Excited-State Solvation and Proton Transfer Dynamics of DAPI in Biomimetics and Genomic DNA

Utilization of Guanidine-Based Ancillary Ligands in Arene-Ruthenium Complexes for Selective Cytotoxicity

A family of three water-soluble half-sandwich arene-ruthenium complexes, depicted as C ₁ -C ₃ , having the general formula [Ru(p-cymene)(L)Cl]Cl has been synthesized, where L represents (1H-benzo[d]imidazol-2-yl)guanidine (L ₁ ) or (benzo[d]oxazol-2-yl)guanidine (L ₂ ) or (benzo[d]thiazol-2-yl)guanidine (L ₃ ). The crystal structure of complex C ₃ has been determined. The complexes show several absorption bands in the visible and ultraviolet regions, and they also show prominent emission in the visible region while excited near 400 nm. Studies on the interaction of ligands L ₁ -L ₃ and complexes C ₁ -C ₃ with calf thymus DNA reveal that the complexes are better DNA binders than the ligands, which is attributable to the imposed planarity of the ruthenium-bound guanidine-based ligand, enabling it to serve as a better intercalator. Molecular docking studies show that the complexes effectively bind with DNA through electrostatic and H-bonding interactions and partial intercalation of the guanidine-based ligands. Cytotoxicity studies carried out on two carcinoma cell lines (PC3 and A549) and on two non-cancer cell lines (BPH1 and WI-38) show a marked improvement in antitumor activity owing to complex formation, which is attributed to improvement in cellular uptake on complex formation. The C ₁ complex is found to exhibit the most prominent activity against the PC3 cell line. Inclusion of the guanidine-based ligands in the half-sandwich ruthenium-arene complexes is found to be effective for displaying selective cytotoxicity to cancer cells and also for convenient tracing of the complexes in cells due to their prominent emissive nature.

Is DAPI assay of cellular nucleic acid reliable in the presence of protein aggregates?

Intracellular amyloid fibrils prevent exclusive staining of nuclei by DAPI.

Micro-solvation of tyrosine-kinase inhibitor AG1478 explored with fluorescence spectroscopy and computational chemistry

Fluorescence quenching of the anticancer AG1478, by at least three explicit water molecules, can be exploited to probe drug–protein binding interactions.

Tuning of resonance energy transfer from 4′,6-diamidino-2-phenylindole to an ultrasmall silver nanocluster across the lipid bilayer

Liposome mediated efficient tuning of FRET between photoexcited 4′,6-diamidino-2-phenylindole (DAPI) and an ultrasmall silver nanocluster (Ag NC) has been demonstrated using steady-state and time-resolved fluorescence spectroscopy.

Effect of compartmentalization of donor and acceptor on the ultrafast resonance energy transfer from DAPI to silver nanoclusters

The mechanism and dynamics of excitation energy transfer (EET) from photo-excited 4',6-diamidino-2-phenylindole (DAPI) to silver nanoclusters (Ag NCs) and its subsequent modulation in the presence of cationic polymer poly(diallyldimethylammonium chloride) (PDADMAC) and Calf Thymus DNA (CT-DNA) have been demonstrated using steady-state fluorescence and femtosecond fluorescence upconversion techniques. The synthesized Ag NCs were characterized using FTIR, mass spectrometry, XPS, HRTEM, DLS, UV-Vis and PL spectroscopy. Mass spectrometric analysis reveals the formation of ultrasmall Ag4 NCs with a small amount of Ag5 NCs. UV-Vis and PL spectra reveal distinct molecular-like optoelectronic behaviour of these ultrasmall Ag NCs. The dihydrolipoic acid-capped Ag NCs strongly quench the fluorescence of DAPI with concomitant increase in its photoluminescence (PL) intensity at 675 nm. This steady-state fluorescence quenching proceeds with a significant shortening of the fluorescence lifetime of DAPI in the presence of Ag NCs, signifying the nonradiative Förster resonance energy transfer (FRET) from DAPI to Ag NCs. Various energy transfer parameters have been estimated from FRET theory. The present FRET pair shows a characteristic Förster distance of 2.45 nm and can be utilized as a reporter of short-range distances in various FRET based applications. Moreover, this nonradiative FRET is completely suppressed in the presence of both 0.2 wt% PDADMAC and CT-DNA. Our results reveal selective compartmentalization of Ag NCs and DAPI in the presence of 0.2 wt% PDADMAC and CT-DNA, respectively. This selective compartmentalization of donor and acceptor and the subsequent modification of the FRET process may find application in various sensing, photovoltaic, and light harvesting applications.

8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research

The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.

Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial

Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.

An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools

The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.

Solvent and rotational relaxation of coumarin-153 and coumarin-480 in ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate) modified sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (NaAOT) micelle

Understanding ion transport dynamics, structure of surfactant aggregates in ionic liquids or ionic liquid/water solutions are quite interesting and potentially important due to widespread applications of surfactant-based systems. In this manuscript we have investigated the effect of 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)) addition on solvent and rotational relaxation of coumarin-153 (C-153) and coumarin-480 (C-480) in aqueous solution of sodium 1,4-bis(2-ethylhexyl) sulfosuccinate (NaAOT) using steady state and picosecond time resolved fluorescence spectroscopy. The strong adsorption of the bmim(+) at the interface and the role of the ionic liquid particularly the cation bmim(+) in the modification of the interfacial geometry were probed by the analysis of decay parameters and the rotational relaxation parameters. Since the addition of the NaAOT in water-bmimBF(4) mixture above critical micellar concentration (48 mM, obtained from observing pyrene fluorescence) causes strong adsorption of the ionic liquid particularly the cation bmim(+), the average solvation time, particularly the slow component increases significantly. More importantly we have found the probe dependent solvation dynamics due to the different location of the probe molecules, C-153 and C-480. C-153 being hydrophobic in nature resides in the stern layer and the adsorption of the bmim(+) at the interface modifies stern layer more effectively. So we have observed more pronounced change in solvation dynamics in case of C-153 compared to that in case of C-480. The fluorescence anisotropy decays of the probe molecules were found to be biexponential in nature. The anisotropy decay was interpreted by using a model which consists of the wobbling (rotational) and translational diffusion of the dye coupled with the rotational motion of the micelle as a whole.

Spectral response of 4-methyl-2,6-dicarbomethoxyphenol, an excited-state intramolecular proton-transfer probe in cyclohexane-ethanol mixtures: signatures of medium microheterogeneity

In this paper, we explore the role of microscopic heterogeneity of the medium on the spectral response of an excited-state proton-transfer (ESIPT) probe, namely, 4-methyl-2,6-dicarbomethoxyphenol (CMOH) using steady-state and time-resolved emission spectroscopy. The mixtures of two solvents with widely different properties, viz., cyclohexane, a nonpolar, and ethanol, a polar protic solvent, were used as microheterogeneous media for spectroscopic studies. Dual fluorescence (normal and tautomer fluorescence) is observed in the nonpolar solvent (cyclohexane), while only a single peak is observed in the protic solvent, ethanol. The spectral responses of CMOH in the binary mixtures have been found to be dependent on the solvent composition and excitation wavelength. The emission spectral properties of CMOH in the cyclohexane-ethanol mixture have been seen to be superposition of spectral properties in their bulk counterparts, indicating the presence of microscopic heterogeneity in the system. A zwitterionic species of CMOH appears to have been detected in binary solvent mixtures with higher ethanol content only through low-energy excitations. The species is converted into an anionic species as excitation energy increases. Density functional theory calculations indicate that two intramolecularly hydrogen bonded rotamers of CMOH have a small energy difference. The formation of a hydrogen bonded 1:1 molecular cluster of CMOH with ethanol has been investigated in the ground state at the same level of theory. Our findings are expected to shed light on the mechanism of many acid-base reactions occurring in microscopically inhomogeneous media that often mimic many biologically relevant processes.