Viscosity Of DNA Research Articles

Spectroscopic and computational approaches to unravel the mode of binding between a isoflavone, biochanin-A and calf thymus DNA

In the present study, attempt was made to explore the interaction between biochanin-A (BioA) and calf thymus DNA (ctDNA) by employing fluorescence spectroscopy, absorption spectroscopy, circular dichroism (CD), DNA melting studies, viscosity measurements, and molecular modeling methods. A well-known fluorescence probe, acridine orange (AO) was used in the present study in order to enhance the emission intensity of weakly fluorescent ctDNA. Quenching in emission intensity of ctDNA-AO system was observed in the presence of different concentrations of BioA, suggesting that BioA has interacted with ctDNA. The hyperchromic effect observed upon the addition of BioA in the absorption spectra of ctDNA-AO without any shift in its absorption maximum revealed that BioA was bound to ctDNA through groove mode of binding. Further the groove mode of binding of BioA to ctDNA was confirmed by DNA melting studies, viscosity measurements, and molecular docking studies. The results of fluorescence measurements that were carried out at different temperature indicated that the BioA has quenched the emission intensity of ctDNA-AO through static mode of quenching mechanism. Thermodynamic parameters revealed that the BioA-ctDNA-AO system was stabilized by van der Waals forces and hydrogen bonding. The effect of binding of BioA on the conformation of ctDNA was examined by circular dichroism studies.

Antiproliferative activities of procainamide and its binding with calf thymus DNA through multi-spectroscopic and computational approaches

The interaction between procainamide with ct-DNA was seen through several experimental and theoretical methods. The fluorescence intensity of procainamide decreased on increasing the concentration of ct-DNA and the quenching process was found to be static with approximately 1:1 binding between ct-DNA and procainamide. UV absorption spectroscopy gave an idea about minor groove binding which was further confirmed by the dye displacement method of DAPI/EtBr bounded ct-DNA interaction. Minor groove binding was also evidenced from the collective information obtained from DNA melting, viscosity and CD spectroscopy. Molecular docking simulations presented that procainamide bound in the minor groove (AT rich) region of B-DNA structures. From thermodynamic point of view the binding interaction between procainamide and ct-DNA was spontaneous process with liberation of energy and overall ordering of system. Hydrogen bonding was found to play important role as suggested by the values of thermodynamic parameters. Whereas from molecular docking simulations it was exposed that hydrogen bonding and hydrophobic interactions were crucial in the binding of ct-DNA and procainamide. DFT method was also used to calculate the Frontier molecular orbitals (HOMO and LUMO) of procainamide which were further used to calculate chemical potential (μ), chemical hardness (η) and fraction number of electrons (ΔN) from procainamide to DNA. Procainamide was found to act as electron donor to DNA bases excpet guanine. Finally, elucidation of anticancer activity revealed that procainamide possesses potential cytotoxicity against MCF-7 breast cancer cells and able to induce significant level of apoptosis at concentrations below IC50 value.

The effect of dimerization on the interaction of ibuprofen drug with calf thymus DNA: Molecularmodeling and spectroscopic investigation

ABSTRACTThe interaction between the dimer structure of ibuprofen drug (D-IB) and calf thymus DNA under simulative physiological conditions was investigated with the use of Hoechst 33258 and methylene blue dye as spectral probes by the methods of UV-visible absorption, fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling study.Using the Job's plot, a single class of binding sites for theD-IB on DNA was put in evidence. The Stern–Volmer analysis of fluorescence quenching data shows the presence of both the static and dynamic quenching mechanisms. The binding constants, Kb were calculated at different temperatures, and the thermodynamic parameters ∆G∘, ∆H∘ and ∆S∘ were given. The experimental results showed that D-IB molecules could bind with DNA via groove binding mode as evidenced by: I. DNA binding constant from spectrophotometric studies of the interaction of D-IB with DNA is comparable to groove binding drugs. II. Competitive fluorimetric studies with Hoechst 33258 have shown that D-IB exhibits the ability of this complex to displace with DNA-bounded Hoechst, indicating that it binds to DNA in strong competition with Hoechst for the groove binding. III. There is no significantly change in the absorption of the MB-DNA system upon adding the D-IB, indicates that MB molecules are not released from the DNA helix after addition of the D-IB and are indicative of a non-intercalative mode of binding. IV. Small changes in DNA viscosity in the presence of D-IB, indicating weak link to DNA, which is consistent with DNA groove binding. As well as, induced CD spectral changes, and the docking results revealed that groove mechanism is followed by D-IB to bind with DNA.

DNA binding and cleavage properties of ponicidin.

Ponicidin, an effective component isolated from Isodon rubescens, possesses anticancer properties. In the present study, we proved its ability to bind to and cleave DNA. DNA binding and cleavage properties are important for designing the rational construction of new and more efficient drugs targeted to DNA, because DNA is the biological target with which many anti-tumor drugs and potential antineoplastic agents interact. The characterization of interaction of ponicidin not only provides insights into its biology, but also gives the opportunity for developing effective therapeutic agents for control of gene expression. The interaction of ponicidin with DNA has been explored by using absorption spectroscopy, fluorescence spectroscopy, viscosity measurement, thermal denaturation and electrophoresis measurement. Firstly, adding ponicidin to a DNA solution could shift the absorption spectra to red. Secondly, ponicidin also raised the melting temperature and viscosity of DNA. Moreover, fluorescence of DNA binding with ethidium bromide was quenched by ponicidin. Finally, ponicidin showed nuclease activity. We propose that the DNA binding and cleavage properties of ponicidin may underlie the mechanism of its cell toxic effects.

Crystal structure, theoretical and experimental electronic structure and DNA/BSA protein interactions of nickel(II) N2O2 tetradentate Schiff base complexes

Nickel(II) allyl arm Schiff base complexes ([NiL1] and [NiL2]) were synthesized and characterized by elemental analysis and ESI-MS, FT-IR, UV–Vis and 1H NMR spectral techniques. The structure of [NiL1] and [NiL2] were analyzed by single crystal X-ray crystallography reveal nickel complexes have slightly distorted square planar geometry around the metal ions. DFT calculations for [NiL1] and [NiL2] in gas phase were performed using SDD basis set for nickel atom and 6-311G(d,p) basis set for the remaining atoms and also at PW91/TZ2P/ZORA level. The electronic transitions of the complexes in acetonitrile were studied by TD-DFT calculations. The energy decomposition analysis was performed to understand the nature of bonding between Ni(II) and Schiff bases (H2L1 and H2L2) suggests that more covalent nature of bonding is in metal complexes. Hypochromism in absorption spectra, emission intensity decrease in EB-DNA complex and DNA viscosity increase by the addition of increasing concentration of the metal complex indicate intercalative mode of binding of the complex with DNA. The binding constants calculated are of the order of 105M−1. The BSA protein binding behavior with [NiL1] and [NiL2] were investigated using absorption and fluorescence titration experiments show alteration in protein’s microenvironment. Also, molecular docking studies were performed to understand the DNA-complex interactions.

Microwave-assisted synthesis of mixed ligands organotin(IV) complexes of 1,10-phenanthroline and l-proline: Physicochemical characterization, DFT calculations, chemotherapeutic potential validation by in vitro DNA binding and nuclease activity

Diorganotin(IV) and triphenyltin(IV) derivatives of L-proline (HPro) having general formula R2Sn(Pro)2 (R=n-Bu (1), Ph (2)) and Ph3Sn(Pro) (3), respectively, and the mixed ligands di-/triorganotin(IV) derivatives of L-proline and 1,10-phenanthroline (phen) with general formula [R2Sn(Pro)(Phen)Cl] and [R3Sn(Pro)(Phen)] (where R=Me (4 and 7), n-Bu (5 and 8), Ph (6 and 9)), respectively, have been synthesized by microwave-assisted method and characterized by elemental analysis, IR, NMR (1H, 13C and 119Sn) and DART-mass spectral studies. The results suggest bicapped tetrahedron or a skew trapezoidal-bipyramid geometry for R2Sn(Pro)2, a distorted tetrahedral geometry for Ph3Sn(Pro) and a distorted octahedral geometry for [R2Sn(Pro)(Phen)Cl] and [Ph3Sn(Pro)(Phen)] around the Sn atom, and the same has been validated by density functional theory calculations (DFT). In vitro DNA binding studies of 1–9 have been investigated by UV–Vis, fluorescence and circular dichroism titrations, viscosity and DNA melting experiments. The observed hypochromic shift in UV–Vis and fluorescence studies evidenced a partial intercalative mode of binding of complexes to CT-DNA. The binding affinity and quenching ability have been quantified in terms of intrinsic binding constant (Kb) and Stern-Volmer quenching constant (Ksv). The determined values suggest that di- and triorganotin(IV) derivatives of L-proline possess lesser affinity to bind with CT-DNA in comparison to the mixed ligands di-/triorganotin(IV) derivatives of L-proline and 1,10-phenanthroline. The partial intercalative mode of binding of these complexes with CT DNA has also been supported by a change in the viscosity and melting point of DNA as well as a change in the intensity of positive and negative bands in circular dichroism spectra. The cleavage studies by agarose gel electrophoresis indicate effective cleavage of supercoiled plasmid DNA into its nicked form by all the complexes and even to its linear form in presence of 9.

DNA Binding with Acetate Bis(1,10-phenanthroline)silver(I) Monohydrate in a Solution and Metallization of Formed Structures.

The study of DNA interaction with the acetate bis(1,10-phenanthroline)silver(I) monohydrate in a solution is of interest both for understanding the mechanism of biological activity of silver compound and for forming ordered structures (DNA fibrils) that can be used to solve various problems in the field of nanotechnology. The analysis of changing the DNA conformation (secondary structure, persistent length and volume effects) during the interaction by the methods of UV spectroscopy with the analysis of DNA melting, circular dichroism, viscosity, flow birefringence, AFM (atomic force microscopy) and SEM (scanning electron microscopy) was performed. The formation of two types of complexes was observed. At lower concentration of compound in DNA solution, silver atoms form the coordination bonds with a macromolecule, while the released phenanthroline ligands intercalate between DNA bases. When the concentration of the compound increases, the phenanthroline ligands form an ordered “layer” around the helix. The excess of silver compounds in the DNA solution (with more than five silver atoms per base pair), DNA precipitation is observed with the formation of long fibrils. It was shown that the binding of silver to DNA during the formation of complexes provides further metallization of the resulting structures with the aid of reducing agents; phenanthroline ligands influence the result of such metallization.

A multi-spectroscopic and molecular docking approach to investigate the interaction of antiviral drug oseltamivir with ct-DNA

ABSTRACTThe possible interaction between the antiviral drug oseltamivir and calf thymus DNA at physiological pH was studied by spectrophotometry, competitive spectrofluorimetry, differential pulse voltammogram (DPV), circular dichroism spectroscopy (CD), viscosity measurements, salt effect, and computational studies. Intercalation of oseltamivir between the base pairs of DNA was shown by a sharp increase in specific viscosity of DNA and a decrease of the peak current and a positive shift in differential pulse voltammogram. Competitive fluorescence experiments were performed using neutral red (NR) as a probe for the intercalation binding mode. The studies showed that oseltamivir is able to release the NR.

Aminoacid-derivatized Cu (II) complexes: Synthesis, DNA interactions and in vitro cytotoxicity

Two different series of copper complexes, [Cu(MFL)(FcAA)H2O] (C1-C4) and [Cu(MFL) (BzAA)H2O] (C5-C8), where FcAA = ferrocenyl amino acid mannich base conjugates and BzAA = benzaldehyde amino acid mannich base conjugates have been synthesized and characterized by spectroscopic methods. The complexes have been investigated for their interactions with DNA by employing fluorescence quenching measurements, UV–Vis spectroscopy and DNA viscosity measurements. High binding constants obtained from the DNA binding studies (Kb = 106 M−1) prompted the in-vitro cytotoxicity assay of complexes on A549 human lung carcinoma cells (employing MTT assay). The IC50 values obtained herein were found to be lower than those of the ligands for A549 cell line. Antiproliferative effects on A549 tumour cells exerted by the complexes were consistent with their intracellular uptake properties. The cellular uptake studies indicated that complexes C1-C8 enter the cytoplasm and accumulate in the nuclei. Rapid change in the nuclear morphology was observed with DAPI staining. Acridine orange/ethidium bromide dual staining revealed that most of the A549 cells enter early apoptosis within 12 h of treatment. Further all the complexes showed effective cell growth inhibition by triggering G0/G1 phase arrest and inducing apoptosis. FACScan results revealed remarkably high percentage of cell death induced by the complexes in the A549 cells, as compared to control. Annexin-V/PI staining of cells also indicated that the complexes induce cell death through the apoptotic pathway. Our data here suggests that the complexes could be good antitumor agents.

Novel mononuclear Cu (II) terpyridine complexes: Impact of fused ring thiophene and thiazole head groups towards DNA/BSA interaction, cleavage and antiproliferative activity on HepG2 and triple negative CAL-51 cell line

Two mononuclear copper (II) terpyridine complexes namely, [Cu(Btptpy) (ClO4)](ClO4) 1, and [Cu(Bttpy) (ClO4)](ClO4) 2, (Btptpy (L1) = 4’-(Benzothiophene)-2,2’:6′,2″-terpyridine, Bttpy (L2) = 4’-(Benzylthiazolyl)-2,2’:6′,2″-terpyridine) have been synthesized and characterized. Single crystal X-ray diffraction shows that, both ligands belong to monoclinic crystal system with space group P21/c (L1) and P21/n (L2). Absorption spectral titration, DNA melting study, circular dichroism and viscosity measurement reveal that, complex 1 and 2 bind with DNA through intercalation. In addition, interaction between the two copper (II) complexes and bovine serum albumin (BSA) has been studied by fluorescence titration, circular dichroism and their protease activity has been investigated using SDS-PAGE gel electrophoresis. Agarose (AGE) and SDS-PAGE gel electrophoresis reveals both complexes have good nucleolytic and proteolytic property in the presence of additive hydrogen peroxide. Both complexes shows remarkable cytotoxic property against triple negative CAL-51 human breast cancer cell line and hepatocellular carcinoma (HepG2) cancer cell lines and bears very less cytotoxicity towards liver normal cell line (Changs). DCF-DA and TBRAS assay also supported that complex 1 and 2 induces elevated level of reactive oxygen species (ROS) and oxidative stress in cancer cells than normal cell line. Furthermore, FACS analysis confirms complex 1 and 2 brings apoptosis by growth phase cell cycle arrest.

DNA interaction, antimicrobial, anticancer activities and molecular docking study of some new VO(II), Cr(III), Mn(II) and Ni(II) mononuclear chelates encompassing quaridentate imine ligand

The present study was conducted to synthesis of some new imine Cr(III), VO(II), Mn(II) and Ni(II) complexes derived from the condensation of 2-amino phenol with 2-hydroxynapthaldehyde were synthesized. The prepared HNPN imine ligand was analyzed by its melting point, IR, 1H NMR and 13C NMR spectroscopies. The investigated HNPN imine complexes were characterized by elemental analysis, FT IR, UV–vis and thermal analysis (TGA) under nitrogen atmosphere from ambient temperature to 750°C. The experimental results revealed that the investigated complexes contain hydrated water molecules. The molar conductance values of complexes are relatively low, indicating the non-electrolytic nature of these complexes. Magnetic susceptibility measurements show that the investigated complexes are paramagnetic. Moreover, the stability constants of the preparing complexes were determined spectrophotometrically. All the complexes were found to be monomeric 1:1 (M:L) stoichiometry in nature with octahedral geometry for Cr(III), tetrahedral for Mn(II), square planner for Ni(II) and square pyramidal for VO(II). Moreover, the prepared HNPN imine ligand and its complexes were evaluated for antimicrobial effect against some types of bacteria such as Bacillus subtilis (+ve), Escherichia coli(−ve) and Staphylococcus aureus (+ve) and some types of fungi such as Aspergillusniger, Candida glabrata and Trichophyton rubrum. The results of these studies indicate that the metal complexes exhibit a stronger antibacterial and antifungal efficiency compared to their corresponding imine ligand. Moreover, the interaction of the investigated complexes with CT-DNA was checked using spectral studies, viscosity measurements and gel electrophoreses. The absorption titration studies revealed that each of these complexes is an avid binder to calf thymus-DNA. Also, there was appreciable changes in the relative viscosity of DNA, which is consistent with enhanced hydrophobic interaction of the aromatic rings and intercalation mode of binding. In addition to, the cytotoxic activity of the prepared imine complexes on human colon carcinoma cells, (HCT-116 cell line), hepatic cellular carcinoma cells, (HepG-2 cell line) and breast carcinoma cells (MCF-7 cell line) has cytotoxicity effect against growth of carcinoma cells compared to the clinically used Vinblastine standard. Furthermore, the molecular docking into TRK (PDB: 1t46) was done for the optimization of the investigated compounds as potential TRK inhibitors.

Synthesis, structural characterization and DNA-binding studies of a new cobalt (II) complex: (HAcr)4[Co(Sal)3

A new cobalt (II) coordination compound was synthesized using proton transfer mechanism. The reaction between CoCl2·2H2O, Salicylic acid (H2Sal) and acridine (Acr) gave a new coordination compound formulated as (HAcr)4[Co(Sal)3], which was characterized by elemental analysis, NMR, IR and UV/Vis spectroscopies. The interaction of this complex with DNA has been investigated in vitro using UV absorption, fluorescence spectroscopy, viscosity measurements and gel electrophoresis methods. The intrinsic binding constant has been estimated to be 5.8 × 105 M−1 using UV absorption. The interaction of DNA–Co (II) complex caused quenching in fluorescence. The binding constant, the number of binding site and Stern–Volmer quenching constant have been calculated to be 7.7 × 104 M−1, 1.143 and 1.5 × 104 Lmol−1, respectively. The increase in the viscosity of DNA with increasing the concentration of the Co (II) complex and the observations of other experiments suggest that the cobalt (II) complex binds to DNA by partial intercalation binding mode. Furthermore, the interaction of DNA–Co (II) complex was confirmed using gel electrophoresis studies. Moreover, molecular docking technique predicted partial intercalation binding mode for the complex.

Caffeic acid binds to the minor groove of calf thymus DNA: A multi-spectroscopic, thermodynamics and molecular modelling study

Caffeic acid (CA) is a plant polyphenol which acts as an antioxidant and has various pharmacological effects. DNA is one of the major cellular targets of therapeutic molecules. Thus, studying the interaction of small molecules with DNA is of great importance. In the current article, we have studied the mode of binding of CA with calf thymus DNA (Ct-DNA) using a series of biophysical techniques. Formation of complex between CA and Ct-DNA is ascertained by analyzing the UV–vis absorbance and fluorescence emission spectra of CA upon successive addition of Ct-DNA. Binding constants of CA with Ct-DNA obtained using multiple experiments was in the order of 103 M-1 which is consistent with known groove binders. Analysis of thermodynamic parameters suggest that hydrogen bonding and van der Waal’s forces played major role in the binding process. Competitive displacement studies confirmed that CA binds to the minor groove of Ct-DNA. These observations were further validated by KI quenching experiment, DNA melting studies, CD and viscosity measurements. In silico molecular docking further provided insight into the mode of binding of CA with Ct-DNA. Through in vitro experiments and in silico molecular docking studies, it was concluded that CA binds to the minor groove of Ct-DNA.

Synthesis and structural characterization of a vanadium(V)-pyridylbenzimidazole complex: DNA binding and anticancer activity

Synthesis and structural characterization of a new pyridylimidazole based vanadyl compound [VO2(L)(L−)] (1) [L=2-(2-pyridyl)benzimidazole] (1) are reported. It crystallizes in P1¯ space group. The molecular geometry of 1 around vanadium(V) is found to be distorted octahedron. 1 interacts with DNA in a intercalative fashion. Hypochromism of the absorption band of the complex with increasing concentration of DNA and the steady increase in DNA viscosity with increasing concentration of 1 indicates intercalative mode of binding. The binding constant is calculated as 2.76×105M−1. 1 also shows cytotoxicity against human breast cancer, human lung cancer and human keratinocyte cancer cell lines.

Experimental and molecular modeling studies on the DNA-binding of diazacyclam-based acrocyclic copper complex

The interaction of a new macrocyclic copper complex, [CuL(NO3)2] in which L is 1,3,6,10,12,15-hexaaza tricyclo[13.3.1.16,10] eicosane was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated the complex interacted with ct-DNA in a groove binding mode while the binding constant of UV–vis and the number of binding sites were 1.0±0.2×104Lmol−1 and 1.01, respectively. The fluorometric studies showed that the reaction between the complex with ct-DNA is exothermic (ΔH=14.85kJmol−1; ΔS=109.54Jmol−1K−1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of DNA in the presence of [CuL(NO3)2] complex. Furthermore, the complex induces detectable changes in the viscosity of DNA. The molecular modeling results illustrated that the complex strongly binds to groove of DNA. Experimental and molecular modeling results showed that Cu(II) complex bound to DNA by a groove binding mode.

Synthesis, characterization and in vitro DNA binding studies of a new copper(II) complex containing an antiviral drug, valganciclovir

A new complex, [Cu(valcyte)2(NO3)2], in which valcyte served as a valganciclovir drug, was synthesized and characterized by different physicochemical methods. Optimization of ligand structures and their complexes with Cu2+ were performed by semi-empirical and DFT methods. Binding interaction of this complex with calf-thymus DNA (ct-DNA) was explored by emission, absorption, circular dichroism and viscosity techniques. Additionally, cell line targeting was studied and cytotoxic effects of [Cu(valcyte)2(NO3)2] (0.0–160 μg) on AGS and MCF-7 cell lines were reported. Percentage of Cell Viability and Apoptotic Index were assessed. The complex displayed significant binding properties to ct-DNA. Undertaking fluorometric studies, the binding mode of the complex with ct-DNA was explored utilizing Hoechst as a fluorescence probe, indicating the binding to be of groove mode. The DNA viscosity altered slightly in presence of the complex. Enthalpy and entropy changes during the interaction showed that the process is endothermic, with the complex mainly bound to ct-DNA by hydrophobic attraction. Values of ΔG revealed a spontaneous reaction between DNA and the complex. Optimized docked model of DNA–complex mixture confirmed the experimental results. The results of MMFF94 calculations indicated stability of [Cu(valcyte)2(NO3)2] after docking with the modeled DNA profile, as compared to the DNA profile and valganciclovir results before the docking process. Cytotoxicity studies showed that an increase in [Cu(valcyte)2(NO3)2] may result in a significant decrease in cell viability and increase apoptosis index in the treated cells, as compared to valganciclovir treated cells (p < 0.05). The findings further showed that [Cu(valcyte)2(NO3)2] has potential for use in cancer therapy.

Synthesis, characterization, and DNA binding studies of the hematoxylin-Zn(II) complex

ABSTRACTThe binding mechanism of Hematoxylin-Zn(II) complex with Herring sperm DNA has been investigated using UV–vis and fluorescence spectroscopies and viscosity measurement. With the increase in the concentration of complex, the viscosity of DNA decreased, and the binding mode is more detailed: there is partially intercalate binding. Furthermore, besides the intercalate binding, the existence of groove binding was confirmed through the ionic strength experiment in Scatchard analysis. Thermodynamic studies provided some thermodynamic parameters: ΔrHmΘ = 1.43 × 105 J mol−1, ΔrSmΘ = 576.14 J mol−1, ΔrGmΘ303K = −3.16 × 104 J mol−1, they illustrated that the binding mechanism between HE-Zn(II) complex and hsDNA was driven mainly by entropy.

Honeycomb-like Ordered Assembly of DNA Induced by Flexible Binuclear Ruthenium(II)-Polypyridyl Complexes.

A series of binuclear ruthenium(II)-polypyridyl complexes of the type [Ru2 (N-N)4 (BPIMBp)]4+ , in which N-N is 2,2'-bipyridine (bpy; 1), 1,10-phenanthroline (phen; 2), dipyrido[3,2-d:2',3-f] quinoxaline (dpq; 3), dipyrido[3,2-a:2',3'-c] phenanzine (dppz; 4), and 1,4'-bis[(2-pyridin-2-yl)-1H-imidazol-1-yl)methyl]-1,1'-biphenyl (BPIMBp) is a bridging ligand, have been synthesized and characterized. These complexes are charged (4+) cations and flexible due to the -CH2 group of the bridging ligand and possess terminal ligands with variable intercalative abilities. The interaction of complexes 1-4 with calf thymus DNA (CT-DNA) was explored by using UV/Vis absorption spectroscopy, steady-state emission, emission quenching with K4 [Fe(CN)6 ], ethidium bromide displacement assay, Hoechst displacement assay, and viscosity measurements and revealed a groove-binding mode for all the complexes through a spacer and an intercalative mode for complexes 3 and 4. A decrease in the viscosity of DNA revealed bending and coiling of DNA, an initial step toward aggregation. Interestingly, a distinctive honeycomb-like ordered assembly of the DNA-complex species was visualized by fluorescence microscopy in the solution state. The use of SEM and AFM confirmed the disordered self-organization of the DNA-complex adduct on evaporation of the solvent. The small orderly nanosized DNA aggregates were confirmed by means of circular dichroism, dynamic light scattering (DLS), and TEM. These complexes are moderately cytotoxic against three different cell lines, namely, MCF-7, HeLa, and HL-60.

Characterization of the binding of neomycin/paromomycin sulfate with DNA using acridine orange as fluorescence probe and molecular docking technique

The binding of neomycin sulfate (NS)/paromomycin sulfate (PS) with DNA was investigated by fluorescence quenching using acridine orange (AO) as a fluorescence probe. Fluorescence lifetime, FT-IR, circular dichroism (CD), relative viscosity, ionic strength, DNA melting temperature, and molecular docking were performed to explore the binding mechanism. The binding constant of NS/PS and DNA was 6.70 × 103/1.44 × 103 L mol−1 at 291 K. The values of ΔHθ, ΔSθ, and ΔGθ suggested that van der Waals force or hydrogen bond might be the main binding force between NS/PS and DNA. The results of Stern–Volmer plots and fluorescence lifetime measurements all revealed that NS/PS quenching the fluorescence of DNA–AO was static in nature. FT-IR indicated that the interaction between DNA and NS/PS did occur. The relative viscosity and melting temperature of DNA were almost unchanged when NS/PS was introduced to the solution. The fluorescence intensity of NS/PS–DNA–AO was decreased with the increase in the ionic strength. For CD spectra of DNA, the intensity of positive band at nearly 275 nm was decreased and that of negative band at nearly 245 nm was increased with the increase in the concentration of NS/PS. The binding constant of NS/PS with double-stranded DNA (dsDNA) was larger than that of NS/PS with single-stranded DNA (ssDNA). From these studies, the binding mode of NS/PS with DNA was evaluated to be groove binding. The results of molecular docking further indicated that NS/PS could enter into the minor groove in the A–T rich region of DNA.

Interaction of biosynthesized gold nanoparticles with BSA and CTDNA: A multi-spectroscopic approach

The interaction between biosynthesized gold nanoparticles (GNP) with bovine serum albumin (BSA) and calf thymus DNA (CTDNA) was investigated from a multi-spectroscopic approach. The apparent binding constant (K) were 2.69×104L/mol and 15.84×104L/mol at 293K, respectively for BSA and CTDNA, and the number of binding sites were ∼1. According to the Van’t Hoff equation, the thermodynamic parameters were calculated (ΔH=−119.496kJ/mol, ΔS=−320.92J/mol/K for BSA and ΔH=−225.89kJ/mol; ΔS=673J/mol/K for CTDNA) and the results indicated hydrogen bonds and van der Waals forces are the main stabilizing force in both of the BSA-GNP and CTDNA-GNP complex. The average binding distance (r=4.45nm) and the critical energy transfer distance (R0=2.94nm) between GNP and BSA were also evaluated according to Förster’s non-radiative energy transfer theory. What is more, UV–Visible, and circular dichroism spectra showed that the addition of GNP changed the secondary structure of BSA and led to a decrease in α-helix. Circular dichroism spectra also indicated conformational changes of CTDNA in the presence of the GNP. Furthermore, the GNP induces small changes in DNA viscosity and melting temperature which is indicative of groove binding mode of GNP with CTDNA.