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Abstract
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 π-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.
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