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New instrument to help scientists examine molecular interactions

Understanding the interactions among DNA, proteins and other molecules will help scientists improve human and animal health and increase the sustainability of agriculture.

Scientists unraveling biological systems have a new state-of-the-art instrument in South Dakota State University’s Functional Genomics Core Facility to analyze molecular interaction, thanks to a three-year, $243,000 National Science Foundation Major Research Instrumentation grant and approximately $100,000 in university matching funds.

genetic evidence of molecular interactions in images
These images show genetic evidence of potential protein-DNA interaction between PatB, a protein that serves as a transcription factor, and nifB promoter DNA. 
graph showing direct interaction among molecules
This graph shows that the two molecules in the images are directly interacting with each other.

“This is the first NSF MRI award for the functional genomics core facility and will greatly boost our research capabilities,” said senior research scientist Liping Gu, who oversees the facility and is principal investigator for the NSF award.

The Octet RED96 BioLayer Interferometry, or BLI, will allow researchers studying biological processes to examine DNA-to-protein, protein-to-protein, virus-to-antibody and ligand-to-protein interactions. “This new equipment enables real-time determination of affinity, kinetic parameters, and concentration, with one of the binding partners immobilized onto the biosensor surface (ligand) and the other in solution (analyte). While the isothermal titration calorimetry available on campus can only determine the affinity—it’s a big step up,” Gu said. “It has eight channels, providing a high-throughput and more sensitive measurement than isothermal titration calorimetry technique.” 

The functional genomics core facility receives annual support from U.S. Department of Agriculture Hatch Act funding through the South Dakota Agricultural Experiment Station; however, outside funding is necessary to purchase new equipment. The NSF MRI award covers 70% of the equipment and training costs, with the remaining 30% coming from SD-AES and the College of Natural Sciences as well as contributions from six departments.

“Liping’s persistent pursuit of this MRI award has made this powerful analytical tool available to SDSU researchers as well as collaborators across the state,” said Distinguished Professor Bill Gibbons, associate dean for research for the College of Agriculture, Food and Environmental Sciences and director of the South Dakota Agricultural Experiment Station.

Increasing research capabilities

Gu and 14 faculty researchers, including one from the University of South Dakota and one from Augustana University, are part of the group that secured the NSF grant.

When the NSF reviewers asked for preliminary data, several team members provided samples and Gu arranged for the manufacturer to scan them. Team member Jaime Lopez, an assistant professor in the Department of Biology and Microbiology, said, “The instrument is very good at measuring protein-protein interactions. It can measure the strength of the binding, how strongly they like each other, how strongly they hug.”

Lopez, whose research focuses on how cells repair DNA damage, sought to compare binding between a protein and DNA. The published data described the protein to DNA binding; however, the BLI results showed the protein binds much more strongly to the other nucleic acid-like molecules.

“The results were clear; the protein prefers to bind to other nucleic acid-like molecules —and that is exactly what we wanted to show,” said Lopez. “This piece of equipment will allow us to publish better data and those publications will indirectly allow us to secure further funding.”

Measuring molecular interactions

With the new instrument, Gu said, “We can directly measure multicomponent interactions, including not only whether they are interacting, but also how fast those interactions happen, how strong the interaction or binding is and, sometimes, how fast that interaction falls apart.”

Professor Sen Subramanian, co-principal investigator on the NSF MRI grant, will use the instrument to examine the DNA-binding actions, or kinetics, of two transcription factor proteins involved in regulating gene expression related to the number of root nodules a soybean plant develops and how quickly those nodules mature.

“This instrument not only measures the final outcome of the binding, but also the rate at which it occurs and how it changes in the presence of a competitor. Seeing the competition between the two proteins will help us understand how plants regulate gene expression and thereby nodulation and maturity outcomes,” Subramanian said. Understanding the signaling involved in nodule development is an essential part of increasing the nitrogen-fixing ability of soybeans and thereby reducing the need for chemical fertilizers.