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Updated: May 12, 2025

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
Published on: July 6, 2016
Synthesis and characterization of a solvatochromic urea-schiff base derivative: Investigating optical properties,
Ibrahim A Alhagri1, Sadeq M Al-Hazmy1, Sarah S Alammari1
1Department of Chemistry, College of Science, Qassim University, Buraydah, Qassim 51452, Kingdom of Saudi Arabia.
Abstract:
This study investigates the fluorescence behavior of the synthesized compound (E)-1-(4-chloro-2-(((2-hydroxynaphthalen-1-yl) methylene) amino) phenyl)-3-(naphthalen-1-yl) urea (3DB) in various solvents. A significant increase in fluorescence intensity was observed when transitioning from ethanol to less polar solvents like CH2Cl2, CHCl3, and CCl4, indicating enhanced fluorescence due to reduced non-radiative processes. Emission wavelengths remained stable with minor shifts (5-6 nm), while significant blue shifts in absorption occurred in water due to strong hydrogen bonding. Fluorescence spectra showed red shifts (519 nm in water, 508 nm in glycerol, and 486 nm in ethylene glycol), highlighting the impact of hydrogen bonding on electronic transitions. Emission intensity in water was six times higher than in ethylene glycol, suggesting that strong hydrogen bonds stabilize the excited state. The study also revealed that 3DB exhibits a large Stokes shift, avoiding reabsorption of emitted light (inner filter effect). Fluorescence was completely quenched by low concentrations of copper ions, demonstrating 3DB's potential as a copper sensor. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations indicated that luminescence quenching in the Cu(II) complex is due to intramolecular charge transfer (ICT). Additionally, 3DB formed stable complexes with DNA and β-cyclodextrin (β-CD), with binding constants (Kb) of 1.30 × 103 M-1 and 1.89 × 103 M-1, respectively, and negative Gibbs free energy values, indicating spontaneous interactions. Fluorescence spectroscopy confirmed DNA binding, showing a 49.62 % increase in intensity and a 4 nm blue shift, consistent with groove-binding. Docking studies further supported favorable interactions with DNA. These results underscore 3DB's potential in sensing, imaging, environmental monitoring, and biological applications.
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