Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System.

@article{Ohara2017NanoporeLO,
  title={Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System.},
  author={Masayuki Ohara and Masahiro Takinoue and Ryuji Kawano},
  journal={ACS synthetic biology},
  year={2017},
  volume={6 7},
  pages={
          1427-1432
        }
}
This paper describes an AND logic operation with amplification and transcription from DNA to RNA, using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously, using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore with single-molecule translocation. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic… 
View on PubMed
web.tuat.ac.jp
27 Citations
Background Citations
1
Methods Citations
4

Figures from this paper

27 Citations

Citation Type

Citation Type

Nanopore Decoding of Oligonucleotides in DNA Computing
TLDR
N nanopore technology, an emerging methodology for single‐molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations.
Serial DNA relay in DNA logic gates by electrical fusion and mechanical splitting of droplets
TLDR
A relay approach for enabling the transfer of DNA from one droplet to another to implement multi-step sequential logic operations and developed Negative-OR operations integrated by a serial connection of the OR gate and NOT gate incorporated in a series of droplets.
A nanopore interface for high bandwidth DNA computing
TLDR
This work presents a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device), and demonstrates this method’s utility in multiplexed detection of clinically relevant microRNA sequences.
Designing logic gates based on 3-way DNAzyme complex
TLDR
This work proposes a 3-way DNAzyme complex composed of three E6 DNAzymes assembled using the biological characteristics of E6DNAzyme, and designs logic gates such as the OR gate, the AND gate, and the INHIBIT gate that will have a wide range of applications in DNA nanoscale programming, biological computing, and nanoscales medicine.
DNA Logic Operation with Nanopore Decoding To Recognize MicroRNA Patterns in Small Cell Lung Cancer.
TLDR
This study proposes 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 and developed a rapid, label-free decoding method for output diagnostic molecules using nanopore measurements.
Nanopore decoding for a Hamiltonian path problem.
TLDR
The results show the feasibility of nanopore measurement as a rapid and label-free decoding method for mathematical DNA computation using parallelSelf-assembly using parallel self-assembly.
Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots.
  • R. Kawano
  • Chemistry, Biology
    Chemphyschem : a European journal of chemical physics and physical chemistry
  • 2018
TLDR
This Minireview focuses on recent research on synthetic ion channels and DNA computing technologies, which are viewed as potential candidate components of molecular robots.
DNA nanotechnology assisted nanopore-based analysis
TLDR
DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis through nanopore sensing technologies.
SURVEY AND SUMMARY DNA nanotechnology assisted nanopore-based analysis
TLDR
A review of recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology shows that DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.
Recent Advances in Liposome-Based Molecular Robots
TLDR
This review describes recent developments of sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots and discusses the emergence of robotics functions by using and functionalizing liposomal membranes.
...
1
2
3
...

References

SHOWING 1-10 OF 29 REFERENCES
Logic Gate Operation by DNA Translocation through Biological Nanopores
TLDR
A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA, and this operation was executed in a four-droplet network.
The potential and challenges of nanopore sequencing
TLDR
A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility.
Hairpin DNA Unzipping Analysis Using a Biological Nanopore Array
This paper describes a method of hairpin DNA (hpDNA) unzipping analysis using a biological nanopore array. Various lengths of hpDNAs were captured and translocated through the nanopore and the…
Enzyme-Free Nucleic Acid Logic Circuits
TLDR
The design and experimental implementation of DNA-based digital logic circuits using single-stranded nucleic acids as inputs and outputs are reported, suggesting applications in biotechnology and bioengineering.
Characterization of nucleic acids by nanopore analysis.
TLDR
Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field and information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade.
Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules.
DNA based arithmetic function: a half adder based on DNA strand displacement.
TLDR
This work designed and realized an XOR logic gate and an AND logic gate based on DNA strand displacement reactions, which utilize ssDNA as input and output signals.
Diagnostic Applications of Nucleic Acid Circuits
TLDR
The Account provides a means of touching on what might seem to be an arcane field, and explains nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly and the hybridization chain reaction.
DNA nanodevices.
The molecular recognition properties of DNA molecules combined with the distinct mechanical properties of single and double strands of DNA can be utilized for the construction of nanodevices, which…
Electrostatic Focusing of Unlabeled DNA into Nanoscale Pores using a Salt Gradient
TLDR
It is shown that application of a 20-fold salt gradient enables detection of picomolar DNA concentrations at high throughput, and the salt gradients enhance the electric field, focusing more molecules into the pore, thereby advancing the possibility of analyzing unamplified DNA samples using nanopores.
...
1
2
3
...