Fluorescent Nucleic Acids

A new modular approach to the design and discovery of fluorophores and sensors built on a DNA backbone is described. Fluorescent designer nucleosides are synthesized into short oligomers; their close interactions results in highly efficient reporters with properties not seen in standard fluorophores. Applications in sensing of molecules, ions, and enzymes in water and in the vapor phase are described. INTRODUCTION, RESULTS AND DISCUSSION, CONCLUSION Fluorescence is perhaps the mostly widely used analytical tool in biology, and hundreds of small molecule fluorophores and sensors now exist for widespread applications. Despite this progress, current smallmolecule fluorophores have the substantial limitation of requiring separate filter sets for multianalyte imaging. Fluorescent sensors also have this spectral limitation, and importantly, are available for a relatively limited set of biological species. Here we describe a new approach to design and discovery of fluorophores and sensors, by use of the DNA backbone to organize multiple chromophores. The close proximity of the chromophores in ssDNA gives rise to sequence-dependent electronic properties that are not present in the components alone. The oligomeric sensors are water soluble, and can be taken up by human cells. Many different sensors can be excited and visualized at one time. Data show that they can show complex fluorescence responses to the recognition of other molecules and ions. We discuss their use in addressing multiple biologically important problems, such as simultaneous sensing of multiple classes of enzymes in cells, and in identifying bacteria by their volatile metabolites. Like DNA, these short DNA-like reporters can be rapidly and conveniently synthesized in automated fashion from a relatively small set of phosphoramidite monomers. REFERENCES 1. Ren, R. X. F., Chaudhuri, N. C., Paris, P. L., Rumney, S., Kool, E. T. Naphthalene, Phenanthrene, and Pyrene as DNA base analogues: Synthesis, Structure, and Fluorescence in DNA, J. Am. Chem. Soc. 1996, 118, 7671-7678. 2. Gao, J., Strässler, C., Tahmassebi, D. C., Kool, E. T. Libraries of Composite Polyfluors Built from Fluorescent Deoxyribosides, J. Am. Chem. Soc. 2002, 124, 1159011591. 3. Wilson, J. N., Teo, Y. N., Kool, E. T. Efficient Quenching of Oligomeric Fluorophores on a DNA Backbone, J. Am. Chem. Soc. 2007, 129, 1542615427. 4. Teo, Y. N., Wilson, J. N., Kool, E. T. Polyfluorophores on a DNA Backbone: A Multicolor Set of Dyes Excited at a Single Wavelength, J. Am. Chem. Soc. 2009, 131, 3923-3933. 5. Dai, N., Teo, Y. N., Kool, E. T. DNA-polyfluorophore Excimers as Sensitive Reporters of Esterases and Lipases, Chem. Commun. 2010, 46, 1221-1223. 6. Samain, F., Ghosh, S., Teo, Y. N., Kool, E. T. Polyfluorophores on a DNA Backbone: Sensors of Small Molecules in the Vapor Phase, Angew. Chem. Int. Ed. 2010, 49, 7025-7029. 7. Tan, S. S., Kool, E. T. Differentiating Between Fluorescence-Quenching Metal Ions with Polyfluorophores on a DNA Backbone, J. Am. Chem. Soc. 2011, 133, 2664-2671. 8. Koo, C. K., Wang, S., Gaur, R. L., Samain, F., Banaiee, N., Kool, E. T. Fluorescent DNA Chemosensors: Identification of Bacterial Species by Their Volatile Metabolites, Chem. Commun. 2011, 47, 11345-11347. 9. Wang, S., Guo, J., Ono, T., Kool, E. T. DNApolyfluorophores for Real-time Multicolor Tracking of Dynamic Biological Systems, Angew. Chem. Int. Ed. 2012, in press. Figure 1. Fluorescent monomer nucleosides incorporated into short oligomeric sensors of enzymes, ions and small molecules. Thursday, 9 August 9.05 am THE SYNTHESIS OF ULTRA-LONG-MER OLIGO POOLS FROM HIGH-FIDELITY MICROARRAYS Siyuan Chen, Jeremy G. Lackey and Emily M. Leproust,* Agilent Technologies – Genomics Division, 5301 Stevens Creek Blvd., Santa Clara, CA, USA, 95051, *Correspondence to: [email protected]