G-quadruplexes in MTOR and induction of autophagy

G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy, a crucial homeostatic mechanism of the cell, is often dysregulated in neurodegenerative diseases and cancers. We used QGRS mapper to identify 470 G4 sequences in MTOR, a key negative regulator of autophagy. We sought to identify a functional context by leveraging the effect of G4-targeting ligands on MTOR G4 sequences. The effect of Bis-4,3, a G4 selective dimeric carbocyanine dye, was compared with the known G4-stabilizing activity of the porphyrin, TMPyP4 in HeLa and SHSY-5Y cells. Our results show that treatment with G4-selective ligands downregulates MTOR RNA and mTOR protein expression levels. This is the first report describing G4 motifs in MTOR. This study indicates a possible role of G4 stabilizing ligands in induction of autophagy by downregulation of mTOR levels, albeit not precluding MTOR independent pathways.

Stabilization and fluorescence light-up of G-quadruplex nucleic acids using indolyl-quinolinium based probes

G-Quadruplexes (G4s) are four-stranded motifs formed by G-rich nucleic acid sequences. These structures harbor significant biological importance as they are involved in telomere maintenance, transcription, and translation. Owing to their dynamic and polymorphic nature, G4 structures relevant for therapeutic applications need to be stabilized by small-molecule ligands. Some of these ligands turn on fluorescence upon binding to G4 structures, which provides a powerful detection platform for G4 structures. Herein, we report the synthesis of fluorescent ligands based on the indolyl-quinolinium moiety to specifically stabilize G4 structures and sense DNA. CD titration and melting experiments have shown that the lead ligand induces the formation of parallel G4 with preferential stabilization of the c-MYC and c-KIT1 promoter G4s over the telomeric, h-RAS1 G4, and duplex DNA. Fluorimetric titration data revealed fluorescence enhancement when these ligands interact with G4 DNA structures. The fluorescence lifetime experiment of the ligand with different DNAs revealed three excited state lifetimes (ns), which indicates more than one binding site. MD studies showed that the ligand exhibits 3 : 1 stoichiometry of binding with c-MYC G4 DNA and revealed the unique structural features, which impart selectivity toward parallel topology. The ligand was found to have low cytotoxicity and exhibited preferential staining of DNA over RNA. Collectively, the results presented here offer avenues to harness indolyl-quinolinium scaffolds for sensing and selective stabilization of G4 structures.

Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay

G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.

Interaction of a dimeric carbocyanine dye aggregate with bovine serum albumin in non-aggregated and aggregated forms

The interaction of fluorescent dyes with serum proteins has garnered significant interest owing to potential for non-covalent labeling and imaging applications. In this work, dimeric benzothiazole-based trimethine cyanine dyes are synthesized and their interaction with bovine serum albumin studied. The dimeric cyanine dyes mainly exist as H-dimers and H-aggregates in aqueous solution. A combination of absorbance, fluorescence, circular dichroism spectroscopy and atomic force and fluorescence microscopy indicate the formation of dye-BSA complexes. Binding of one of the dimeric dyes on BSA with a K_a of 1.49×10⁵M^-1 results in disruption of dye self-aggregates and unfolding of the dyes into the monomeric or open conformation. Fluorescence enhancement experienced by the dimeric dyes upon interaction with BSA is superior to that registered by Thioflavin T. Surfactant SDS has been used to further tune the self-aggregation of the dimeric dye resulting in a 200-fold fluorescence enhancement in presence of BSA. Interaction of a dimeric dye with BSA under conditions favoring protein aggregation is found to result in faster dye binding and the resulting fluorescence enhancement is easily visualized by fluorescence microscopy. The interaction of a dimeric cyanine dye aggregate with BSA is promising for non-covalent labeling applications in sharp contrast to the monomeric dye counterpart.

Cationic red emitting fluorophore: A light up NIR fluorescent probe for G4-DNA

Guanine (G) quadruplexes (G4) are nucleic acid secondary structures formed by G-rich sequences, commonly found in human telomeric and oncogene-promoter regions, have emerged as targets for regulation of multiple biological processes. Considering their importance, targeting the G-quadruplex structure with small molecular binders is extremely pertinent. In this work, red emitting water soluble fluorophores bearing push-pull substituents were synthesized and examined for their interaction with human telomeric G4 and duplex (ds) -DNAs. The presence of a strong electron donating (dimethylamino) and electron withdrawing (cationic pyridinium) groups linked through a conjugated double bond helps in water solubility and enabling the emission in the near IR region (>700-nm). Binding of this cationic dye to the G4-DNA yields multiple-fold emission enhancement (~70 fold with G4-DNA vs. ~7 fold with ds-DNA) along with hypsochromic wavelength shifts (35 nm with G4-DNA and 8 nm with ds-DNA). The remarkable emission changes, ~2-4 fold enhanced binding efficiency noted with the antiparallel conformation of G4-DNA indicates preferential selectivity over ds-DNA. The molecular docking and dynamics studies of the ligands with duplex and G4-DNA were performed, and they provide insights into the mode of binding of these dyes with G4-DNA and supplement the experimental observations.

Template-free H-dimer and H-aggregate formation by dimeric carbocyanine dyes

Dimeric cyanine dyes self-assemble into H-dimers and H-aggregates, which experience de-aggregation with specific biomolecules.