.

Abstract

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Computer Simulation
DNA / chemistry*
DNA, Complementary / genetics
Logic*
Nanopores*
Nucleic Acid Conformation
Reproducibility of Results
Thermodynamics

Substances

DNA, Complementary
DNA

Grants and funding

This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas “Molecular Robotics” (No. 24104002) to RK and MT; a Grant-in-Aid for Challenging Exploratory Research (No. 26540160) to RK; a Grant-in-Aid for Young Scientists (A) (No. 25708024) to RK; the Regional Innovation Strategy Support Program to ST; a Grant-in-Aid for Scientific Research (A) (No. 25246017) to ST of The Ministry of Education, Culture, Sports, Science, and Technology, Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.