Selective, pH‐Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4‐Dimethylamino(phenyl)‐Substituted Berberine Derivatives

Abstract

The 9‐ and 12‐dimethylaminophenyl‐substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki‐Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4‐DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA‐melting analysis. Both ligands bind to duplex DNA by intercalation and to G4‐DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb=105−106 M−1) to representative quadruplex forming oligonucleotides 22AG, c‐myc, c‐kit, and a2, than to duplex calf thymus (ct) DNA (Kb=5‐7×104 M−1). At pH 5, however, the affinity of 3 a towards G4‐DNA 22AG is higher (Kb=1.2×106 M−1), whereas the binding constant towards ct DNA is lower (Kb=3.9×103 M−1) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light‐up effect was observed upon association to duplex (Φfl=0.01) and quadruplex DNA (Φfl=0.04) at pH 5. This fluorimetric response to G4‐DNA association in combination with the distinct, red‐shifted absorption under these conditions provides a simple and conclusive optical detection of G4‐DNA at lower pH.

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

“…For example, in the crystal structure, C13 on berberine’s concave site is positioned centrally above the tetrad. Thus, position 13 has commonly been substituted with bulky aromatic moieties, for example, phenylalkyl, diphenylalkyl, dimethylaminophenyl, or pyridine containing groups, to improve stacking interactions or avoid the berberine dimerization. ,,, However, in the solution structure of the berberine–G-quadruplex complex, C13 is located at the edge of the tetrad close to the negatively charged quadruplex groove. Therefore, the more flexible and often cationic alkyl side chains − could be better suited for the berberine concave side, such as position 13 as well as positions 1, 11, and 12, to facilitate backbone interactions and improve binding affinity.…”

“…For example, the recruited A6 of the MycG4 has its 6-amino group as a hydrogen-bond donor and N1, N3, or N7 as hydrogen-bond acceptors. Judicial substituents of berberine C4–C8 or O9, which has been derivatized before, ,, may facilitate hydrogen-bond interactions with the recruited adenine. Similar strategies can be used to target G23 at the 3′ binding site of MycG4 or other bases if alternative G-quadruplexes are targeted.…”

“…In 2017, a paper by Moraca et al in PNAS using computational simulation also suggested a dimer binding mode . Subsequently, the crystal structure and the dimer binding mode have been actively used as a basis to design G4-targeted berberine derivatives. − …”

Structural modifications of berberine and their binding effects towards polymorphic deoxyribonucleic acid structures: A review

“…In 2021, Ihmels’s group successfully synthesized 9-dimethylaminophenyl BBR and 12-dimethylaminophenyl BBR ( 26 and 27 , Figure 12 ) ( Wickhorst and Ihmels, 2021 ). They bond to G4 DNAs with high affinities, both at neutral conditions and at pH 5.…”

Major Achievements in the Design of Quadruplex-Interactive Small Molecules

“…However, in most cases, this light-up effect is merely coincidental between emission and DNA-binding properties. Nevertheless, 9- and 12-dimethylaminophenyl-substituted berberine derivatives showed potential as pH dependent probes for optical detention of G4s [ 279 ]. Moreover, the derivatives Berb9 upon binding to DNA G4 also exhibited pronounced fluorescent light-up effects, namely, with the alkyl chain n = 4 (with a2) and n = 5 (with 22AG) [ 276 ].…”