Selective visualization of DNA G-quadruplex structures in live cells with 1-methylquinolinium-based molecular probes: The importance of indolyl moiety position towards specificity

Abstract

A class of small 1-methylquinolinium-based molecular fluorescent probes with high specificity in DNA G-quadruplex structures imaging in live cells was developed through the structural inclusion with an indolyl moiety. The study reveals that the scaffold of 1-methylquinolinium and indole ring is a distinctive combination for molecular design of new probes with effective and sensitive fluorescent signal switch-on functionality, particularly for identifying telomeric DNA, recognizing G-quadruplexes in promoters, and imaging or visualization of DNA G-quadruplex from other DNA structures. In addition, the experimental results demonstrate a rarely investigated factor on the importance of the indolyl moiety and its position when conjugating with a 1-methylquinolinium scaffold though a ethylene bridge in molecular probe design and synthesis; and these factors are determined as the crucial root leading to the excellent fluorescent signal switch-on property for the specific discrimination of DNA G-quadruplexes against other nucleic acids in live human prostate cancer cells (PC-3 cells) experiments. The characteristics of the new probes were comprehensively investigated with fluorescence titration, native PAGE experiments, and CD analysis to validate the selectivity, sensitivity, and stability while interacting with DNA G-quadruplex structures.