Visualization of G-quadruplexes in gel and in live cells by a near-infrared fluorescent probe

Abstract

G-quadruplexes, one of the most significant secondary structure of nucleic acid, are formed by stacking G quartets, which received broad interests due to their involvement in telomere function, gene transcription and recombination. As for ligand, better selectivity for G-quadruplex against other DNA or RNA structures and higher ability to stabilize G-quadruplex are necessary. In addition, developing a new probe to recognize G-quadruplex is desired for utilizing G-quadruplex structure to relevant biological processes. In this study, we report a Cy5 labelled ligand (named PDP-Cy5) developed as a near-infrared fluorescent ligand for G-quadruplexes both in DNA and RNA. The results indicated that PDP-Cy5 selectively induced the formation of intramolecular G-quadruplexes with strong binding affinity. Furthermore, this Cy5 labelled ligand can effectively stabilize G-quadruplexes. Moreover, the direct visualization of G-quadruplexes in gel, even on cell level is realized by using PDP-Cy5.

Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS

“…1 C) at higher concentrations of KCl (2 M and 3 M) may be because of the coexistence of a minor population of the hybrid quadruplex conformation 28 , 29 , 31 . The formation of quadruplex structure is further confirmed through the hypochromic thermal melting pattern, which is a characteristic feature of quadruplex structure 28 , 32 (Supplementary Fig. S1 ).…”

Design of Modular G‐quadruplex Ligands

“…This probe has also been tested in DNA staining gel experiments, which have confirmed 119 fluorescence and selectivity . Alternatively, 46 d has been conjugated with another fluorophore (Cy5), and resulting probe 120 shows high selectivity for DNA and RNA G4s, allowing their visualization in vitro (native gel electrophoresis) and in cells …”

“…[65] Alternatively, 46 d has been conjugated with another fluorophore (Cy5), and resulting probe 120 shows high selectivity for DNA and RNA G4s, allowing their visualization in vitro (native gel electrophoresis) and in cells. [66]…”

Design and Synthesis of a Dimethylindole Red Trimer: A New Light‐Up Red‐Emitting Fluorescent Probe for G‐Quadruplexes

“…The results in aqueous solution show that Dir‐Trimer has highly selective binding towards G‐quadruplexes, especially trimeric G‐quadruplex. As exogenous prefolded G‐quadruplexes that were transferred into cells could remain their conformations, we chose HT70 as an unlabeled G‐quadruplex sequence and transfected it into cells by transfection reagent. As shown in Figure , the fluorescence signal of cells incubated with Dir‐Trimer only is very weak.…”