Studying the interactions between biomolecules at the single molecule level contributes significantly to our understanding of biological phenomena, but a key challenge has been the complexity of single-molecule experiments and the lack of high throughput methods.

Now, researchers from the University at Albany, State University of New York developed a benchtop centrifugal force microscope (CFM) that can perform high throughput single-molecule experiments. This plug-and-play device is designed to fit into a commercial centrifuge and can be controlled wireless using an external computer. Dr. Ken Halvorsen at SUNY Albany's RNA Institute had previously developed the CFM, a custom-built sample-holding chamber with an inbuilt microscope that can fit into a centrifuge bucket. From its original conception in 2010, the team has upgraded the instrument to fit into a commercially available centrifuge bucket. In the sample chamber, the researchers attached DNA handles to a surface which can then interact with different types of biomolecules. They demonstrated the function of the CFM using another DNA molecule that interacts with the DNA handle by base pair hybridization. Once the samples are in the chamber, the CFM module is placed inside the centrifuge bucket. Running the centrifuge exerts a centrifugal force on the interacting molecules. To "view" the interactions, they attached microscopic beads at the end of the interacting DNA molecules. At a certain force, if the DNA-DNA interaction is pulled apart, the beads fall off. The team studied the effect of force over time to characterize DNA interactions based on the beads in the microscope view.

Traditional single-molecule methods include techniques such as optical tweezers, magnetic tweezers, and atomic force microscopy (AFM), where force is applied to a biomolecule tethered between two surfaces via optical forces, magnetic forces, or mechanical forces. While these techniques are well-established and have contributed to biophysical studies, they require complex equipment with frequent alignment, and can study only one molecule at a time, making data collection tedious. The Centrifuge Force Microscope overcomes some of these limitations by studying hundreds of such interactions in the sample chamber simultaneously, allowing high throughput data collection for single molecule analysis. The current study by Halvorsen and co-workers further advances the instrument by adding wi-fi and live-streaming capabilities to make the technique more user-friendly.

Dr. Jibin Abraham Punnoose, lead author on the study says “The use of Wi-Fi to achieve wireless communication is a key factor in making the devise user-friendly for programming and upgrading. Connecting the CFM and the computer enables the user to use any programming language with Gigabit Ethernet (GigE) protocol support to control the CFM. In this version of the CFM we used LabVIEW to develop a graphical user interface (GUI) to control the instrument, but other common programming languages like MATLAB can be also used.”

While allowing massively parallel single-molecule experiments, the CFM faces challenges in the timescales of observation and real-time focusing. However, the researchers built the Wi-Fi CFM for ~$2200, a cost that might make the technique more easily adaptable in other laboratories for research and educational purposes.

“One of our goals is to make single molecule experiments more accessible to researchers. The version we have developed here is the easiest CFM to build and use so far, and with a cost that is reasonable for even a small lab,” said Dr. Halvorsen.

Their study was released in issue 119/11 of Biophysical Journal titled "Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments".

- Arun Richard Chandrasekaran