*September 16, 2024*
In a groundbreaking development, an interdisciplinary research team from the University of Pennsylvania has unveiled the first-ever reusable coupled nanopore platform designed for both detecting and guiding molecules. This innovative technology promises significant advancements in DNA sequencing and molecular identification, offering a glimpse into the future of molecular research.
### A Revolutionary Leap in Nanopore Technology
The team, led by physicist Marija Drndić from the University of Pennsylvania and her long-time collaborator Dimitri Monos from the Perelman School of Medicine and the Children’s Hospital of Philadelphia (CHOP), has introduced a dual-layer nanopore system. This novel design, which features two or more nanopores stacked just a few nanometers apart, allows for unprecedented precision in detecting and controlling molecules like DNA as they traverse through the system.
Drndić, who specializes in synthetic versions of biological pores that regulate ion and molecule exchange in the body, highlights that controlling and monitoring molecular flow through these nanopores has revolutionized research in the past two decades. Advances in synthetic nanopores, made from materials such as graphene and silicon, have already significantly impacted DNA sequencing.
### A New Design for Enhanced Accuracy
In a paper published in *NatureNanotechnology *, Drndić and Monos detail their new nanopore technology, which promises to overcome many limitations of current systems. “Current platforms can be likened to cooking spaghetti in a pot—molecules like DNA are tangled and challenging to manage, let alone guide through a single pore,” Monos explains. Typically, proteins are used to unwind and straighten DNA, but this method has limitations due to degradation, which affects sensitivity and operational lifespan.
“With our new design,” Monos adds, “we are essentially guiding molecules through two coupled nanopores, providing a smoother and more controlled passage, making them easier to detect and analyze.” This new platform, named GURU—short for “Guided and Reusable”—represents a significant step forward in molecular study, offering key benefits like improved assessment of molecular length and conformation as they pass through the nanopores.
### Precise Measurements and New Signal Patterns
The GURU platform allows researchers to use the precise distance between the two nanopores as a “ruler” to determine the exact length of DNA passing through. This level of precision provides a clearer view of molecular shapes and structures, including DNA, RNA, and proteins.
Unlike traditional single-pore systems, GURU extends the time molecules spend in the sensing zone, enhancing the detection process. This extended interaction has led to the discovery of unique signal patterns resembling the letters “W” and “T”—a finding first observed by Chih-Yuan (Scottie) Lin, the paper’s first author.
“These patterns reflect how molecules interact with the dual-pore system,” Lin notes. “When we see signals resembling a ‘W,’ it indicates that the molecule interacts sequentially with both the top and bottom nanopores, reflecting how it enters the lower pore, exits slightly, and then reengages with the upper layer.”
The T-shaped signal occurs when a molecule is long enough to block both nanopores simultaneously, providing a clear indication of its full length. “These signals offer real-time data on the molecule’s length and position,” Lin adds.
### Future Prospects and Clinical Applications
As the team continues to refine their system, they believe it could lead to more efficient, accurate, and cost-effective sequencing technologies that address the limitations of current protein-based nanopore systems. Monos emphasizes, “What solidified our collaboration was the shared goal of advancing sequencing technology, particularly for applications like human leukocytic antigen (HLA) genes, which require long DNA reads.” As the director of the Immunogenetics Laboratory at CHOP, Monos works extensively with HLA genes, which are crucial for immune system compatibility in organ transplantation.
“HLA genes are among the most complex regions of the human genome, and precise long-read sequencing is essential to understanding their variations,” Monos explains. “Nanopore technology like GURU offers the potential for more accurate and comprehensive sequencing in this challenging area.”
By eliminating the need for proteins and developing a purely solid-state system, their combined efforts have produced a platform that advances nanopore technology and opens new possibilities for clinical applications.
Drndić concludes, “Solving problems like DNA sequencing and molecular detection with nanopores requires expertise from diverse fields. It’s not just about physics or materials science. We need input from biologists to understand the molecules, chemists to help with reactions, and medical professionals to explore real-world applications.”