Specific Recognition of G-Quadruplexes Over Duplex-DNA by a Macromolecular NIR Two-Photon Fluorescent Probe

Abstract

The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. Herein, we report on a near-infrared (NIR) two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA. In particular, the striking changes in its linear and third-order nonlinear optical properties, combined with the emergence of a strong induced electronic circular dichroism (ECD) signal upon binding to canonical and noncanonical DNA secondary structures allowed for a highly specific detection of several different G4s. Furthermore, through a detailed computational analysis we bring compelling evidence that our probe intercalation within G4s is a thermodynamically favored event, and we fully rationalize the spectroscopic evolution resulting from this complexation event by providing a reasonable explanation regarding the origin of the peculiar ECD effect that accompanies it.

Selective parallel G-quadruplex recognition by a NIR-to-NIR two-photon squaraine

“…S24 † ). This result is in agreement with recent results from Goodson and co-workers 39 and some of us 40 , 41 that relate the changes in the TPA cross-section to the different DNA binding modes. In particular, groove binders exhibit an enhanced TPA cross-section due to the DNA electric field induced enhancement of the transition dipole moment, while intercalators or end-stackers show a decrease in the TPA cross-section when complexed with DNA.…”

“… 42 Indeed, the native conformation of the parallel G4s was almost not affected by the presence of the squaraine dye indicating no or very weak perturbation on the quadruplex morphologies. By analogy with previously reported data for a G4 intercalator, 41 the absence of conformational changes observed for CAS-C1 -parallel G4 systems constitutes a clear evidence of the ability of CAS-C1 to coordinate the external G-tetrads, ruling out the possible intercalative binding behavior of our probe known to give rise to pronounced structural changes associated with a partially disruption of the stacking interactions that govern G4 formation.…”

The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis

“…DFT calculations Ground state geometry optimizations have been performed at the M052X/6‐311G(d,p) level of theory, imposing C s symmetry, for all the calculations not including explicit water molecules. M052X has been selected because it has been tailored to produce a fairly accurate description of stacking interactions and has previously been profitably used to study oligonucleotides, including guanine‐based quadruplexes . We have performed test calculations using the geometries optimized by M052X with a smaller basis set (6‐31G(d)) or by CAM‐B3LYP or B3LYP functionals, checking that the computed spectra do not significantly depend on these details.…”

Reversible Photocontrol of DNA Melting by Visible‐Light‐Responsive F4‐Coordinated Azobenzene Compounds

“…The binding ability of the azo compounds was also tested in the presence of higher‐order DNA structures that form G‐quadruplex (G4) motifs. In this study, the archetypical guanine‐rich telomeric DNA sequence (5′‐A(GGGTTA)3GGG‐3′, henceforth denoted as Tel‐22) was used as a model system . In solution, Tel‐22 adopted a single antiparallel conformation under a high concentration of Na + , whereas a (3+1) hybrid architecture, in which three of the four strands were parallel and the fourth pointed in the opposite antiparallel direction, occurred under K + conditions.…”