Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

Abstract

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2–7 × 105 M−1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.

G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

“…Moreover, in the same study, they also investigated the orientation of the ligand with G4s by analyzing the ICD signals [ 137 ]. The same research group reported the binding modes of a selective fluorescent probe of DNA G4s [ 138 ].…”

Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution

“…Berberine has a long history of use in traditional Chinese medicine, and its anticancer activity is related to its binding to DNA . Berberine and derivatives bind G-quadruplex (G4) DNA structures with higher affinity than duplex DNA. − As such, the G4-binding of berberine has been extensively studied. Berberine has an asymmetric scaffold of four fused rings with a methylenedioxy group at one end (ring A) (Figure C).…”

Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex

“…Then, the fluorescence emission of these solutions was recorded by exciting at 443 nm (at the isosbestic point observed in the UV/Vis spectra, where both the free berberine and the complex have the same extinction coefficient, see Figure 2 ) and collecting the emission at λ max (~536 nm). Fluorescence spectroscopy was chosen to follow the binding because berberine is almost not fluorescent in aqueous solution, whereas a strong fluorescence increase is observed upon binding to G4Qs [ 28 , 29 ]. Thus, the fluorescence intensity is directly related to complex formation.…”