Study on the interaction between aglycon of daunorubicin and calf thymus DNA by spectroscopy

Study on the electrochemical and spectroscopic characteristics of holmium ion and its interaction with DNA

Metal ion-DNA interactions play a crucial role in modulating the structure and function of genetic material in the natural environment. In this study, we report on the favorable electrochemical activity of holmium(III) (Ho3+) on a glassy carbon electrode (GCE) and its interaction with double-stranded DNA. The interaction between DNA and Ho3+ was investigated for the first time using cyclic voltammetry and differential pulse voltammetry. The electrochemical behavior of Ho3+ ions on a GCE exhibited a reversible electron transfer process, indicative of its redox activity. A linear correlation between the peak current and the square root of the scan rate was observed, suggesting a diffusion-controlled kinetic regime for the electrochemical process. Additionally, fluorescence and absorption spectroscopy were employed to confirm the binding of Ho3+ to DNA. Our findings demonstrate that, at pH 7.2, specific DNA bases and phosphate groups can interact with Ho3+ ions. Moreover, electrochemical measurements suggest that Ho3+ ions bind to DNA via a groove binding mode, with a calculated binding ratio of 1:1 between Ho3+ and DNA. Notably, under optimal conditions, an increase in the amount of DNA leads to a significant reduction in the current intensity of Ho3+ ions.

DNA binding studies of antifungal drug posaconazole using spectroscopic and molecular docking methods

The binding studies of DNA with small molecules have been an emerging field of research all the time since DNA as the genetic material is a major biological target for various drugs. Interpretation of small molecule-DNA binding helps in understanding their interactions with designing new drugs of greater medicinal activity. Posaconazole is an antifungal drug in the class of triazoles which are known to possess numerous pharmacological properties. In this work, the nature of the binding of posaconazole with calf-thymus DNA has been studied using spectroscopic techniques and molecular docking studies. A binding constant of the order of 10³ M^-1 was observed from UV-visible and fluorescence studies for the interaction between posaconazole and calf-thymus DNA. The fluorescence property of posaconazole was found to be quenched by calf-thymus DNA with a quenching constant of the order of 10³ M^-1. Competitive displacement of ethidium bromide and Hoechst 33258 by posaconazole using fluorescence technique suggested minor groove binding of posaconazole in calf-thymus DNA. Confirmation of the binding mode was further complemented by the viscosity measurement and DNA melting studies followed by KI quenching experiments. The studies on the effect of ionic strength on the binding suggested a possible role of electrostatic force in the interaction. Molecular docking studies reflected a crescent shape of the posaconazole within the minor groove of calf-thymus DNA validating the experimental findings showing the residues involved in the interaction.

Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA

Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and ³¹P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 10⁴ M^-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG⁰ < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH⁰ < 0 and ΔS⁰ > 0). The up-field shift in the ³¹P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.

Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA

Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. In aqueous solutions, the interaction with DNA leads to the formation of noncovalent complexes of K1 and K2 with DNA, which is accompanied by a significant increase in the fluorescence intensity. The results of the molecular docking experiments showed the possibility of several types of binding, which was confirmed by the data obtained from other experiments. The effects of temperature and additions of NaCl on the stability of the dye-DNA complexes were studied. The spectral-fluorescent data were used to estimate the binding constants of the dyes with DNA and other characteristics of the dyes that are important for their use as probes. Upon flash photolysis of the dyes in complexes with DNA, photoisomerization is not observed, but the quantum yield of intersystem crossing to the triplet state increases. The decay of the triplet states occurs by a two-exponential law. The rate constants for quenching of the triplet states of the dyes complexed with DNA by oxygen were found to be lower than the expected values for diffusion-controlled quenching (taking into account the spin statistical factor 1/9), which is explained by the steric factor of complexation.

DNA/Lysozyme-binding affinity study of novel peptides from TAT (47-57) and BRCA1 (782-786) in vitro by spectroscopic analysis

SISLL-TAT and TAT-SISLL were synthesized by modifying the N- or C-termini of cell-penetrating peptides as transacting activator of transcription TAT (47-57) by attaching BRCA1 (782-786) (SISLL). The novel peptides were synthesized through Fmoc solid-phase synthesis procedures and characterized by LCQ Fleet MS, ¹H NMR and ¹³C NMR. SISLL-TAT and TAT-SISLL displayed forceful antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Salmonella typhimurium with low hemolysis. SISLL-TAT showed better antibacterial activity than TAT-SISLL, with the minimum inhibitory concentration (MIC) values of 10-33 μg·mL^-1. The results of the DNA-binding activities showed that both SISLL-TAT and TAT-SISLL could interact with DNA via the minor groove mode, and the binding constants were 4.97 × 10⁵ L·mol^-1 and 4.42 × 10⁵ L·mol^-1 at 310 K, respectively. Circular dichroism analysis showed slight transformation of the lysozyme secondary structure caused by SISLL-TAT and TAT-SISLL. We also found that the novel peptides SISLL-TAT and TAT-SISLL targeted bacterial DNA resulting in cell death. This explains the antibacterial mechanism of SISLL-TAT and TAT-SISLL, and is a solid theoretical basis for further designing novel and highly effective antibiotics for clinical application.

Probing the Characterization of the Interaction of Aflatoxins B1 and G1 with Calf Thymus DNA In Vitro

The binding characterization of aflatoxins with calf thymus DNA (ctDNA) under physiological conditions was investigated. Multispectroscopic techniques, ctDNA melting, viscosity measurements, and molecular docking techniques were employed to elucidate the binding mechanism of the aflatoxins with DNA. The fluorescence results indicated that both aflatoxin B1 (AFB1) and aflatoxin G1 (AFG1) bound to the ctDNA, forming complexes through hydrogen bonding. The binding constants of AFB1 and AFG1 with ctDNA reached up to 10³ L·mol-1 and 10⁴ L·mol-1, respectively, and AFG1 exhibited a higher binding propensity than that of AFB1. Furthermore, both AFB1 and AFG1 bound to the ctDNA through groove binding, as evidenced by the results of the spectroscopic, iodide quenching effect, viscosity, and ctDNA melting measurements. Changes in the circular dichroism signal manifested that both AFB1 and AFG1 induced an increase in the right-handed helicity, but only minimally influenced the base stacking of the DNA. A molecular docking study of the aflatoxin's binding with the DNA revealed a groove binding mode, which was driven mainly by hydrogen bonding. This study of aflatoxin-ctDNA interaction may provide novel insights into the toxicological effect of the mycotoxins.

Interaction of indomethacin with calf thymus DNA: a multi-spectroscopic, thermodynamic and molecular modelling approach

Indomethacin belongs to the acetic acid derivative class of non-steroidal anti-inflammatory drugs with diverse pharmacological and biological activities. Understanding the mechanism of interaction of drugs with possible target and off-target biomolecules can prove useful in the development of a rational drug designing system. In this paper, we have attempted to ascertain the mode of binding of indomethacin with calf thymus DNA (Ct-DNA) through various biophysical techniques and in silico molecular docking. Analysis of the UV-visible absorbance spectra and fluorescence emission profile of indomethacin upon addition of Ct-DNA indicates the formation of a drug-DNA complex. UV-visible absorbance and steady state fluorescence experiments revealed a binding constant on the order of 103 L mol-1, which is consistent with those of well-known groove binders. Competitive displacement studies with ethidium bromide, acridine orange and Hoechst 33258 further suggested that indomethacin binds to the minor groove of the Ct-DNA. The above observations were further confirmed by KI induced quenching experiments, DNA melting studies, CD spectral analysis and viscosity measurements. The thermodynamic parameters like spontaneous free energy (ΔG < 0) and large favourable enthalpy (ΔH < 0) obtained from isothermal calorimetry indicated the involvement of hydrogen bonding and van der Waals forces in the binding process. Molecular docking further corroborated the experimental results.

Evaluation of interaction between imidazolium-based chloride ionic liquids and calf thymus DNA

With ionic liquids (ILs) being widely used, the toxicity of many ILs has been studied and verified. However the mechanism underlying the interaction between ILs and DNA needs to be investigated. In this study, the interaction of three imidazolium-based ILs ([C8mim]Cl, [C12mim]Cl, and [C16mim]Cl) with calf thymus DNA (ctDNA) was investigated by UV absorption spectroscopy and fluorescence spectroscopy. An intense interaction between [Cnmim]Cl and ctDNA was observed, involving a hypochromic effect or even a hyperchromic effect, in the UV absorption spectrum of ctDNA at 260nm. The Tm of ctDNA increased over 10°C after binding with [Cnmim]Cl, and the KSV values of [Cnmim]Cl-ctDNA quenched by potassium iodide (KI) were lower than those of [Cnmim]Cl. The fluorescence intensity of ctDNA-ethidium bromide (EB) was gradually quenched as the [Cnmim]Cl concentration increased. The results indicated that ctDNA interacted with [Cnmim]Cl through an intercalation binding mode. The mechanism of fluorescence quenching of [Cnmim]Cl with ctDNA involved static quenching. The binding constant between [Cnmim]Cl and ctDNA were 1443, 11169, and 67189, and the number of binding sites were 0.89, 1.10, and 1.27 at 298K, for [C8mim]Cl, [C12mim]Cl, and [C16mim]Cl, respectively. The results indicated that the intercalation binding between the three [Cnmim]Cl and ctDNA increased with increasing IL-alkyl chain length. These results will aid in the understanding of the mechanism of toxicity and of the biologically mediated environmental processes of ILs.

Unraveling multiple binding modes of acridine orange to DNA using a multispectroscopic approach

The interaction of acridine orange (AOH(+)) with calf thymus DNA (ct-DNA) under different dye-DNA conditions has been investigated in detail using multispectroscopic techniques, unraveling a number of hitherto unexplored intricacies of dye-DNA binding. The observed results intriguingly show contrasting binding features when low (2.4 μM) and significantly high (23 μM) dye concentrations are used. It is conclusively inferred from absorption, steady-state fluorescence, circular dichroism, fluorescence decay and anisotropy decay studies that at low [DNA] to [dye] ratio, especially with higher dye concentration, dimeric AOH(+) predominantly binds externally to DNA surfaces through electrostatic interactions. At sufficiently high [DNA] to [dye] ratios, however, the interaction intriguingly changes to monomeric AOH(+) bound to DNA, predominantly in the intercalative mode between DNA base pairs, with partly an electrostatic binding on DNA surfaces. With very low initial dye concentration, monomeric (AOH(+)) mostly binds to DNA through intercalative and electrostatic modes for most DNA to dye ratios. The present study demonstrates a systematic correlation of the striking changes in the photophysical properties of the dye upon multimode binding with DNA. The observed results are of great significance in understanding the fundamental insights of dye/drug binding to DNA hosts, of use in the design of effective therapeutic agents.

Study on the interaction of berberine with nucleic acids in the presence of silver nanoparticles, and the fluorometric determination of nucleic acids

The partial intercalation binding between BER and ctDNA, and the anti-photobleaching ability of BER were both strengthened by AgNPs. A metal enhanced fluorescence-based sensitive method for the determination of nucleic acids was obtained.

Interaction of Cd(ii) and Ni(ii) terpyridine complexes with model polynucleotides: a multidisciplinary approach

The study of the intercalation of both complexes, evidenced by CD and fluorescence spectroscopy and supported by QM/MM calculations, broadens the experimental and theoretical background on drugs/DNA interactions.

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.

Interaction of three new tetradentates Schiff bases containing N2O2 donor atoms with calf thymus DNA

Interaction of 1,3-bis(2-hydroxy-benzylidene)-urea (H2L1), 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea (H2L2) and 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea nickel(II) (NiL2) with calf-thymus DNA were investigated by UV-vis absorption, fluorescence emission and circular dichroism (CD) spectroscopy as well as cyclic voltammetry, viscosity measurements, molecular docking and molecular dynamics simulation. Binding constants were determined using UV-vis absorption and fluorescence spectra. The results indicated that studied Schiff-bases bind to DNA in the intercalative mode in which the metal derivative is more effective than non metals. Their interaction trend is further determined by molecular dynamics (MD) simulation. MD results showed that Ni derivative reduces oligonucleotide intermolecular hydrogen bond and increases solvent accessible surface area more than other compounds.

Ibuprofen causes photocleavage through ROS generation and intercalates with DNA: a combined biophysical and molecular docking approach

Ibuprofen is an important nonsteroidal anti inflammatory drug which intercalates with DNA and causes phototoxicity through ROS generation.

Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies

DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

Interaction of doxorubicin with polynucleotides. A spectroscopic study

The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (polyAT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV-vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.

Binding characteristics of sodium saccharin with calf thymus DNA in vitro

The binding characteristics of sodium saccharin (SSA), an artificial sweetener, with calf thymus DNA (ctDNA) were investigated by multispectroscopic techniques, chemometrics, and molecular simulation. A combined fluorescence and UV-vis spectroscopic data matrix was resolved by the multivariate curve resolution-alternating least-squares (MCR-ALS) chemometrics algorithm. The MCR-ALS analysis extracted simultaneously the concentration profiles and spectra for the three components (SSA, ctDNA, and SSA-ctDNA complex) to quantitatively monitor the SSA-ctDNA interaction, which is difficult to perform by conventional spectroscopic approach. The binding mode of SSA to ctDNA was principally through groove binding as revealed by ctDNA melting temperature studies, viscosity measurements, and iodide and salt quenching effects. Analysis of the Fourier transform infrared and circular dichroism spectra as well as molecular docking indicated that SSA preferentially bound to the guanine base of ctDNA and led to a transformation from B-like DNA structure to A-like conformation. Moreover, gel electrophoresis results suggested that SSA did not induce any significant cleavage in plasmid DNA.

Spectroscopic and Modelling Analysis on the Interaction of 3'-Azidodaunorubicin Semicarbazone with ctDNA

The synthesis and characterisation of a new anthracycline, 3′-azidodaunorubicin semicarbazone (ADNRS) is reported. The interaction between ADNRS and calf thymus DNA (ctDNA) was investigated by absorption and fluorescence spectroscopy in combination with melting temperature (Tm) curves and molecular modelling in physiological buffer (pH 7.4). Evidence indicates that ADNRS binds in the groove of ctDNA and the fluorescence quenching mechanism is a static quenching type. Calculated thermodynamic parameters show that hydrophobic interactions may play a predominant role in the binding. Furthermore, molecular modelling results corroborate the spectroscopic investigations.

Spectroscopic, viscositic and molecular modeling studies on the interaction of 3'-azido-daunorubicin thiosemicarbazone with DNA

A new daunorubicin has been synthesized and structurally characterized. The interaction of native calf thymus DNA (ctDNA) with 3′-azido-daunorubicin thiosemicarbazone (ADNRT) was investigated under simulated physiological conditions by multi-spectroscopic techniques, viscometric measurements and molecular modeling study. It concluded that ADNRT could intercalate into the base pairs of ctDNA, and the fluorescence quenching by ctDNA was static quenching type. Thermodynamic parameters calculated suggested that the binding of ADNRT to ctDNA was mainly driven by hydrophobic interactions. The relative viscosity of ctDNA increased with the addition of ADNRT, which confirmed the intercalation mode. Furthermore, molecular modeling studies corroborate the above experimental results.