DFAME is a red fluorophore for RNA nanostructure research

**Background**

The development of sophisticated RNA nanostructures has opened new avenues in the fields of synthetic biology and precision medicine. RNA assemblies, characterized by their ability to organize molecules into specific spatial arrangements, are particularly valuable for studying intracellular molecular interactions and developing advanced delivery systems. Such DNA/RNA nanostructures are increasingly recognized as essential tools in cell and gene therapy (CGT) research, where precise control over molecular architecture can enhance therapeutic efficacy and targeting. To visualize and study these assemblies within the complex environment of living cells, high-performance fluorescent probes are required. In this context, we will introduce a red fluorophore designed for RNA aptamer labeling – DFAME.

**Definition**

DFAME is a red fluorophore with an excitation wavelength of 508 nm and an emission wavelength of 641 nm, used to label dimeric fluorescent RNA aptamers.

**In Vitro Studies**

According to the DFAME description, this compound is characterized by a molecular weight of 322.26 and the DFAME formula $\text{C}_{15}\text{H}_{12}\text{F}_2\text{N}_2\text{O}_4$. DFAME exhibits specific binding affinities for dimeric fluorescent RNA aptamers, specifically Beetroot and Corn. In vitro binding assays demonstrate that DFAME binds to the Beetroot aptamer with a dissociation constant ($K_d$) of 460 nM and to the Corn aptamer with a $K_d$ of 3600 nM. These interactions result in the formation of Beetroot-DFAME and Corn-DFAME complexes. These labeled aptamers can be further utilized to create multivalent RNA assemblies within living cells, providing a powerful method for the study of RNA nanostructures. By leveraging the DFAME biological activity, researchers can monitor the self-assembly of intracellular RNA complexes with high sensitivity. In conclusion, DFAME is a specialized red fluorophore that enables the visualization and construction of RNA nanostructures for biomedical research.

Keywords

DFAME, 1420815-55-9, Fluorescent Dye, fluorophore, Beetroot, Corn, dimeric fluorogenic aptamers, RNA assemblies, Inhibitor, inhibitor, inhibit

References

[1] Jiahui Wu, et al. Self-Assembly of Intracellular Multivalent RNA Complexes Using Dimeric Corn and Beetroot Aptamers. J Am Chem Soc. 2022 Mar 30;144(12):5471-5477.