DNA Logic Operation with Nanopore Decoding To Recognize MicroRNA Patterns in Small Cell Lung Cancer.

Although DNA computation has traditionally been developed for parallel calculations in molecular analyses, this approach has recently been considered for use in diagnostic or medical applications in living systems. In this study, we propose that the DNA logic operation may be a powerful tool for the recognition of microRNA patterns, which may have applications for the early diagnosis of cancers. We developed a rapid, label-free decoding method for output diagnostic molecules using nanopore measurements. We designed diagnostic DNAs that autonomously recognized two microRNAs, miR-20a and miR-17-5p, and formed a four-way junction structure that was captured in the nanopore, showing long blocking currents. We analyzed the blocking duration based on the central limit theorem and found that four different operations, i.e., (0, 0), (0, 1), (1, 0), and (1, 1), could be discriminated. This pattern recognition method has been differentiated from simple detection methods based on DNA computing and nanopore technologies.

[1]  Ryuji Kawano,et al.  Hairpin DNA Unzipping Analysis Using a Biological Nanopore Array , 2016 .

[2]  Yong Wang,et al.  Nanopore-based detection of circulating microRNAs in lung cancer patients , 2011, Nature nanotechnology.

[3]  Jason Campbell,et al.  Disease detection and management via single nanopore-based sensors. , 2012, Chemical reviews.

[4]  Shoji Takeuchi,et al.  Metal-Organic Cuboctahedra for Synthetic Ion Channels with Multiple Conductance States , 2017 .

[5]  Ryuji Kawano,et al.  Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots. , 2018, Chemphyschem : a European journal of chemical physics and physical chemistry.

[6]  R. Kawano,et al.  Channel Current Analysis for Pore-forming Properties of an Antimicrobial Peptide, Magainin 1, Using the Droplet Contact Method , 2016, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.

[7]  Conrad Steenberg,et al.  NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..

[8]  Michele Zagnoni,et al.  Miniaturised technologies for the development of artificial lipid bilayer systems. , 2012, Lab on a chip.

[9]  Y. Benenson.  Biomolecular computing systems: principles, progress and potential , 2012, Nature Reviews Genetics.

[10]  Shoji Takeuchi,et al.  A polymer-based nanopore-integrated microfluidic device for generating stable bilayer lipid membranes. , 2010, Small.

[11]  Yaakov Benenson,et al.  Biocomputers: from test tubes to live cells. , 2009, Molecular bioSystems.

[12]  Norihisa Miki,et al.  Automated Parallel Recordings of Topologically Identified Single Ion Channels , 2013, Scientific Reports.

[13]  Andrew D. Ellington,et al.  Diagnostic Applications of Nucleic Acid Circuits , 2014, Accounts of chemical research.

[14]  Rui Gao,et al.  Nanopore-based sequencing and detection of nucleic acids. , 2013, Angewandte Chemie.

[15]  Sean Conlan,et al.  Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter , 1999, Nature.

[16]  C. Croce,et al.  MicroRNAs in Cancer. , 2009, Annual review of medicine.

[17]  A. Meller,et al.  Nanopore unzipping of individual DNA hairpin molecules. , 2004, Biophysical journal.

[18]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.

[19]  Ryuji Kawano,et al.  Amplification and Quantification of an Antisense Oligonucleotide from Target microRNA Using Programmable DNA and a Biological Nanopore. , 2017, Analytical chemistry.

[20]  Shoji Takeuchi,et al.  Lipid bilayer formation by contacting monolayers in a microfluidic device for membrane protein analysis. , 2006, Analytical chemistry.

[21]  Norihisa Miki,et al.  Serial DNA relay in DNA logic gates by electrical fusion and mechanical splitting of droplets , 2017, PloS one.

[22]  Norihisa Miki,et al.  A Portable Lipid Bilayer System for Environmental Sensing with a Transmembrane Protein , 2014, PloS one.

[23]  K. Tsumoto,et al.  Analysis of Pore Formation and Protein Translocation Using Large Biological Nanopores. , 2017, Analytical chemistry.

[24]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Wallace,et al.  Direct detection of membrane channels from gels using water-in-oil droplet bilayers. , 2007, Journal of the American Chemical Society.

[26]  C. Croce,et al.  MicroRNAs in cancer. , 2014, Annual review of pathology.

[27]  Masahiro Takinoue,et al.  Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System. , 2017, ACS synthetic biology.

[28]  Rukshan T. Perera,et al.  Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. , 2016, Biophysical journal.

[29]  Satoshi Kobayashi,et al.  Molecular robots with sensors and intelligence. , 2014, Accounts of chemical research.

[30]  Li-Qun Gu,et al.  Programming Nanopore Ion Flow for Encoded Multiplex MicroRNA Detection , 2014, ACS nano.

[31]  Norihisa Miki,et al.  Logic Gate Operation by DNA Translocation through Biological Nanopores , 2016, PloS one.

[32]  Z. Siwy,et al.  Nanopore analytics: sensing of single molecules. , 2009, Chemical Society reviews.

[33]  D. Branton,et al.  Characterization of nucleic acids by nanopore analysis. , 2002, Accounts of chemical research.

[34]  E. Shapiro,et al.  Programmable and autonomous computing machine made of biomolecules , 2001, Nature.

[35]  Susan Daniel,et al.  Single ion-channel recordings using glass nanopore membranes. , 2007, Journal of the American Chemical Society.

[36]  M. Troll,et al.  Ionic Current Blockades from DNA and RNA Molecules in the α-Hemolysin Nanopore , 2007 .

[37]  Norihisa Miki,et al.  Droplet split-and-contact method for high-throughput transmembrane electrical recording. , 2013, Analytical chemistry.