MFB: Programmable RNA Targeting and Engineering using Pentatricopeptide Repeat Proteins

About This Grant

With this award, the Molecular Foundations for Biotechnology (MFB) Program is funding Drs. Chaolin Zhang and Harris H. Wang from Columbia University to engineer modular proteins that can be programmed to precisely edit sequences of RNA messages or control the expression of genes encoded in these messenger RNAs in human cells. This project adapts a unique class of plant proteins, called pentatricopeptide repeat (PPR) proteins that naturally recognize RNA sequences through a modular code. Such proteins will overcome limitations of current RNA-targeting technologies, including imprecise binding and difficulties in introducing them into cells. PPR proteins will be custom designed to bind specific RNA targets with high accuracy, and their performance tested in human cells and compared to existing technologies. In parallel, the project will include community outreach and education through workshops hosted with a public biology lab in New York City, offering hands-on experiences in RNA biology and biotechnology to citizen scientists. Overall, this work could lead to powerful new RNA-based tools with broad applications in biotechnology, agriculture and medicine, while also promoting public understanding and engagement with cutting-edge biological science. The technical goal of this research is to establish a versatile and high-performance platform for programmable RNA targeting using engineered PPR proteins. The team will apply computational approaches to decipher the natural code that allows PPR proteins to bind specific RNA sequences, and then use synthetic biology and high-throughput screening to optimize designer PPR variants (dPPRs) for use in human cells. These tools will be evaluated in terms of binding specificity, efficiency, and functional versatility, and benchmarked against state-of-the-art RNA technologies such as CRISPR and RNA interference. The project integrates computational modeling, synthetic DNA assembly, and RNA functional assays to explore the full potential of PPR-based RNA engineering. By addressing key technical limitations of current platforms—such as off-target effects and delivery complexity—this research will significantly advance molecular tool development. It also offers new insight into how modular RNA-binding proteins function, which may inform future efforts to engineer RNA recognition in diverse biological systems. This project is supported by the Division of Chemistry in the Mathematical and Physical Sciences Directorate, by the Division of Molecular and Cellular Biosciences and the Genetic Mechanisms program in the Biological Sciences Directorate and by the Division of Information and Intelligent Systems in the Directorate for Computer and Information Science and Engineering. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.