The synthesis and characterization of a universal and fluorescent nucleoside, 4-cyanoindole-2′-deoxyribonucleoside (4CIN), and its incorporation into DNA is described. 4CIN is a highly efficient fluorophore with quantum yields >0.90 in water. When incorporated into duplex DNA, 4CIN pairs equivalently with native nucleobases and has uniquely high quantum yields ranging from 0.15 to 0.31 depending on sequence and hybridization contexts, surpassing that of 2-aminopurine, the prototypical nucleoside fluorophore. 4CIN constitutes a new isomorphic nucleoside for diverse applications.
Bibliographical noteFunding Information:
We thank David Cullen (University of Minnesota, UMN) for assistance performing the DNA thermal melting experiments shown in Table S1. This work was supported by NIH R01-GM110129 and R01-GM118000 and a 3M Graduate Research Fellowship to K.T.P. Mass spectrometry was performed at the Analytical Biochemistry Core Facility of the UMN Masonic Cancer Center, which is supported by the NIH (P30-CA77598). Fluorescence lifetime and circular dichroism experiments were performed at the UMN Biophysical Technology Center.
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