New Size-Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application.

Here, the synthesis, photophysical characterization, and application of a new size-expanded thymine nucleoside, diox T, is described. diox T has desirable qualities as a T surrogate, including excellent quantum yield (0.36) and high environmental sensitivity. When incorporated into single- and double-stranded DNA, diox T showed excellent photophysical characteristics including a high quantum yield (average 0.20), and unlike BgQ, demonstrated dependence on neighboring bases without significant destabilization of the duplex. Interestingly, the matched base pair of adenine (A) and diox T has the unique property that it exhibits higher fluorescence than mismatched base pairs, and diox T has self-quenching effects. As one example of the possible applications of these promising features, single nucleoside polymorphism typing is demonstrated for discrimination of A by using diox T. The results suggest that diox T can be used for a broad range of applications in chemical biology.