Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

Chilka, Pallavi; Patlolla, Prathap Reddy; Datta, Bhaskar

doi:10.1039/c6ra05474a

Cited by 9 publications

(7 citation statements)

References 42 publications

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“…We have recently reported the distinctive self-assembly and G4 recognition by dimeric cyanine dyes [ 20 ]. The aggregates of these dyes are fluorescence-quenched in aqueous media and exhibit significant fluorescence enhancement upon interaction with G4 DNA.…”

Section: Resultsmentioning

confidence: 99%

“…We compare the performance of B6,5 with TO as part of this work. TO is a suitable control for B6,5 in the present experiments based on its established end-stacking mode of binding to G4 structures that is also followed by the dimeric cyanine dyes [ 20 , 40 ]. To this end, we calculated the percentage fluorescence decrease of B6,5 and compared it with the same of thiazole orange.…”

Section: Resultsmentioning

confidence: 99%

“…In this study, we report a dimeric cyanine small molecule, B6,5, which can be used in fluorescence displacement assays to screen G4-specific ligands for DNA and RNA G-quadruplexes. We have previously reported the ability of dimeric carbocyanine dye to selectively bind DNA G4 structures [ 20 ]. B6,5 is a benzothiazole-based dimeric dicarbocyanine dye and we examine it as an alternative to TO considering the modest selectivity of the latter for G-quadruplex over duplex DNA [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

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

2021

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

2021

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“…These results shed light on the propensity of dimeric dicarbocyanine dyes to self‐assemble and suggest uses of such dye aggregates in fluorescence sensing applications. Work on the development and optimization of such dyes is ongoing in our laboratory …”

Section: Discussionmentioning

confidence: 99%

Template‐Free Self‐Assembly of Dimeric Dicarbocyanine Dyes

2017

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Symmetrical dicarbocyanine dyes are known to cooperatively assemble on DNA templates. With the goal of developing dyes that are capable of template‐free self‐assembly, two N‐linked dimeric benzothiazole containing pentamethine cyanine dyes have been synthesized. UV‐visible spectroscopy of the dimeric dyes reveals very strong propensities for self‐assembly unlike their monomeric dye counterparts. The N‐propyl linked dye exhibits pronounced H‐aggregation at micromolar dye concentrations with the absorption maxima blue‐shifted by nearly 200 nm. In contrast, an N‐hexyl linked dye preferentially folds into H‐dimers. Similar aggregates of the monomeric dicarbocyanine dyes are known to be observed at much higher dye concentrations or in presence of suitable templates such as DNA molecules. The aggregate species of the dimeric dyes are identified based on shifts in their absorbance maxima and quenched fluorescence. The calculated electronic structure of the dimeric dyes supports their observed aggregation behaviour. Further, introduction of DNA molecules with AT‐tracts leads to transformation of the spontaneously formed dimeric dye H‐aggregates and H‐dimers into DNA‐bound dye species.

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“…We have previously reported the G4-binding behaviour of a novel dimeric carbocyanine dye, Bis-4,3 [Fig. 1F] that displayed strong propensity to selectively bind parallel G4 with concomitant fluorescence turn-on 31,32 . While our previous work focused on the G4-selective fluorescent reporting potential of Bis-4,3, interest in its ligand-like behaviour led to the formulation of the current work.…”

Section: G4 Stabilization By Tmpyp4 and A Di-carbocyanine Ligand Bis-43mentioning

confidence: 99%

G4-Selective Ligand Induced Autophagy

Majumder¹,

Shukla²,

Datta

2021

Preprint

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G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy is a housekeeping cellular homeostatic mechanism and deregulation of autophagy is common in cancer and in neurodegenerative diseases. In this study, we identified the presence of 46 putative G4 sequences in the MTOR gene by use of QGRS mapper tool. We sought to connect these putative G4 sequences to a functional context by leveraging G4-targeting ligands. A G4-selective dimeric carbocyanine dye Bis-4,3 and the porphyrin TMPyP4 were used to affect the replication, transcription and translation of the MTOR gene. The ligand-induced induction of autophagic pathway via MTOR gene regulation was monitored upon treatment of HeLa and SHSY-5Y cells with G4-targeting ligands. The use of Bis-4,3 was compared with the known G4-stabilizing activity of TMPyP4. Our results show that treatment with G4-selective ligands downregulates mTOR activity and leads to the induction of excessive autophagy. This is first report on effect of G4-selective ligands on MTOR regulation and mTOR expression. mTOR being the key negative regulator of autophagy, the current work suggests potential of G4 stabilizing ligands towards induction of autophagy through the downregulation of mTOR.

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Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

Abstract: A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

Cited by 9 publications

References 42 publications

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

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

Template‐Free Self‐Assembly of Dimeric Dicarbocyanine Dyes

G4-Selective Ligand Induced Autophagy

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