Surfing the Nano Wave: Dramatic Leap in DNA Sensing with Surfactant-Coated Nanopores

Solid-state nanopores (ssNPs) are nanoscopic apertures, fabricated in ultrathin solid membranes made of silicon or graphene. These devices can be fabricated with an adjustable size, enabling the selective passage of individual molecules one at a time. This capability makes them useful in various technological applications, particularly in biosensing, where ssNPs can detect and analyze individual molecules, such as DNA, RNA, proteins, or other biological molecules. Nanopore plays a crucial role in high-precision biomedical research, diagnostics and emerging single proteins molecule sensing applications. The underlying working principle of these nano devices involves time-dependent measurement of the ion flux through the nanopore during the electro-kinetic passage of bio-analyte molecules. For example, when a single DNA strand passes through the narrow orifice, changes in ionic current can provide information about the sequence of bases DNA is composed of. Another advantage for ssNPs is that they can perform real-time analysis which is much faster than traditional methods. In all nanopore sensing applications, the speed at which the bio-analytes translocate is crucial in determining the method’s sensitivity and resolution. To that end, many efforts have been invested to engineer the nanopores’ specific physical and chemical properties, such as their size, shape, or surface chemistry, allowing them to be tailored for specific sensing applications.

The ability to modulate the characteristics of these nanopores, especially their surface charges, has opened new avenues in biopolymer analysis. The study in question hinges on this principle, using ssNPs modified with an anionic surfactant coating to significantly alter the DNA translocation dynamics. In a new study published in ACS’s Nano Letters led by Professor Amit Meller and conducted by PhD candidate Neeraj Soni, Dr. Navneet Chandra Verma and Ms. Noam Talor from the Faculty of Biomedical Engineering at Technion – Israel Institute of Technology, the researchers focused on enhancing the capabilities of ssNPs in DNA translocation dynamics. The team used silicon nitride (SiN_x) nanopores as the base in their experiments. The nanopores were then coated with the anionic surfactant, sodium dodecyl sulfate (SDS), which greatly enhances the negative surface charge of the nanopores. This modification aimed to manipulate the Electro-Osmotic Flow (EOF) within the nanopores, creating movement of liquid in the opposite direction to the motion of the DNA molecules inside the nanopore, hence slowing down their overall speed. This results in a much-improved sensing resolution.

To evaluate the effects of this surfactant coating, the researchers used double-stranded DNA (dsDNA) of varying lengths. These molecules were passed through the modified nanopores to observe changes in translocation dynamics. In a novel approach, the team also used uncharged analytes (small zwitterion organic dyes) for real-time visualization of voltage-dependent Electro-osmotic flow in custom electro-optical apparatus capable of sensing single fluorophores flow in the ssNP. This was done to de-couple the effects of EOF from electrophoretic forces, thereby providing a clearer and quantitative understanding of EOF’s role in DNA translocation by a direct electro-optical measurement.

The authors found over 30-fold increase in the translocation dwell-times (t_D) of dsDNA through the SDS-coated nanopores. This meant that the DNA molecules spent a much longer time within the nanopores compared to uncoated nanopores. Importantly, this enhancement in dwell-time did not come at the cost of increased nanopore noise. Maintaining a low noise level is crucial for the accuracy and reliability of measurements in nanopore sensing. The researchers also observed that the SDS coating did not negatively impact the capture rates of shorter DNA fragments (unlike, for example increasing the medium viscosity). This is important for applications in biomedical research where short DNA sequences are often the subject of analysis.

The ability to slow down DNA translocation significantly enhances the potential for detailed analysis of DNA sequences. This is particularly valuable for applications such as detecting and characterizing short DNA fragments, which are important in various biomedical contexts, such as cell-free genomic DNA. Moreover, the study provided valuable insights into the behavior of EOF within planar ssNPs. Understanding the mechanics of EOF in such systems is essential for both theoretical knowledge and practical applications in biosensing. In summary, Meller’s research team successfully manipulated the EOF in nanopores by coating them with an anionic surfactant, leading to a significant improvement in the capabilities of these nanopores for DNA sensing. Indeed, the enhanced functionality of ssNPs due to surfactant coating opens up new possibilities in nanopore technology. The authors’ findings could pave the way for more sensitive and accurate biosensors, capable of detecting a wide range of biomolecules with high precision. In statement to Advances in Engineering, Neeraj said: ‘’These SDS coated nanopores represent the advanced iteration of solid-state nanopores, providing precise control and manipulation of small molecule dynamics through these minute apertures with higher accuracy’’. Co-author Navneet told Advances in Engineering: “The integration of nanopores with single molecule optical methods hold promise for investigating nanoscale dynamics, including the visualization of electro-osmotic flow via individual fluorophores”.