Interaction studies of DNA binding of ruthenium(II) mixed-ligand complexes: [Ru(phen)2(dtmi)]2+ and [Ru(phen)2(dtni)]2+

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs

DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.

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.

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.

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.

Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA

We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.

Spectroscopic and molecular docking studies on the interaction of troxerutin with DNA

Troxerutin (TXER) is a derivative of naturally occurring bioflavonoid rutin. It possesses different biological activities in rising clinical world. The biological activity possessed by most of the drugs mainly targets on macromolecules. Hence, in the current study we have examined the interaction mechanism of TXER with calf thymus DNA (CT-DNA) by using various spectroscopic methods, isothermal titration calorimetry (ITC) and molecular docking studies. Further, DNA cleavage study was carried out to find the DNA protection activity of TXER. UV-absorption and emission spectroscopy showed low binding constant values via groove binding. Circular dichroism study indicates that TXER does not modify native B-form of DNA, and it retains the native B-conformation. Furthermore, no effective positive potential peak shift was observed in TXER-DNA complex during electrochemical analysis by which it represents an interaction of TXER with DNA through groove binding. Molecular docking study showed thymine guanine based interaction with docking score -7.09 kcal/mol. This result was compared to experimental ITC value. The DNA cleavage study illustrates that TXER does not cause any DNA damage as well as TXER showed DNA protection against hydroxyl radical induced DNA damage. From this study, we conclude that TXER interacts with DNA by fashion of groove binding.

DNA-interacting and biological properties of copper(ii) complexes from amidino-O-methylurea

Two copper(ii) complexes from the water-soluble amidino-O-methylureas exhibit interesting activities which are of paramount importance for biological applications.

Interaction of 6 mercaptopurine with calf thymus DNA--deciphering the binding mode and photoinduced DNA damage

DNA is one of the major intracellular targets for a wide range of anticancer and antibiotic drugs. Elucidating the binding between small molecules and DNA provides great help in understanding drug-DNA interactions and in designing of new and promising drugs for clinical use. The ability of small molecules to bind and interfere with DNA replication and transcription provides further insight into how the drugs control the expression of genes. Interaction of an antimetabolite anticancer drug 6mercaptopurine (6MP) with calf thymus DNA was studied using various approaches like UV-visible spectroscopy, fluorescence spectroscopy, CD, viscosity and molecular docking. UV-visible spectroscopy confirmed 6MP-DNA interaction. Steady state fluorescence experiments revealed a moderate binding constant of 7.48×10³ M⁻¹ which was consistent with an external binding mode. Competitive displacement assays further confirmed a non-intercalative binding mode of 6MP which was further confirmed by CD and viscosity experiments. Molecular docking further revealed the minimum energy conformation (−119.67 kJ/mole) of the complex formed between DNA and 6MP. Hence, the biophysical techniques and in-silico molecular docking approaches confirmed the groove binding/electrostatic mode of interaction between 6MP and DNA. Further, photo induced generation of ROS by 6MP was studied spectrophotometrically and DNA damage was assessed by plasmid nicking and comet assay. There was a significant increase in ROS generation and consequent DNA damage in the presence of light.

DNA intercalating studies of [Ru(bpy)2dmt]2+ with two vacant nitrogen atoms by introducing copper(II) ions

A novel, yet effective method for identifying DNA-binding modes of [Ru(bpy)(2)dmt](2+) (where bpy = 2,2'-bipyridine and dmt = 2,3-dimethyl-1,4,8,9-tetra-aza-triphenylene) on an indium tin oxide electrode has been successfully developed by introducing Cu(2+) ion and ethylenediaminetetraacetic acid. The results from emission spectra and fluorescence microscopic images suggested that [Ru(bpy)(2)dmt](2+) not only associates with Cu(2+) ion in both the absence and presence of DNA but also shows strong affinity with DNA in the presence of Cu(2+). Evidence for the strong binding of [Ru(bpy)(2)dmt](2+) to DNA was determined from the interface studies using electrochemical methods. The present study suggests that a combination of photoluminescence measurement with electrochemical methods identifies the DNA-binding behavior of luminescent molecules with redox activities. [Ru(bpy)(2)dmt](2+) binds to DNA via an intercalative mode.

Synthesis, characterization, DNA binding properties, fluorescence studies and toxic activity of cobalt(III) and ruthenium(II) polypyridyl complexes

The new ligand 4-(isopropylbenzaldehyde)imidazo[4,5-f ][1,10]phenanthroline (ippip) and its complexes [Ru(phen)(2)(ippip)](2+)(1),[Co(phen)(2)(ippip)](3+)(2),[Ru(bpy)(2)(ippip)](2+)(3),[Co(bpy)(2)(ippip)](3+)(4)(bpy=2,2-bipyridine) and (phen=1,10-phenanthroline) were synthesized and characterized by ES(+)-MS, (1)H and (13)C NMR. The DNA binding properties of the four complexes were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that complexes bind to calf thymus DNA (CT-DNA) through intercalation. When irradiated at 365 nm, the complexes promote the photocleavage of pBR322 DNA, and complex 1 cleaves DNA more effectively than 2, 3, 4 complexes under comparable experimental conditions. Furthermore, photocleavage studies reveal that singlet oxygen ((1)O(2)) plays a significant role in the photocleavage.

Luminescence properties of [Ru(bpy)(2)MDHIP](2+) modulated by the introduction of DNA, copper(II) ion and EDTA

The luminescence properties of [Ru(bpy)(2)MDHIP](2+) (bpy=2,2'-bipyridine, MDHIP=2,4-dihydrophenyl-imidazo[4,5-f][1,10]phenanthroline) in the absence and presence of DNA modulated by the introduction of Cu(2+) ion and EDTA have been investigated. It is found that the ruthenium(II) complex can insert and stack between the base pairs of calf thymus DNA with MDHIP ligand, and the intramolecular hydrogen bond is located inside of the DNA. The presence of DNA can enhance the luminescence intensities of [Ru(bpy)(2)MDHIP](2+) both in buffer solution and on an ITO surface. Moreover, the luminescence intensities of [Ru(bpy)(2)MDHIP](2+) and DNA-bound [Ru(bpy)(2)MDHIP](2+) are quenched by Cu(2+), and next recovered by the addition of EDTA. The repetitive luminescence-modulations have been achieved through the introduction of equimolar Cu(2+) and EDTA, respectively. In addition, it becomes evident that the number of luminescence-modulation cycles for [Ru(bpy)(2)MDHIP](2+) in the absence and presence of DNA is influenced by the cumulative concentrations of CuEDTA, generated successively by the strong coordination of Cu(2+) to EDTA.

Synthesis, characterization, DNA binding and cleavage studies of chiral Ru(II) salen complexes

Interaction of chiral Ru(II) salen complexes (S)-1 and (R)-1 with Calf Thymus DNA (CT-DNA) was studied by absorption spectroscopy, competitive binding study, viscosity measurements, CD measurements, thermal denaturation study and cleavage studies by agarose gel electrophoresis. The DNA binding affinity of (S)-1 (6.25 x 10(3)M(-1)) was found to be greater than (R)-1 (3.0 x 10(3)M(-1)). The antimicrobial studies of these complexes on five different gram (+)/(-) bacteria and three different fungal organisms showed selective inhibition of the growth of gram (+) bacteria and were not affective against gram (-) and fungal organisms. Further, the (S)-1 enantiomer inhibited the growth of organisms to a greater extent as compared to (R)-1 enantiomer.