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 (Kabs = 6.3 × 105 M-1, 5.6 × 104 M-1, 4.3 × 104 M-1 and Kemiss = 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.

pH-Induced Biophysical Perspectives of Binding of Surface-Active Ionic Liquid [BMIM][OSU] with HSA and Dynamics of the Formed Complex.

The influence of pH on the human serum albumin (HSA) interaction with ionic liquid (IL)1-butyl 3-methylimidazolium octyl sulfate ([BMIM][OSU]) at its sub-micellar concentration of 5 mM (well below CMC ∼31 mM at 25 °C) in aqueous solution has been monitored employing different methods, viz., circular dichroism (CD), fluorescence, electrokinetic determination of the zeta potential (ZP), nuclear magnetic resonance (NMR), small-angle neutron scattering (SANS), and molecular docking (MD). CD analysis indicated a noticeable reduction of the α-helical content of HSA by IL at pH 3. A significant interaction of the anionic part of IL with HSA was evident from the 1H chemical shifts and saturation transfer difference (STD) NMR. A strong binding between IL and HSA was observed at pH 3 relative to pH 5, revealing the importance of electrostatic and hydrophobic interactions assessed from global binding affinities and molecular correlation times derived from STD NMR and a combined selective/nonselective spin-relaxation analysis, respectively. ZP data supported the electrostatic interaction between HSA and the anionic part of IL. The nature of IL self-diffusion with HSA was assessed from the translational self-diffusion coefficients by pulse field gradient NMR. SANS results revealed the formation of prolate ellipsoidal geometry of the IL-HSA complex. MD identified the preferential binding sites of IL to the tryptophan centers on HSA. The association of IL with HSA was supported by fluorescence measurements, in addition to the structural changes that occurred in the protein by the interaction with IL. The anionic part of IL contributed a major interaction with HSA at the pH levels of study (3, 5, 8, and 11.4); at pH > 8 (effectively 11.4), the protein also interacted weakly with the cationic component of IL.

Effect of ancillary ligand on DNA and protein interaction of the two Zn (II) and Co (III) complexes: experimental and theoretical study.

In the present work we have developed one mononuclear Zn(II) complex [Zn(L)(H2O)] (Complex 1) by utilizing a tetracoordinated ligand H2L, formed by simple condensation of 2, 2 dimethyl 1,3 diamino propane and 3- ethoxy salicylaldehyde and one newly designed mononuclear Co (III) complex [Co(L)(L1)] (complex 2) by utilizing (H2L) and 3- ethoxy salicylaldehyde(HL1) as an ancillary ligand. The newly developed complex 2 have been spectroscopically characterized. An interesting phenomenon has been noticed that in presence of ancillary ligand, the solubility in buffer solution and the thermal stability of complex 2 comparatively increases than 1. To check the effect of ancillary ligand, present in complex 2 towards the DNA and HSA binding efficacy, both the complexes have been taken into consideration to inspect their binding potentiality with the macromolecules. The 'on', 'off' fluorescence changes in presence of DNA and HSA, the binding constant values, obtained from electronic spectral titration, iodide induced quenching, competitive binding assay, circular dichroism (CD) spectral titration, time resolved fluorescence experiment unambiguously assure the better binding efficacy of complex 2 with the signal of minor groove binding mode with DNA along with no significant conformational changes of the macromolecules. The strong and spontaneous binding of complex 2 with CT-DNA is further supported by the Isothermal Titration Calorimetry (ITC) study. Furthermore TDDFT calculation of DNA with and without complex 2 significantly authorize the formation of complex 2-DNA adduct during the association. Finally Molecular Docking study properly verifies the experimental findings and provides justified explanation behinds experimental findings.

Active Bromoaniline-Aldehyde Conjugate Systems and Their Complexes as Versatile Sensors of Multiple Cations with Logic Formulation and Efficient DNA/HSA-Binding Efficacy: Combined Experimental and Theoretical Approach.

Two fluorescence active bromoaniline-based Schiff base chemosensors, namely, (E)-4-bromo-2-(((4-bromophenyl)imino)methyl)phenol (HL1 ) and (E)-2-(((4-bromophenyl)imino)methyl)phenol (HL2 ), have been employed for the selective and notable detection of Cu2+ and Zn2+ ions, respectively, with the simultaneous formation of two new metal complexes [Cu(L1)2] (1) and [Zn(L2)2] (2). X-ray single crystal analyses indicate that complexes 1 and 2 are tetra-coordinated systems with substantial CH...π/π...π stacking interactions in the solid-state crystal structures. These two complexes are exploited for the next step detection of Al3+ and Hg2+ where complex 2 exhibits impressive results via turn-off fluorescence quenching in (DMSO/H2O) HEPES buffer medium. The sensing phenomena are optimized by UV-vis spectral analyses as well as theoretical calculations (density functional theory and time-dependent density functional theory). The combined detection phenomena of the ligand (HL2 ) and complex 2 are exclusively utilized for the first time to construct a molecular memory device, intensifying their multisensoric properties. Furthermore, the DNA- and human serum albumin (HSA)-binding efficacies of these two complexes are examined by adopting electronic and fluorometric titration methods. Complex 2 shows a higher DNA-binding ability in comparison with complex 1, whereas in the case of HSA, the reverse situation is observed. Finally, the binding modes of both the complexes with DNA and HSA have been investigated through molecular docking studies, suggesting good agreement with the experimental results.

Insights on the interaction of phenothiazinium dyes methylene blue and new methylene blue with synthetic duplex RNAs through spectroscopy and modeling.

The ubiquitous influence of double stranded RNAs in biological events makes them imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situations wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of this study is to delve into the interactive pattern of two small molecule phenothiazinium dyes, methylene blue and new methylene blue, with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic and molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules was evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding patterns of the dye molecules within the RNA duplexes. The novelty of the present work lies towards a new contribution of the phenothiazinium dyes in dysfunctioning double stranded RNAs, advancing our knowledge to their potential use as RNA targeted small molecules.

Understanding the Effect of Single Cysteine Mutations on Gold Nanoclusters as Studied by Spectroscopy and Density Functional Theory Modeling.

Fluorescent metal nanoclusters have generated considerable excitement in nanobiotechnology, particularly in the applications of biolabeling, targeted delivery, and biological sensing. The present work is an experimental and computational study that aims to understand the effects of protein environment on the synthesis and electronic properties of gold nanoclusters. MPT63, a drug target of Mycobacterium tuberculosis, was used as the template protein to synthesize, for the first time, gold nanoclusters at a low micromolar concentration of the protein. Two single cysteine mutants of MPT63, namely, MPT63Gly20Cys (mutant I) and MPT63Gly40Cys (mutant II) were employed for this study. The experimental results show that cysteine residues positioned in two different regions of the protein induce varying electronic states of the nanoclusters depending on the surrounding amino acids. A mixture of five-atom and eight-atom clusters was generated for each mutant, and the former was found to be predominant in both cases. Computational studies, including density functional theory (DFT), frontier molecular orbital (FMO), and natural bond orbital (NBO) calculations, validated the experimental observations. The as-prepared protein-stabilized nanoclusters were found to have applications in the imaging of live cells.

CB7 as a drug vehicle and controlled release of drug through non ionic surfactant: Spectroscopic technique.

A study of the comparative drug carrier properties of cucurbituril[7] (CB7) and ß-cyclodextrin (ß-CD) with a naphthalimide derivative, [2-(2-aminoethyl)-1H-benzo[deisoquinoline-1,3(2H)-dione] (NAP) and its release in aqueous solution using micellar environment, is the key research interest of this work. The profound changes in the different spectroscopic behavior have been attributed to the formation of a 1:1 inclusion complex for NAP:CB7 system. Several experimental outcomes clearly interpreted that CB7 has better drug carrier properties for NAP compared to ß-CD. It has been also focused on the systematic release of NAP molecule from CB7 by using different ionic and non ionic surfactants. Before releasing the drug molecules from CB7 the interaction between NAP and the three different types of surfactants has also been investigated separately. The selectivity of drug carrier and releaser has been monitored, using different spectroscopic techniques like absorbance, fluorescence, fluorescence decay life time and 1H NMR spectroscopy. Besides, a theoretical approach has been followed for a proper geometrical optimized structure of NAP molecule and molecular arrangement of NAP:CB7 inclusion complex. From Density Functional Theory (DFT) it has been seen that NAP molecule is oriented as a t-bone like structure in its optimized form.

Photoinduced Electron Transfer Switching Mechanism of a Naphthalimide Derivative with its Solvatochromic Behaviour: An Experimental and Theoretical Study with In Cell Investigations.

The sole existence of a t-bone-shaped naphthalimide derivative [2-(2-aminoethyl)-1H-benzo[de]isoquinoline-1,3(2H)dione] (NAP), which gives rise to a photoinduced electron transfer (PET) mechanism, has been established using a combination of experimental and theoretical studies. In parallel an in vitro-in cell PET mechanism has also been shown. To understand the photophysics of NAP, solvent studies have been carried out in different solvents. In addition, theoretical calculations have been conducted to explain the spectroscopic properties through optimized structures. A "turn off" PET mechanism has also been observed in the presence of specific metal ions, namely, Cr3+ , Fe3+ and Hg2+ among a series of metal ions. Theoretical studies reveal that NAP-Cr3+ , NAP-Fe3+ and NAP-Hg2+ have their HOMO energy states lying in between a HOMO-LUMO energy state of the t-bone-type NAP molecule. On the contrary, the HOMO state of the other metal ion-NAP conjugate (NAP-Mn+ ) does not lie in between the HOMO-LUMO energy gap of the t-bone-type NAP molecule. Coupled with in vitro studies, in cell investigations reveal an enhancement of fluorescence intensity of NAP upon cytosolic metal sensing. Furthermore, a very high cell viability of NAP treated cells as tested by MTT assay and a fast permeation of the said compound as revealed by flow cytometry suggest NAP to be a potential candidate in metal sensing and bioimaging applications.

Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach.

This study focuses on the understanding of the interaction of phenothiazinium dyes methylene blue (MB), new methylene blue (NMB), azure A (AZA) and azure B (AZB) with tRNAPhe with particular emphasis on deciphering the mode and energetics of the binding. Strong intercalative binding to tRNAPhe was observed for MB, NMB and AZB, bound by a partial intercalative mode. AZA has shown groove binding characteristics. From spectroscopic studies binding affinity values of the order of 105 M-1 were deduced for these dyes; the trend varied as MB > NMB > AZB > AZA. The binding was characterized by an increase of thermal melting temperatures and perturbation in the circular dichroism spectrum of tRNA. All the dyes acquired optical activity upon binding to tRNA. The binding was predominantly entropy driven with a favorable enthalpy term that increased with temperature in all the cases. Dissection of the Gibbs energy to polyelectrolytic and non-polyelectrolytic terms revealed a major role of the non-electrostatic forces in the binding. The small but significant heat capacity changes and the observed enthalpy-entropy compensation phenomenon confirmed the involvement of multiple weak non-covalent forces driving the interaction. The mode of binding was confirmed from quenching, viscosity and cyclic voltammetric results. Using density functional theory, ground state optimized structures of the dyes were calculated to provide insight into theoretical docking studies to correlate the experimental approaches. The modeling results verified the binding location as well as the binding energy of complexation. The results may provide new insights into the structure-activity relationship useful in the design of effective RNA targeted therapeutic agents.

Aggregation-induced fabrication of fluorescent organic nanorings: selective biosensing of cysteine and application to molecular logic gate.

Self-aggregation behavior in aqueous medium of four naphthalimide derivatives has exhibited substitution-dependent, unusual, aggregation induced emission enhancement (AIEE) phenomena. Absorption, emission, and time-resolved study initially indicated the formation of J-type fluorescent organic nanoaggregates (FONs). Simultaneous applications of infrared spectroscopy, theoretical studies, and dynamic light scattering (DLS) measurements explored the underlying mechanism of such substitution-selective aggregation of a chloro-naphthalimide organic molecule. Furthermore, transmission electron microscopy (TEM) visually confirmed the formation of ring like FONs with average size of 7.5-9.5 nm. Additionally, naphthalimide FONs also exhibited selective and specific cysteine amino acid sensing property. The specific behavior of NPCl aggregation toward amino acids was also employed as a molecular logic gate in information technology (IT).

Spectroscopic and quantum mechanical approach of solvatochromic immobilization: modulation of electronic structure and excited-state properties of 1,8-naphthalimide derivative.

Photophysical and spectroscopic properties of a fluorescent analogue, 2-(5-selenocyanato-pentyl)-6-chlorobenzo- [de]isoquinoline-1,3-dione (NP) in different solvents has been described in this paper using steady-state, time resolved spectroscopy and density functional theory (DFT) calculation. Stoke's shifted emission band in different solvents clearly demonstrate the highly polar character of the excited state, which is also supported by the enhancement of dipole moment of the molecule upon photoexcitation. Spectroscopic studies and multiple linear regression analysis method reveal that the solvatochromic behavior of the probe depends not only on the polarity of the medium but also on the hydrogen bonding interaction with the solvents. When the solvent effect was taken into account, the computed results show encouraging agreement with known experimental data. This article reveals the excellent correlation between the predicted and experimental spectral data of 1,8-naphthalimide derivative, providing a useful tool in the design of new fluorogenic probes having potential therapeutic activity.

An efficient, Schiff-base derivative for selective fluorescence sensing of Zn²âº ions: quantum chemical calculation appended by real sample application and cell imaging study.

Since zinc ions (Zn(2+)) are involved in numerous biological phenomena and go through subsequent interactions with zinc-binding proteins, we have attempted a sensitive fluorescence based detection of this second most abundant metal ion using an engineered and synthesized Schiff-base ligand, namely 2,4-bis((Z)-2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)pyrimidine (PyHP). The ligand exhibits a zinc-induced fluorescence response when investigated in a MeOH-buffer (10 mM HEPES, pH = 7) (4 : 1) solvent mixture. The presence of zinc ions (λ(ex) = 410 nm, quantum yield, ϕ = 0.20) causes approximately 45 fold fluorescence enhancement at 489 nm. Formation of the metal-ligand complex was ascertained by (1)H NMR and mass spectra analysis. 1 : 1 binding affinity was ascertained according to Job's plot. Apart from this, theoretical interpretation of the experimental outcome was also obtained by applying density functional theory (DFT) to the PyHP-Zn(2+) complex formation. The practical applicability of the ligand has been tested in bacterial cells as well as in mammalian cell imaging and also by measuring and comparing the amount of Zn(2+) in some real samples such as liquid milk, tomato juice, banana stem juice and commercial fruit juice.

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.

Self-aggregation of MEGA-9 (N-nonanoyl-N-methyl-D-glucamine) in aqueous medium: physicochemistry of interfacial and solution behaviors with special reference to formation energetics and micelle microenvironment.

Self-aggregation of MEGA-9 (N-nonanoyl-N-methyl-D-glucamine), a nonionic sugar-based surfactant, was studied with respect to the effect of salt (NaCl) and ionic liquid (1-butyl-3-methylimidazolium tetrafluoroborate) on its critical micelle concentration (cmc), aggregation number, hydrodynamic dimensions, energetics of micellization, and micellar microenvironment. Fluorimetry (both steady state and time resolved) was used to understand the microenvironments under the influence of additives. NaCl was found to decrease cmc, increase aggregation number (N), increase micellar size, and decrease enthalpy of micelle formation; the IL effect on the parameters was mostly opposite. The microscopic properties of micelles were probed using two fluorophores: one nonpolar C-153 (2,3,5,6-1H,4H-tetrahydro-8-trifluormethylquinolizino-(9,9a,1-gh)coumarin) and the other fairly polar ANS (8-anilinonaphthalene-1-sulfonate); they delivered information on the palisade layer and the peripheral region of the micelle interface, respectively. Energy of activation and entropy of activation of the dynamics of the probes were evaluated from their decay time, lifetime, and rotational movements in the regions of residency in the micelles. Density functional theory (DFT) calculations showed that the ternary combination MEGA-9/IL/H2O had the maximum interaction energy compared to any of the binary combinations. Thus, the ionic liquid reduced MEGA-9 self-association to a large extent.

Explicit spectral response of the geometrical isomers of a bio-active pyrazoline derivative encapsulated in ß-cyclodextrin nanocavity: a photophysical and quantum chemical analysis.

The existence of two geometrical isomers (cis- and trans-) of a biologically significant pyrazoline derivative [5-(-1'-(4-bromo-phenyl)-3a',7a'-hexahydro-1'H-indazol-3'-yl)-3-methyl-1-phenyl-1H-pyrazole-4-carbonitrile] (PZ) has been established using a combined theoretical and experimental investigation. Solvatochromic analysis of PZ revealed the existence of said cis- and trans- isomers. The unique solvatochromic response of the PZ isomers and their preferential encapsulation within ß-cyclodextrin (ß-CD) nanocavity clearly shows the difference in the behavioral nature of the isomers of PZ in homogeneous and heterogeneous medium. Solvent polarity, time-resolved study, and anisotropy results also reinforce in favor of the existence of the isomers. To evaluate the actual orientation of cis and trans-PZ, the ground and excited state geometry of these isomers were optimized by the DFT/LanL2DZ and CIS/LanL2DZ methods, respectively. The experimentally observed results and the theoretically calculated results are found to be in close agreement.

Differential contribution of Igepal and CnTAB micelles on the photophysics of nonsteroidal drug Naproxen.

Spectroscopic studies of Naproxen (NP), a nonsteroidal drug have been carried out in well characterized, micellar media of cationic surfactants of a homologous series having general formula C(n)TAB (alkyl trimethyl ammonium bromide) and of nonionic surfactants of Igepal (Ig) series (poly(oxyethylene) nonyl phenol). The fluorescence behavior of the drug molecule in C(n)TAB micelles has been found to be opposite to that in Igepal micelles. The binding constants during probe micelle binding have been evaluated from relevant fluorescence data. Location and nature of the surrounding medium of the probe in micellar media have been ascertained from fluorescence quenching study. Fluorescence anisotropy parameter has been monitored for exploring the imposed motional restriction of the microenvironment around the probe. Contrasting behavior of the drug molecule has been observed in two different types of micelles. Based on the experimental and theoretical studies, an attempt has been made to explain the different behavior of the probe in different media.