Squash FL Aptamer is a compact, highly stable fluorogenic RNA aptamer evolved from a naturally occurring bacterial adenine riboswitch scaffold, rather than selected from a random-sequence library, to leverage the riboswitch's exceptional in vivo folding efficiency and structural stability. Its ligand-binding pocket was randomized to strongly bind and activate the fluorescence of GFP-like fluorophores such as DFHBI-1T (excitation ~430 nm, emission ~500 nm, green channel). Crystal structure studies at 2.7 Å resolution revealed that Squash sandwiches its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket, notably without a G-quadruplex, distinguishing it mechanistically from other GFP-like aptamers such as Spinach and Broccoli. This superior cellular folding makes Squash well-suited for live-cell RNA imaging as an encodable fluorescent tag. It is also readily engineered into RNA-based sensors for real-time intracellular detection of small molecules such as S-adenosylmethionine (SAM), and is orthogonal to other fluorogenic aptamers (e.g., Pepper) enabling multiplexed dual-color imaging. More recently, Squash has been paired with novel near-infrared fluorophores for in vivo RNA imaging and sensing in mice.
Applications:
If you desire custom RNA fused with Squash FL Aptamer, please use the custom RNA tab and fill in the details to get a custom quote.
1) Dey, S.K., Filonov, G.S., Olarerin-George, A.O., Jackson, B.T., Finley, L.W.S., & Jaffrey, S.R. (2022). "Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag." Nature Chemical Biology, 18, 180–190
2) Truong, L., Kooshapur, H., Dey, S.K., Li, X., Tjandra, N., Jaffrey, S.R., & Ferré-D'Amaré, A.R. (2022). "The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold." Nature Chemical Biology, 18, 191–198
3) Yin, P., Ge, M., Xie, S., Zhang, L., Kuang, S., & Nie, Z. (2023). "A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers." Chemical Science, 14(48), 14131–14139
4) Chen, Z., et al. (2025). "Near-infrared fluorogenic RNA for in vivo imaging and sensing." Nature Communications, 16, 518
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