Fluorescence Light-Up Probe for Parallel G-Quadruplexes

Abstract

Putative G-quadruplex-forming sequences (PQS) are highly prevalent in human genome; however, the structures and functions of most PQSs in genome are poorly understood. Therefore, selective recognition of certain types of G-quadruplexes (G4s) is important for the study of G4s. A new light up fluorescent probe, BPBC composed of benzimidazole and carbazole moieties was designed and synthesized. BPBC possesses a crescent-shaped π-conjugated planar core that is slightly larger than the dimension of the G-quartet plane in G4s. This structure endows BPBC with excellent selectivity to parallel G4s. BPBC exhibits almost no fluorescence in the aqueous buffer condition, its fluorescence increases approximately 330-1800-fold in the presence of parallel G4s but only about 30-fold in the presence of single/double-stranded (ss/ds) DNA and 30-110-fold in the presence of antiparallel G4s. Binding studies indicate that the highly selective fluorescent response of BPBC arises from end-stack binding model to G-quartet.

A comparative study for recognizing G-quadruplexes using dimeric cyanine dyes with different sizes of aromatic substituents

“…24 However, the affinities and uorescence enhancements are not directly correlated, due to the different microenvironments in the binding sites, which avoid the nonradiative relaxation process to different extents. 32 Here, we observed that these cyanine dyes could selfassemble aggregation and result in self-quenching in PBS, and also can recover high uorescence in the presence of G-quadruplex by transformation among different aggregations. It is well known that aggregation-caused quenching (ACQ) oen limits the label to analyte ratio and narrows the practical application.…”

DNA interaction, cellular localization and cytotoxicity of quinacridone derivatives

“…The Φ f values of QA and QAB greatly increased in the presence of parallel G-quadruplexes (EAD, Pu22, ckit2, and c-myc); and that of QAT and QAP increased in the presence of all forms of DNA. The Circular dichroism spectra of G-quadrplexes sequences in the presence of QAs did not show significant change ( Figure S5) compared with the CD spectra of these sequences in the absence of QAs [29,30], suggesting that the interaction of QAs with G-quadrplexes did not cause the conformation change of G-quadruplexes.…”

“…The fluorometric titration curves were further fitted to an independent-site model [29][30][31] (eq 1, Materials and Methods). All the data of QA/QAB against parallel G-quadruplexes fitted well by using 1:1 stoichiometry with R 2 higher than 0.98, however, the data of QAP and QAT could not satisfactorily fitted using any stoichiometry of 2:1, 1:1, 1:2 and 1:3…”

“…Based on the structure of G-quadruplexes, the loops distribute on the side faces of parallel G-quadruplexes, or on the top and bottom G-quartet plane of the antiparallel G-quadruplexes. Therefore, the parallel structure is in favor of the end-stacking of ligands because of less interference from loops [29,30]. In current case, QAs have a large π-conjugated core, thus QA and QAB could strongly end-stack on the G-quartets planes of parallel G-quadruplexes, which caused the transition from aggregates to monomers and resulted in the intensity change and red-shift of their absorption bands, as well as 10 assay showed that QA and QAB had good selectivity to parallel G-quadruplexes; but the selectivity was almost completely lost after added more than one amine group on QAs although the affinity was greatly increased.…”

“…included a single-stranded DNA (ssDNA), a duplex DNA (dsDNA) formed by ssDNA and its complementary sequence; four parallel G-quadruplex sequences (EAD, c-myc, c-kit2, Pu22); and two antiparallel G-quadruplex sequences (TBA and 22AG)[29,30].…”