Fluorescent probes for G-quadruplex structures

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• Biologically relevant G-quadruplexes are confirmed in single-cell organisms, but their existence in mammalian cells is debated.
• A key limitation is the lack of in vivo tools to characterize DNA structures, hindering studies on nucleic acid structure-function relationships.
• Nucleic acids are often misconceived as passive carriers, overlooking their complex structures and functions.

Purpose of the Study:

• To review advancements in direct G-quadruplex structure detection using fluorescent probes.
• To highlight the challenges and motivations for developing these probes.
• To present an orthogonal approach using internal fluorescent probes to avoid perturbing native conformations.

Main Methods:

• Development of cell-permeable fluorescent probes for selective G-quadruplex binding.
• Utilizing modified oligonucleotides and fluorescent base analogues as internal probes.
• Characterizing photophysical, biophysical, and biological properties of reported probes.

Main Results:

• Small molecule and modified oligonucleotide probes show promise for G-quadruplex detection.
• Cell-permeable probes can induce G-quadruplex folding, complicating native structure assessment.
• Internal probes offer an orthogonal method to detect conformational changes without perturbing equilibria.

Conclusions:

• Direct detection of endogenous G-quadruplexes in mammalian cells requires sensitive and non-perturbing methods.
• Fluorescent probes, particularly internal ones, are crucial for overcoming current limitations.
• Further development is needed to fully elucidate the role of G-quadruplex structures in mammalian systems.