Dr. Samie Jaffrey is a Professor of Pharmacology at the Weill Medical College of Cornell University. He received an M.D. and Ph.D. from Johns Hopkins School of Medicine where he also conducted postdoctoral work. Dr. Jaffrey’s laboratory focuses on identifying novel RNA regulatory pathways the control protein expression in normal cellular function and in disease processes. His research uses novel imaging, sequencing, microfluidic, and chemical biology approaches to address these questions. Dr. Jaffrey’s laboratory developed a novel class of RNAs referred to as “RNA mimics of green fluorescent protein,” which are used to image RNA localization and monitor RNA processing in living cells. The Jaffrey laboratory extended this technology to create a new class of genetically encoded biosensors composed of RNA that allows signaling molecules to be imaged in living cells.
Imaging RNA and RNA biology using RNA mimics of green fluorescent protein
Green fluorescent protein (GFP) and its derivatives have transformed the use and analysis of proteins for diverse applications. Like proteins, RNA has complex roles in cellular function and is increasingly used for various in vitro and in vivo applications, but a comparably robust and simple approach for fluorescently tagging RNA is lacking. We will describe the creation of RNA aptamers that bind fluorophores resembling the fluorophore in GFP. These fluorophores are nonfluorescent in vitro and in cells, but become fluorescent upon binding specific aptamers. A variety of fluorophores have been designed that mimic fluorophores naturally found in GFP and red fluorescent protein (RFP), and the corresponding RNA-fluorophore complexes, termed Spinach, Corn, and Red Broccoli, exhibit green, yellow and red fluorescence. These aptamers function as genetically encodable imaging tags, but also enable visualization of other cellular processes such as real-time imaging of transcription in single cells. Another use of these aptamers is for the creation of genetically encoded sensors composed of RNA that report on the endogenous metabolite and protein levels. We will discuss the various strategies for the design of these sensors as well as novel structure-guided, directed evolution, and massively parallel biochemical approaches for optimizing the use of these RNA-based sensors.
Paige, J.S., Wu, K.Y., Jaffrey, S.R. RNA mimics of green fluorescent protein, Science, 333:642-646, 2011.
Paige, J.S., Nguyen-Duc, T., Song, W., Jaffrey, S.R. Fluorescence imaging of cellular metabolites with RNA, Science, 335:1194, 2012.
Strack, R.L., Disney, M.D., Jaffrey, S.R. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nature Methods, 10:1219-1224, 2013.
Filonov, G.S., Moon, J.D., Svensen, N, Jaffrey, S.R. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. Journal of the American Chemical Society, 136:16299-16308, 2014.