By Dave DeFusco
At the Katz School鈥檚 Graduate Symposium on Science, Health and Technology, Rutu Jagtap and Andres Romero, both students in the M.S. in Biotechnology Management and Entrepreneurship, presented an ambitious research project with big implications for medicine, molecular biology and even developmental biology.
Their presentation, 鈥淯sing PNA Oligomers for RNA Visualization and Function Inhibition,鈥 explored how synthetic molecules called peptide nucleic acids鈥攐r PNAs鈥攃ould help scientists better track and control messenger RNA (mRNA), one of the body鈥檚 most important biological messengers.
Their faculty mentor, Dr. Irina Catrina, a clinical associate professor of chemistry at Yeshiva College, praised the project as 鈥渁n exciting demonstration of how synthetic biology tools can open new doors in understanding gene expression and cellular behavior.鈥
The process by which cells make proteins from RNA鈥 mRNA translation鈥攊s a central mechanism in every living cell. It鈥檚 not just about producing proteins; the when and where of this translation deeply affects how organisms grow, respond to stress and fight disease.
鈥淚f we can visualize where RNA is going and stop it from making proteins at the right moment,鈥 said Romero, 鈥渨e can potentially develop better treatments for genetic diseases, cancers or even viral infections.鈥
To do that, Jagtap and Romero worked with PNAs, lab-made molecules that mimic DNA or RNA but with a twist: they have a peptide-like backbone that makes them much more stable and resistant to being broken down by enzymes in the body. 鈥淧NAs are like supercharged genetic tools,鈥 said Jagtap. 鈥淭hey bind more strongly and more precisely to their targets.鈥
The student project had three main goals: Understand how PNAs interact with double-stranded DNA (dsDNA); test whether PNAs could stop mRNA from being translated into proteins; and explore whether PNAs could be used to actually see RNA as it moves through cells.
To mimic real RNA structures, the team created model DNA hairpins鈥攕hort pieces of DNA folded into tight, looped shapes鈥攂ased on the sequence of oskar mRNA, a gene essential for establishing body patterns in fruit fly embryos (Drosophila).
鈥淲e used hairpin structures to model what might happen in real RNA under natural conditions,鈥 said Jagtap. 鈥淭hey gave us a simple but powerful test system.鈥
In the lab, the students folded their DNA hairpins by heating them up and cooling them slowly, then mixed them with different concentrations of PNA. To see whether the PNA bound to the hairpins, they used a method called polyacrylamide gel electrophoresis (PAGE), which separates molecules based on size and shape.
Their results showed that the PNA molecules could efficiently bind and 鈥渋nvade鈥 the DNA hairpins鈥攆orming stable complexes, even at salt concentrations (100 mM NaCl) close to what鈥檚 found in the human body. That鈥檚 important because many previous studies needed milder conditions for similar results.
鈥淲e showed that you don鈥檛 need a huge excess of PNA to get strong duplex invasion,鈥 said Romero. 鈥淭hat鈥檚 a big step toward making these systems usable in real cells.鈥
They also tracked how quickly the PNA-DNA complexes formed and used a type of analysis called pseudo-first-order kinetics to study the rate of binding. The more PNA they added, the faster the binding happened鈥攁 predictable and encouraging result. Some hairpin sequences, particularly ones called HP1, HP1 MUT and HP2, performed better than others, forming complexes more easily.
Still, not all results were clear-cut. 鈥淪tatistically, we didn鈥檛 see significant differences between the hairpins,鈥 said Jagtap, 鈥渂ut that might be because we only had three data points per sample. We鈥檙e planning to run more experiments with better pipetting and more precise loading to improve our data.鈥
Dr. Catrina emphasized the broader implications of the work. 鈥淯nderstanding how PNAs interact with nucleic acids is vital,鈥 she said. 鈥淭his research doesn鈥檛 just help us figure out how to stop translation or image RNA; it could contribute to gene therapies, personalized medicine and real-time cellular diagnostics.鈥
