Unusual photophysical properties of fluorescent cytosine analogues utilized in real-time detecting i-motif DNA: A theoretical study

In this work, we report a theoretical study on the optical properties of a set of fluorescent cytosine analogues as indicators to examine the structural changes during the four-stranded intercalated motif (i-motif) formation. Herein, the neutral bases, protonated monomers and hemiprotonated base pairs corresponding to different stages of the forming process are considered. The calculated results reveal that the modified cytosine analogues show red-shifted absorption and bright fluorescence emission arisen from the increased pi-conjugation characters. Especially, the 1,3-diaza-2-oxophenoxazine (tCO) possesses high fluorescence intensity, large Stokes shift and distinct wavelengths for all considered configurations (445 nm for neutral base, 546 nm for protonated monomer and 509 nm for hemiprotonated base pair), in which the tCO becomes potential candidate for application in detecting i-motif structure. Besides, the fluorescence quenching induced by the proton transfer is observed depending on base pairing, which is another efficient optical probe during the i-motif formation. Also examined are the effects of binding to deoxyribose, which can red-shift the fluorescence emissions and enhance fluorescence intensities for both monomers and base pair.

Automated summary

This theoretical study investigates the optical properties of a set of fluorescent cytosine analogues as indicators to analyze structural changes during the formation of a four-stranded intercalated motif (i-motif). The modified cytosine analogues exhibit red-shifted absorption and bright fluorescence emission, making them potential candidates for detecting i-motif structure. The study also reveals fluorescence quenching induced by proton transfer depending on base pairing, serving as an efficient optical probe during the i-motif formation process.