Detection of cancer biomarkers from blood samples

Pattern recognition of miRNA expression using DNA computing and nanopore decoding
Credit: Ryuji Kawano, Tokyo University of Agriculture and Technology

… using nanopore-based DNA computing technology.

Cholangiocarcinoma, also known as bile duct cancer, is a cancer type with a characteristically high mortality. At the time of diagnosis, most bile duct cancers are typically already incurable. This is why methods for the early diagnosis of bile duct cancer are urgently needed.

Liquid biopsy, the sampling of non-solid biological tissue like blood, is gaining interest as a quick and non-invasive method for diagnosing cancers. Unlike traditional biopsies that require surgery and often general anesthesia, a liquid blood biopsy only requires a couple of milliliters of blood, with minimal harm to the patient.

After sampling, the blood is screened for specific markers indicating the presence of cancerous tissue. For example, specific patterns of microRNA (miRNA), short non-coding strands of RNA, are associated with different types of cancer and can be used to diagnose cancers from liquid biopsies with high precision. However, the low concentration of miRNA in the blood samples makes their detection challenging.

Researchers at the Tokyo University of Agriculture and Technology have developed a new method for the detection of cancer miRNA patterns based on DNA computing technology. The developed method shows potential as a promising tool for simple and early cancer diagnosis from liquid biopsies with low concentrations of target biomarkers. The findings were published in the peer-reviewed journal JACS Au on June 26th, 2022.

“DNA computing uses the biochemical reactions of the information-encoding DNA molecules to solve problems based on formal logic, in the same way that normal computers do,” said corresponding author Ryuji Kawano, professor in Tokyo University of Agriculture and Technology (TUAT) in Japan. “In this case, a diagnostic DNA molecule was designed to be able to bind five different kinds of miRNA associated with bile duct cancer. In the process of binding the miRNA molecules, the diagnostic DNA converts the expression pattern of the miRNAs into the information contained in the form of a nucleic acid structure.”

To read this information, the scientists use a method called nanopore decoding. In this method, the DNA is passed through a nano-sized hole, or “pore”. As the molecule transits the pore, it will obstruct the flow of electrical current through the pore. These perturbations in the current through the pore can be then measured and used to deduce the properties of the passing molecule. In the case of the diagnostic DNA, the bound miRNAs will be “unzipped” from the DNA, resulting in a current inhibition of characteristic amplitude and duration. Through statistical analysis of the unzipping data of the miRNA patterns, the scientists were able to recognize cancer-specific expression patterns even from clinical samples with extremely low concentrations of miRNA. This is a significant improvement in the field of nanopore diagnosis, as nanopore measurements have generally been considered unable to detect nucleic acids at such low levels, which has undermined the use of the technology in clinical applications.

For more information about the Kawano laboratory, please visit

Original publication:

Nanami Takeuchi, Moe Hiratani and Ryuji Kawano*,
Pattern Recognition of microRNA Expression in Body Fluids using Nanopore Decoding at Sub-femtomolar Concentration
JACS Au, 2022,
*: corresponding author


About Tokyo University of Agriculture and Technology (TUAT):

TUAT is a distinguished university in Japan dedicated to science and technology. TUAT focuses on agriculture and engineering that form the foundation of industry, and promotes education and research fields that incorporate them. Boasting a history of over 140 years since our founding in 1874, TUAT continues to boldly take on new challenges and steadily promote fields. With high ethics, TUAT fulfills social responsibility in the capacity of transmitting science and technology information towards the construction of a sustainable society where both human beings and nature can thrive in a symbiotic relationship. For more information, please visit

Journal: JACS Au
DOI: 10.1021/jacsau.2c00117
Article Title: Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations
Article Publication Date: 26-Jun-2022

Media Contact

Ken-ichiro Saitoh
Tokyo University of Agriculture and Technology

Media Contact

Ken-ichiro Saitoh
Tokyo University of Agriculture and Technology

All latest news from the category: Life Sciences and Chemistry

Articles and reports from the Life Sciences and chemistry area deal with applied and basic research into modern biology, chemistry and human medicine.

Valuable information can be found on a range of life sciences fields including bacteriology, biochemistry, bionics, bioinformatics, biophysics, biotechnology, genetics, geobotany, human biology, marine biology, microbiology, molecular biology, cellular biology, zoology, bioinorganic chemistry, microchemistry and environmental chemistry.

Back to home

Comments (0)

Write a comment

Newest articles

Compact QKD system

… paves the way to cost-effective satellite-based quantum networks. Researchers demonstrate successful quantum key distribution between space lab and four ground stations. Researchers report an experimental demonstration of a space-to-ground…

Exploring quantum electron highways with laser light

Spiraling laser light reveals how topological insulators lose their ability to conduct electric current on their surfaces. Topological insulators, or TIs, have two faces: Electrons flow freely along their surface…

First image of antigen-bound T-cell receptor at atomic resolution

Immune system: Antigen binding does not trigger any structural changes in T-cell receptors – Signal transduction probably occurs after receptor enrichment. The immune system of vertebrates is a powerful weapon…

Partners & Sponsors