Probing the binding mode of psoralen to calf thymus DNA

Exploring the interaction between calf thymus DNA and 11H-Indeno[1,2-b]quinoxalin-11-one Thiosemicarbazones: Spectroscopies and in vitro antitumor activity

Understanding the interactions between small molecules and calf thymus deoxyribonucleic acid (ctDNA) is critical for certain aspects of drug discovery. In this study, three 11H-indeno[1,2-b]quinoxalin-11-one thiosemicarbazones were synthesized and their interaction with ctDNA was examined through various spectroscopic techniques, including ultraviolet (UV) spectroscopy, fluorescence spectroscopy, and circular dichroism (CD) spectrum, and through physicochemical methods, including viscosity measurements. In addition, the effects of these thiosemicarbazone compounds 4a, 4b and 4c on several cancer cell lines were explored. The results of UV absorption, fluorescence quenching and CD experiments indicated that compounds 4a, 4b and 4c primarily bound to ctDNA by an intercalation. This mode of interaction was further corroborated by viscosity measurements. Docked poses of compound 4a revealed that it formed a crucial N position hydrogen bond with the DNA receptor. The chemical structure of compound 4a was further confirmed by X-ray crystallographic analysis. Through biological evaluation, it was found that the in vitro cytotoxicity of three compounds agreed with the order of their binding strength to ctDNA, indicating that the antitumor activity of these compounds correlated with their binding affinity to ctDNA.

Elucidating the Interaction of Indole-3-Propionic Acid and Calf Thymus DNA: Multispectroscopic and Computational Modeling Approaches

Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.

Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and multispectroscopic techniques

In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT-ctDNA complex was calculated, Ka = 9.91 × 104 M-1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.

Intercalation of anticancer drug Palbociclib with calf-thymus DNA: new insights from molecular spectroscopic, molecular dynamic simulations and cleavage studies

The interaction between the anti-cancer drug Palbociclib (PAL) and calf-thymus DNA (CT-DNA) was investigated using various biophysical techniques in a physiological buffer (pH 7.4). It was found that PAL intercalated into the base pairs of CT-DNA as evidenced from the results of UV-Vis, fluorescence, circular dichroism (CD), competitive binding assay with ethidium bromide (EB) and Hoechst 33258, KI quenching study, the effect of denaturing agent and viscosity measurements. The magnitude of binding constants (106 M-1) at different temperatures suggested strong binding between PAL and CT-DNA during complexation. The observed ΔHo > 0 and ΔSo > 0 indicated that the binding process is primarily driven by hydrophobic interactions. Molecular docking studies indicated partial intercalation of pyridopyrimidine ring between the base pairs of DNA. Free energy surface (FES) analysis derived from metadynamics simulation studies revealed the PAL-induced cleavage of DNA, which was confirmed by gel electrophoresis experiments.Communicated by Ramaswamy H. Sarma.

Non-covalent binding interaction of bioactive coumarin esculetin with calf thymus DNA and yeast transfer RNA: A detailed investigation to decipher the binding affinities, binding location, interacting forces and structural alterations at a molecular level

Esculetin is a well-known coumarin derivative found abundantly in nature possessing an extensive array of pharmacological and therapeutic properties. Consequently, to comprehend its molecular recognition mechanism, our objective is to conduct a complete investigation of its interactions with the nucleic acid, specifically ct-DNA, and t-RNA, using spectroscopic and computational techniques. The intrinsic fluorescence of esculetin is quenched when it interacts with ct-DNA and t-RNA, and this occurs through a static quenching mechanism. The thermodynamic parameters demonstrated that the interaction is influenced by hydrogen bonding and weak van der Waals forces. CD and FT-IR results revealed no conformational changes in ct-DNA and t-RNA structure on binding with esculetin. Furthermore, competitive displacement assay with ethidium bromide, melting temperature, viscosity measurement, and potassium iodide quenching experiments, reflected that esculetin probably binds to the minor groove of ct-DNA. The molecular docking results provided further confirmation for the spectroscopic findings, including the binding location of esculetin and binding energies of esculetin complexes with ct-DNA and t-RNA. Molecular dynamics simulation studies demonstrated the conformational stability and flexibility of nucleic acids.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Economical gold recovery cycle from bio-sensing AuNPs: an application for nanowaste and COVID-19 testing kits

We report the controlled growth of biologically active compounds: gold nanoparticles (AuNPs) in various shapes, including their green synthesis, characterization, and studies of their applications towards biological, degradation and recycling. Using spectroscopic methods, studies on responsive binding mechanisms of AuNPs with biopolymers herring sperm deoxyribonucleic acid (hsDNA), bovine serum albumin (BSA), dyes degradation study, and exquisitely gold separation studies/recovery from nanowaste, COVID-19 testing kits, and pregnancy testing kits are discussed. The sensing ability of the AuNPs with biopolymers was investigated via various analytical techniques. The rate of degradation of various dyes in the presence and absence of AuNPs was studied by deploying stirring, IR, solar, and UV-Vis methods. AuNPs were found to be the most active cytotoxic agent against human breast cancer cell lines such as MCF-7 and MDAMB-468. Furthermore, an economical process for the recovery of gold traces from nanowaste, COVID-19 detection kits, and pregnancy testing kits was developed using inexpensive and eco-friendly α-cyclodextrin sugar. This method was found to be easy and safest in comparison with the universally accepted cyanidation process. In the future, small gold jewelry makers and related industries would benefit from the proposed gold-recycling process and it might contribute to their socio-economic growth. The methodologies proposed are also beneficial for trace-level forensic investigation.

Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis

A series of biophysical experiments like UV-Vis, fluorescence, circular dichroism (CD), competitive displacement assays, voltammetric studies, viscosity measurements and denaturation effect and metadynamics simulation studies were performed to establish the mode of binding of diafenthiuron (DF) insecticide with calf thymus DNA (CT-DNA). Analysis of absorption and fluorescence spectra in Tris-HCl buffer of pH 7.4 indicates the formation of a complex between DF and CT-DNA and the binding constant of which is in the order of 10⁴ M^-1. Competitive displacement assay with ethidium bromide (EB) and Hoechst 33258 suggests that the most probable mode of binding of DF with CT-DNA may be via intercalation mode. The results of other experiments such as CD spectral studies, viscosity measurements and the effect of denaturation agent urea support the intercalation of DF with CT-DNA. Thermodynamic parameters (ΔH^o, ΔS^o and ΔG^o) reveal that hydrogen bonds (H-bonds) or van der Waals (vdW) force is the main binding force in the spontaneous interaction between DF and CT-DNA. Molecular dynamics (MD) simulation studies confirmed the intercalation of DF into the base pairs of CT-DNA.Communicated by Ramaswamy H. Sarma.

Targeting Natural Polymeric DNAs with Harmane: An Insight into Binding and Thermodynamic Interaction Through Biophysical Approach

DNA is one of the major molecular targets for a broad range of anticancer drugs. Hence, interaction studies involving cellular DNA and small molecules can be highly beneficial as they often lead to rational and efficient drug design. In this study, the binding interaction of Harmane (a naturally occurring, bioactive indole alkaloid) with two natural polymeric DNAs, that is, Calf thymus (CT) DNA and Herring testis (HT) DNA has been elucidated using biophysical techniques. A ground state, 1:1 complexation, was revealed by steady-state fluorescence spectroscopy. The thermodynamic profile and energetics of the associated reaction were evaluated by temperature-dependent fluorescence spectroscopy. The spontaneity of the binding was confirmed by the negative ΔG° values in both cases. Negative enthalpy change, along with stronger positive entropic contribution, indicated the dominant electrostatic nature of the interaction and finally the entropy-driven exothermic binding process throughout. Salt-dependent studies further demonstrated the significant contribution of electrostatic interactions in ligand binding toward DNA. Infrared data substantiated the structural information of the said interactions, leading to the exploration of the structure-function relationship.

Interaction of aflatoxin G1 with free DNA in vitro and possibility of its application in removing aflatoxin G1

The present study sought to evaluate the interaction between aflatoxin G₁ and free DNA in vitro through different analytical techniques. The UV-visible spectra results showed that the structure of DNA might be changed with a new aflatoxin G₁-DNA complex forming, which indicated that the interacting mode between them was the intercalating mode. The DNA melting temperature increased by 12.80 °C, suggesting that the DNA double helix structure was more compact and stable through intercalation. The circular dichroism (CD) spectra results indicated that the interaction of aflatoxin G₁ with DNA induced the DNA base stacking changes. The results of agarose gel electrophoresis and fluorescence microscope further verified that the interacting mode between aflatoxin G₁ and DNA was intercalation mode. According to the fluorescence spectrum data, the binding constant was calculated 6.24 × 10⁴ L·mol^-1. The thermodynamic results demonstrated that the reaction of aflatoxin G₁ intercalating to DNA was a spontaneous reaction. The elimination results suggested that aflatoxin G₁ could be enriched and removed by DNA intercalation through magnetic beads separation, with the removal efficiency of 93.73%. The study results would provide a theoretical basis for establishing a new aflatoxin removal method based on DNA intercalation.

A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation

The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.

Change of benzo(a)pyrene during frying and its groove binding to calf thymus DNA

Benzo[a]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92-27.82 μg kg^-1 and increased with increasing frying time. The detected BaP levels were 3.64-4.00 μg kg^-1, exceeding the upper limit (2 μg kg^-1) set by European Union (EU), though below the limiting value (10 μg kg^-1) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.

Interacting mechanism of benzo(a)pyrene with free DNA in vitro

Polycyclic aromatic hydrocarbons are environmental pollutants with strong carcinogenicity, indirect teratogenicity, and mutagenicity. This study explored the interaction mechanism of benzo(a)pyrene with free DNA in vitro by using various analytical methods. UV-vis spectra showed that benzo(a)pyrene and DNA formed a new benzo(a)pyrene-DNA complex. The thermal melting temperature of DNA increased by 12.7 °C, showing that the intercalation of benzo(a)pyrene into DNA could promote the stability of the DNA double helix structure. The intercalation of benzo(a)pyrene with DNA in vitro was further confirmed by fluorescence microscopy with magnetic beads. Fluorescence spectra showed that the interaction between DNA and benzo(a)pyrene decreased the fluorescence intensity of benzo(a)pyrene, and the maximum quenching rate was 27.89%. The quenching mode of benzo(a)pyrene was static quenching. Thermodynamic data showed that the main driving forces were van der Waals forces and hydrogen bonds, and the reaction was spontaneous. The results of this study provided a novel insight for the establishment of polycyclic aromatic hydrocarbon capture and elimination through polycyclic aromatic hydrocarbon-DNA intercalation.

Physicochemical Investigation of Psoralen Binding to Double Stranded DNA through Electroanalytical and Cheminformatic Approaches

This work showcased the first physicochemical investigation of psoralen (PSO) binding to double stranded DNA (dsDNA) through electroanalytical methods. Results evidenced that PSO presents one non-reversible anodic peak at electric potential (E_pa) ≈ 1.42 V, which is associated with its oxidation and the formation of an epoxide derivative. Moreover, PSO analytical signal (i.e., faradaic current) decreases linearly with the addition of dsDNA, while the electric potential associated to PSO oxidation shifts towards more positive values, indicating thence that dsDNA addition hinders PSO oxidation. These findings were corroborated by the chemoinformatic study, which evidenced that PSO intercalated noncovalently at first between base-pairs of the DNA duplex, and then irreversibly formed adducts with both DNA strands, leading up to the formation of a cross-link which bridges the DNA helix, which explains the linear dependence between the faradaic current generated by PSO oxidation and the concentration of DNA in the test-solution, as well as the dependence between E_p and the addition of dsDNA solution. Therefore, the findings herein reported evidence of the applicability of electroanalytical approaches, such as voltammetry in the study of DNA intercalating agents.

In vitro spectroscopic investigation of groove binding interaction of Fe3O4@CaAl-LDH@L-Dopa with calf thymus DNA

The principal goal of this study is to evaluate the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with calf thymus DNA. The magnetic nanoparticles were previously prepared by a chemical co-precipitation method, and the surface of the Fe₃O₄ nanoparticles was coated with CaAl layered double hydroxides. The antiparkinsonian drug "L-Dopa" was carried by this core-shell nanostructure to achieve the drug delivery system with suitable properties for biological applications. Also, the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with CT-DNA was studied using, UV-Visible spectroscopy, viscosity, circular dichroism (CD), and fluorescence spectroscopy techniques. The results of investigations demonstrated that Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles have interacted via minor groove binding and intercalated to CT-DNA, respectively.

Binding characteristics of aflatoxin B1 with free DNA in vitro

In this paper, the binding characteristics of aflatoxin B₁ (AFB₁) with the herring sperm deoxyribonucleic acid (DNA) in vitro were investigated through different analytical methods. The ultraviolet-visible spectroscopy (UV-vis), fluorescence, and circular dichroism (CD) spectra results showed that a new AFB₁-DNA complex was formed. All the results suggested that AFB₁ interacted with free DNA in vitro in an intercalating binding mode. The results of the DNA melting experiments also showed that the melting temperature of DNA increased by about 12.1 °C due to the addition of AFB₁, which was supposed to be closely related to the intercalation of AFB₁ into DNA. The agar gel electrophoresis experiments further confirmed that the binding mode of AFB₁ and free DNA in vitro was indeed intercalation. In addition, the fluorescence quenching induced by adding AFB₁ to the ethidium bromide-DNA (EB-DNA) mixture indicated the presence of competitive non-covalent intercalating binding interaction with a competitive binding constant of 5.58 L/mol between AFB₁, EB, and DNA. The thermodynamic data demonstrated that the main driving forces of the binding reaction were van der Waals forces and hydrogen bond. The resonance light scattering (RLS) assay results showed that the DNA binding saturation values of AFB₁, EB, psoralen (PSO), and angelicin (ANG) were 2.14, 15.59, 0.74, and 0.74, respectively. These results indicated that the DNA binding capacity of AFB₁ was weaker than that of EB, but stronger than those of PSO and ANG.

Influence of DMβCD on the Interaction of Copper(II) Complex of 6-Hydroxychromone-3-carbaldehyde-3-hydroxybenzoylhydrazine with ctDNA

The interaction mechanism between a scarcely soluble copper(II) complex of Cu(II)-6-hydroxychromone-3-carbaldehyde-(3'-hydroxy)benzoylhydrazone (CuCHz) in aqueous solution and its DMβCD complex was studied in the presence of ctDNA through spectroscopy and thermodynamic methods. The thermodynamic results indicate that the binding process of the CuCHz-DMβCD inclusion complex is a spontaneous process and the inclusion is enthalpy-driven. The binding constants of CuCHz and CuCHz-DMβCD with ctDNA are 2.69 × 10³ and 14.7 × 10³ L mol^-1, respectively. The stoichiometry of the complex is 1:1, and the determined thermodynamic indicates that the process of binding is spontaneous and entropy-driven. A competitive binding titration with ethidium bromide revealed that CuCHz efficiently displaces EB from the EB-DNA system. In addition to the thermal denaturation experiments and docking studies, we can confirm that the mode of binding of this complex to ctDNA is intercalation mode. The presence of DMβCD enhances the aqueous solubility of CuCHz; nevertheless, the cyclodextrin did not affect the interaction of CuCHz with ctDNA because the inclusion complex breaks down when it binds with ctDNA.

Study on the interactions between B-norcholesteryl benzimidazole compounds with ct-DNA

The study of molecule-DNA interaction is very important for designing an improved therapeutic agent. In previous studies, we synthesized some B-norcholesteryl benzimidazole compounds, and the tests on cancer cells showed that these compounds had good in vitro anti-cancer activities. In order to further investigate mechanism of their actions, three different B-norcholesteryl benzimidazole compounds were selected and interaction of these compounds with the calf thymus DNA (ct-DNA) was monitored by using various methods including UV-Vis and fluorescence spectroscopic techniques, viscosity measurement, and circular dichroism (CD). The results proved a hypochromic effect accompanied with a slight red-shift due to the interaction of the molecules with ct-DNA. According to the UV-Vis and fluorescence spectra, the mentioned compounds were bound to DNA, preferentially through partial intercalation into the DNA helix. Moreover, the ethidium bromide (EB) and Hoechst 33258 competitive binding experiments were also used to confirm the interaction mode of the compounds with ct-DNA. In the Hoechst 33258 displacement experiment, no significant change in the fluorescence intensity was observed. Additional assays such as iodide quenching, viscosity, and CD spectroscopy further confirmed that intercalation should be the major binding mode of the selected compounds with DNA. The cytotoxicity of these three compounds was also evaluated by MTT method, and the results confirmed that binding ability of these compounds to DNA was consistent with their cytotoxicity behavior. The experimental results indicated a higher binding affinity for compound 3 compared to the other compounds. This research provided a better understanding on the molecular mechanism of the interaction between B-norcholesteryl benzimidazole compounds and tumor cells, and offered a beneficial perspective to the designation of novel B-norsteroidal anticancer compounds.

Synthesis, characterization and DNA binding studies of a new ibuprofen-platinum(II) complex

The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density functional theory. Using the continuous variation method, the stoichiometry of Pt(HIb)₂(Cl)₂ binding on DNA (ct-DNA) determines as a single class of binding. Based on the results of Stern-Volmer analysis on the fluorescence quenching data, the quenching mechanism was determined to be static in nature. The studies indicated that the complex could bind DNA molecules via groove binding for four major reasons. Initially, the complex-DNA binding constant determined based on spectrophotometric data were found to be comparable to those of groove-binding drugs. In addition, the competitive fluorimetric based on the applications of Hoechst 33258 proved the ability of Pt(HIb)₂(Cl)₂ to displace with Hoechst in its DNA-bounded form, reflecting the competition between Pt(HIb)₂(Cl)₂ and Hoechst for groove binding. Further, no considerable changes were observed in the intensity of the methylene blue (MB)-DNA system after adding the Pt(HIb)₂(Cl)₂ complex, reflecting the stability of MB molecules in the DNA helix and a non-intercalative bonds of Pt(HIb)₂(Cl)₂ interaction on DNA. Finally, minor changes in the viscosity of DNA in the presence of Pt(HIb)₂(Cl)₂, indicated that changes in the length of DNA in the presence of the complex are negligible, supporting the assumption of DNA groove-binding. Also induced CD spectral changes and docking simulations were in favor of the groove mechanism for the Pt(HIb)₂(Cl)₂-DNA binding.Communicated by Ramaswamy H. Sarma.

Spectrophotometric study on binding of 2-thioxanthone acetic acid with ct-DNA

Thioxanthone and its derivatives are the most remarkable molecules due to their vast variety of application such as radiation curing that is, until using them as a therapeutic drug. Therefore, in this study it was intended to use 2-Thioxanthone acetic acid with and without NaCl in Tris HCl buffer solution (pH:7.0) to represent the interaction with ct-DNA. The UV-vis absorption spectra of TXCH₂COOH in the presence of ct-DNA showed hypochromism and the intrinstic binding constant (K_b) was determined as 6 × 10³ L mol^-1. The fluoresence intensity of TXCH₂COOH with ct-DNA clearly increased up to 101% which indicated that the fluorescence intensity was very sensitive to ct-DNA concentration. The binding constant (K) and the values of number of binding sites (n) and were calculated as 1.8 × 10³ L mol^-1 and 0.69, respectively. When the quenching constants (K_sv) of free TXCH₂COOH and TXCH₂COOH, which were bonded with ct-DNA were compared, slightly changed values of Ksv were seen. Moreover, displacement assay with Hoechst 33,258 and viscosity measurements in the presence and absence of NaCl salt also confirmed the binding mode which noted the electrostatic interaction following groove binding between TXCH₂COOH and ct-DNA. Last but not least, the salt effect was examined on ct-DNA binding with TXCH₂COOH. The results of the experiments indicated that the groove binding was strengthened by NaCl whereas in the high NaCl concentration, the binding ability of TXCH₂COOH to ct-DNA was inversely affected.

hsDNA groove binding, photocatalytic activity, and in vitro breast and colon cancer cell reducing function of greener SeNPs

Selenium nanoparticles (SeNPs) have attracted great attention because of their superior optical properties and wide utilization in biological and biomedical studies. This paper reports an environmentally benign procedure of greener monodispersible SeNP synthesis using the reducing power of Trigonella foenum-graecum extract, characterization and their protective effect against unfolded (Herring sperm DNA) hsDNA. We investigated the anti-cancer activity of SeNPs against MCF-7, MDA MB 435 and COLO-205 cells. The photocatalytic activity of SeNPs was investigated for the degradation of a Sunset Yellow FCF (SYFCF) dye using ultraviolet-B light. The reduction of the Se ion to SeNPs was monitored by ultraviolet-visible spectroscopy (UV-vis). The size and morphology of the SeNPs were characterized by high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), and Dynamic Light Scattering (DLS). The SeNPs were stable, and the diameter was homogeneous at around 5-12 nm. Interactions of various concentrations of SeNPs with hsDNA were systematically investigated by UV-vis, fluorescence, circular dichroism (CD), polarimetry and FTIR spectroscopy under physiological conditions. The results from fluorescence spectroscopy indicated that SeNPs quenched the fluorescence intensity of hsDNA with increasing concentrations. The modified Stern-Volmer quenching rate constant Ksv, binding constant K and binding sites n at different temperatures and the corresponding thermodynamic parameters ΔH°, ΔG° and ΔS° were calculated. Hoechst 33258 and methyl green (MG) site markers, melting experiment (Tm), viscosity measurements and sequence specificity verification by DNA bases clarified that SeNPs bind to hsDNA via a groove site. The rate of photocatalytic degradation of the SYFCF dye in the presence and absence of photocatalysts (SeNPs) was studied using UV-vis, the results showed appreciable degradation of the SYFCF dye. Our results suggested that nano Se can be used as a promising selenium species with potential application in cancer treatment. These nanoparticles were found to be the most active cytotoxic agent prepared in a new green synthesis manner, causing >50% inhibition of MCF-7, MDA MB-435 and COLO-205 cell proliferation at concentrations <10(-7) M. Hence these SeNPs could be recognized as promising materials for biomedical applications.

Insight into the binding of a non-toxic, self-assembling aromatic tripeptide with ct-DNA: Spectroscopic and viscositic studies

The report describes the synthesis, self-association and DNA binding studies of an aromatic tripeptide H-Phe-Phe-Phe-OH (FFF). The peptide backbone adopts β-sheet conformation both in solid and solution. In aqueous solution, FFF self-assembles to form nanostructured aggregates. Interactions of this peptide with calf-thymus DNA (ct-DNA) have been studied using various biophysical techniques including ultraviolet (UV) absorption spectroscopy, fluorescence spectroscopy and circular dichroism (CD) spectroscopy. The value of mean binding constant calculated from UV and fluorescence spectroscopic data is (2.914 ± 0.74) x 103 M-1 which is consistent with an external binding mode. Fluorescence intercalator displacement (FID) assay, iodide quenching study, viscosity measurement and thermal denaturation study of DNA further confirm the groove binding mode of peptide, FFF with ct-DNA. MTT cell survival assay reveals very low cytotoxicity of the peptide toward human lung carcinoma cell line A549.

Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA

The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.

Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study

Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waal's forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted.

Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

Alteration in DNA binding pattern of conformationally locked NC(O)N system: A spectroscopic investigation

The binding mode of a conformationally locked NC(O)N planar system with deoxyribonucleic acid (DNA) is investigated using various spectroscopic and enzymatic assays. Compound 1 and its four different salts (comp. 2-5) were prepared for this purpose. They showed certain changes in their respective DNA-compound complex at ground state and excited state as measured by UV-vis and fluorescence emission spectra. The Stern-Volmer quenching constant (KSV) for the neutral species (1) is found 8545 M(-1), whereas, for its salts 2, 3, 4 and 5 the quenching constants were 33510 M(-1), 11352 M(-1), 19693 M(-1) and 27270 M(-1) respectively. Nevertheless, the binding constant values remain comparable in neutral and salt forms except for 5. To elucidate the reason we took their CD spectra and ran a topoisomerase I (Topo I) assay. These experimental data revel the fact that compound 1 (neutral form) binds at the minor groove of DNA, whereas, its salt (2) has an extended intercalating property.

Intercalation of the daphnetin–Cu(ii) complex with calf thymus DNA

The daphnetin–Cu(ii) complex binds to the A–T bases region of ctDNA and causes cleavage of plasmid DNA.

Interaction of a synthesized pyrene based fluorescent probe with CT-DNA: spectroscopic, thermodynamic and molecular modeling studies

The present study demonstrates the synthesis of a new pyrene based water soluble fluorescent probe and its interaction with Calf-thymus DNA.

Multispectral studies of DNA binding, antioxidant and cytotoxic activities of a new pyranochromene derivative

The binding properties of a new pyranochromene derivative, 2-amino-4-(3-hydroxyphenyl)-5-oxo-4H, 5H-pyrano-[3, 2-c] chromene-3-carbonitrile (3-HC) with calf thymus DNA (ctDNA) have been investigated by UV-vis absorption, circular dichroism, fluorescence spectroscopy and viscosity measurement. These results indicated that 3-HC can interact with DNA through non-intercalative mode and the intrinsic binding constant (Kb) for 3-HC with DNA was estimated to be 3.6 × 10(3)M(-1). The antioxidant activity experiments show that 3-HC also exhibit good antioxidant activity in DPPH free radical scavenging and ferric reducing ability methods. Moreover, 3-HC exhibited cytotoxic activity against K562, human chronic myelogenous leukemia cells, with IC50 value of 146 μM and the cells responded to the treatment with mostly through apoptosis.

Interactions of Isophorone Derivatives with DNA: Spectroscopic Studies

Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods. All the studied compounds interact with DNA through intercalative binding mode. The stoichiometry of the isophorone/DNA adducts was found to be 1:1. The fluorescence quenching data revealed a binding interaction with the base pairs of DNA. The CD data indicate that all the investigated isophorones induce DNA modifications.

Characterization of the interaction between resmethrin and calf thymus DNA in vitro

Resmethrin preferentially binds to the G–C rich region of the ctDNA groove, and the UV-vis spectral matrix is decomposed by MCR-ALS.

Multi-spectroscopic and molecular modelling studies on the interaction of esculetin with calf thymus DNA

Minor groove binding of esculetin with Ct-DNA was established by a series of in vitro experiments and in silico analyses.