Synthesis of a novel fluorescent probe and investigation on its interaction with nucleic acid and analytical application

Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study

Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding preference with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (K_abs = 6.3 × 10⁵ M^-1, 5.6 × 10⁴ M^-1, 4.3 × 10⁴ M^-1 and K_emiss = 6.1 × 10⁵ M^-1, 5.7 × 10⁴ M^-1 and 3.5 × 10⁴ M^-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5^/-GCGAATTCGC-3^/ and 3^/-CGCTTAAGCG-5^/). Cell viability assays (86.13 % in 6.58 μM and 84.01 % in 9.88 μM concentrations) and confocal microscopy revealed low cytotoxicity (IC₅₀ 25.86 μM) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encompassing nucleic acid therapeutics.

Multispectroscopic and Computational Investigation of ct-DNA Binding Properties with Hydroxybenzylidene Containing Tetrahydrocarbazole Derivative

Mode of interaction of a new tetrahydrocarbazole derivative with ct-DNA has been investigated systematically using fluorescence spectroscopy, UV-Vis spectroscopy and circular dichroism spectroscopy. It is concluded that TAH could intercalate into the base pairs of ct-DNA, and the fluorescence quenching by ct-DNA was static quenching type. Beside the multispectroscopic results, computational studies were done. Molecular docking results revealed that the TAH-DNAs complexes might be classified as druggable molecule in drug design. Additionally, DNA binding studies exhibited that TAH complexes have different interaction and orientation abilities to each DNA isomer. Combination of experimental and computational data showed that reported TAH is promising structure and deserves further applications.

Unveiling the groove binding mechanism of a biocompatible naphthalimide-based organoselenocyanate with calf thymus DNA: an "ex vivo" fluorescence imaging application appended by biophysical experiments and molecular docking simulations

The present study embodies a detailed investigation of the binding modes of a potential anticancer and neuroprotective fluorescent drug, 2-(5-selenocyanato-pentyl)-6-chloro benzo[de]isoquinoline-1,3-dione (NPOS) with calf thymus DNA (ctDNA). Experimental results based on spectroscopy, isothermal calorimetry, electrochemistry aided with DNA-melting, and circular dichroism studies unambiguously established the formation of a groove binding network between the NPOS and ctDNA. Molecular docking analysis ascertained a hydrogen bonding mediated 'A-T rich region of B-DNA' as the preferential docking site for NPOS. The cellular uptake and binding of NPOS with DNA from "Ehrlich Ascites Carcinoma" cells confirmed its biocompatibility within tumor cells. Experimental and ex vivo cell imaging studies vividly signify the importance of NPOS as a potential prerequisite for its use in therapeutic purposes.

Biochemical investigation of yttrium(III) complex containing 1,10-phenanthroline: DNA binding and antibacterial activity

Characterization of the interaction between yttrium(III) complex containing 1,10-phenanthroline as ligand, [Y(phen)2Cl(OH2)3]Cl2⋅H2O, and DNA has been carried out by UV absorption, fluorescence spectra and viscosity measurements in order to investigate binding mode. The experimental results indicate that the yttrium(III) complex binds to DNA and absorption is decreasing in charge transfer band with the increase in amount of DNA. The binding constant (Kb) at different temperatures as well as thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), were calculated according to relevant fluorescent data and Vant' Hoff equation. The results of interaction mechanism studies, suggested that groove binding plays a major role in the binding of the complex and DNA. The activity of yttrium(III) complex against some bacteria was tested and antimicrobial screening tests shown growth inhibitory activity in the presence of yttrium(III) complex.

An investigation on the fluorescence quenching of 9-aminoacridine by certain pyrimidines

The fluorescence quenching of 9-aminoacridine by certain substituted uracils in water was studied using absorption, steady state and time resolved measurements. The bimolecular quenching rate constants (k(q)), binding constant K and number of binding sites (n) were calculated based on the fluorescence quenching data. The free energy change (ΔG(et)) for electron transfer process was calculated by Rehm-Weller equation. From lifetime measurement we observed that the quenching was mainly due to static mechanism involving ground state complex formation.

Study on fluorescence and DNA-binding of praseodymium(III) complex containing 2,2'-bipyridine

The fluorescence of praseodymium(III) complex containing 2,2'-bipyridine, [Pr(bpy)2Cl3·OH2] has been investigated in details. Also, the biological activity of [Pr(bpy)2Cl3·OH2] has been evaluated by examining its ability to bind to DNA with UV-vis, fluorescence as well as viscosity measurement. The fluorescence of [Pr(bpy)2Cl3·OH2] is strongly quenched through static mechanism in the presence of DNA. DNA intrinsic binding constant, Kb the binding site number, n the Stern-Volmer quenching constant, KSV and the thermodynamic parameters have been determined by fluorescence spectroscopy. For characterization of bonding mode, the effect of various experimental parameters were investigated on the interaction of [Pr(bpy)2Cl3·OH2] with DNA.

Characterization of the aminated agarose nanoparticles labeled with fluorescein isothiocyanate

Incorporating an organic fluorescence agent into nanoparticles can significantly promote its fluorescent efficiency. In this article, a novel fluorescein isothiocyanate labeling aminated agarose (FITC-AA) was synthesized and tested as an effective fluorescent labeling agent. FITC-AA could spontaneously form nanoparticles with a diameter less than 200 nm below 37°C due to gelling effect of the agarose. Cell culture experiments confirmed that 3T3 fibroblast cells could be marked by fluorescent FITC-AA nanoparticles and the labeling time sustained longer than by FITC alone. This finding demonstrates that the fluorescent labeling of cells can be enhanced when fluorescent nanoparticles are used as markers.

Spectrofluorimetric determination of 5-fluorouracil by fluorescence quenching of 9-anthracenecarboxylic acid

Photo-induced intermolecular electron transfer (PET) interaction between excited singlet (S(1)) state of 9-anthracene carboxylic acid (9-ANCA) and DNA bases of pyrimidines as uracil and 5-fluorouracil (5-FU) has been studied in water and ethanol solutions using steady-state fluorescence spectroscopy. The intensity of all emission bands of 9-ANCA was quenched in presence of uracil and 5-FU by electron transfer reaction without formation of an exciplex. It was found that uracil and 5-fluorouracil acts as effective electron donors and simultaneously quench the fluorescence of electron-accepting sensitizer 9-ANCA. The quenching by diffusion-controlled rate coincides well with the dynamic Stern-Volmer correlation. The bimolecular quenching rate constant (k(q)(ss)) and electron transfer rate constant (k(et)) observed are seen to be much higher for 5-fluorouracil than those for uracil. The thermodynamic parameters estimated by using the Rehm-Weller equation were used to propose a suitable mechanism for PET occurring between uracils and 9-ANCA. The proposed method was used to determine 5-fluorouracil from pharmaceutical samples with satisfactory results. The technique is more selective, sensitive and relatively free from coexisting substances.

Fluorescence and DNA-binding spectral studies of neodymium(III) complex containing 2,2'-bipyridine, [Nd(bpy)2Cl(3)xOH2]

The interaction of [Nd(bpy)(2)Cl(3)xOH(2)], where bipy is 2,2'-bipyridine, with DNA has been studied by absorption, emission, and viscosity measurements. [Nd(bpy)(2)Cl(3)xOH(2)] showed absorption decreasing in charge transfer band with increasing of DNA. The binding constant, K(b) has been determined by absorption measurement and found to be (1.5+/-0.1)x10(5)M(-1). The fluorescent of [Nd(bpy)(2)Cl(3)xOH(2)] has been investigated in detail. The interaction was also studied by fluorescence quenching technique. The results of fluorescence titration revealed that DNA had the strong ability to quenching the intrinsic fluorescence of Nd(III) complex at 327 nm. The binding site number n, apparent binding constant K(b) and the Stern-Volmer quenching constant K(SV) have been determined. Thermodynamic parameters have been calculated according to relevant fluorescent data and Van't Hoff equation. Characterization of bonding mode has been studied. The results suggested that the major interaction mode between [Nd(bpy)(2)Cl(3)xOH(2)] and DNA was groove binding.