Double-stranded Calf Thymus DNA Research Articles

Experimental, Density Functional Theory and Molecular Docking Studies about the Interaction between 6-MP and DNA: A Biosensor Study

In the paper presents a new DNA biosensor including 6-Mercaptopurine (6-MP), a well-known anticancer drug. Interactions with single-stranded and double-stranded calf thymus DNA (ct ds DNA and ct ss DNA) of the mentioned drugs were checked via experimental and theoretical tools. The experimental part of the article includes the voltammetric analyses made to see the interaction between 6-MP and DNA. Impedance Spectroscopy (EIS) measurements were performed to evaluate changes in charge transfer resistance (Rct) due to interactions on the PGE surface. The limit of detection (LOD) was determined as 2.43 µg/mL and 1.13 µg/mL for ct -dsDNA and ct -ssDNA interaction, respectively. In the experiments, a low-cost electrode frequently used in electrochemical analysis, was preferred the pencil graphite electrode (PGE) was preferred. In the theoretical section, the chemical reactivity of 6-MP was highlighted in the light of Conceptual Density Functional Theory (CDFT) based reactivity descriptors and electronic structure principles. The nature of DNA-drug interaction was highlighted through Molecular Docking analysis and obtained docking results supported the experimental observations. Our study shows the interaction of 6-MP with DNA biosensors. It is an original study as it is being studied for the first time. Therefore, the results obtained will guide researchers in future studies on biosensors.

Spectroscopic, electrochemical, and molecular docking studies of the interaction between the antihistamine drug desloratadine and dsDNA

Through the utilization of fluorescence spectroscopy, electrochemical, and molecular docking methods, this research investigates the interaction between the antihistamine drug desloratadine and calf thymus double-stranded DNA (ct-dsDNA). Deoxyguanosine (dGuo) and deoxyadenosine (dAdo) oxidation signals were diminished by incubation with varying concentrations of desloratadine, as determined by differential pulse voltammetry (DPV). This change was ascribed to desloratadine's binding mechanism to ct-dsDNA. The binding constant (Kb) between desloratadine and ct-dsDNA was determined to be 2.2 × 105 M−1 throughout electrochemical experiments. In order to further develop our comprehension of the interaction mechanism between desloratadine and ct-dsDNA, a series of spectroscopic experiments and molecular docking simulations were conducted. The Kb value was found to be 8.85 × 104 M−1 at a temperature of 25 °C by the use of fluorescence spectroscopic techniques. In summary, the utilization of electrochemical and spectroscopic techniques, alongside molecular docking investigations, has led to the prediction that desloratadine has the capability to interact with ct-dsDNA by groove binding.

DOX-DNA Interactions on the Nanoscale: In Situ Studies Using Tip-Enhanced Raman Scattering.

Chemotherapeutic anthracyclines, like doxorubicin (DOX), are drugs endowed with cytostatic activity and are widely used in antitumor therapy. Their molecular mechanism of action involves the formation of a stable anthracycline-DNA complex, which prevents cell division and results in cell death. It is known that elevated DOX concentrations induce DNA chain loops and overlaps. Here, for the first time, tip-enhanced Raman scattering was used to identify and localize intercalated DOX in isolated double-stranded calf thymus DNA, and the correlated near-field spectroscopic and morphologic experiments locate the DOX molecules in the DNA and provide further information regarding specific DOX-nucleobase interactions. Thus, the study provides a tool specifically for identifying intercalation markers and generally analyzing drug-DNA interactions. The structure of such complexes down to the molecular level provides mechanistic information about cytotoxicity and the development of potential anticancer drugs.

Electrochemical Investigations and Molecular Docking Analysis to Evaluate the Molnupiravir-Calf Thymus dsDNA Interaction

Molnupiravir (MLP) is an important antiviral drug recommended for the treatment of COVID-19. In order to design new pharmaceuticals, exploring drug and DNA interaction is crucial. This study aimed to determine the interaction of MLP with calf thymus double-stranded DNA (ct-dsDNA) by electrochemical methods. Investigation of these interactions was carried out using the differential pulse voltammetry technique (DPV) on the biosensor surface and in-solution studies. Changes in ct-dsDNA between deoxyguanosine (dGuo) and deoxyadenosine (dAdo) oxidation signals were examined before and after the interaction. It was found that MLP interacts significantly with bases of ct-dsDNA dAdo. Limits of detection and quantification for MLP-ct-dsDNA interaction were calculated as 2.93 and 9.67 μM in the linear range of 10–200 μM, respectively, based on dAdo’s decreasing peak current. To calculate the binding constant of MLP and ct-dsDNA, cyclic voltammetry was used, and it was found to be 8.6 × 104 M. As for molecular docking techniques, the binding energy of MLP with DNA is −8.1 kcal mol−1, and this binding occurred by a combination of strong conventional hydrogen bonding to both adenine and guanine base pair edges, which indicates the interaction of MLP with DNA.

Design, synthesis and characterization of tetra substituted 2,3-dihydrothiazole derivatives as DNA and BSA targeting agents: advantages of the visible-light-induced multicomponent approach.

This report describes the visible-light-induced one-pot multicomponent regioselective synthesis of a series of 5-aroyl-3-((arylidene)amino)-2-((arylidene)hydrazono)-4-methyl-2,3-dihydrothiazoles as DNA and BSA targeting agents. The multicomponent condensation of thiocarbohydrazide and aldehydes with α-bromo-1,3-diketones, generated in situ by the bromination of unsymmetrical 1,3-diketones with NBS using white LED light as an environmental friendly source in the presence of EtOAc solvent furnished the titled 2,3-dihydrothiazole derivatives in excellent yields. The exact regioisomeric structure was identified unambiguously by employing multinuclear 2D-NMR spectroscopy [1H-13C] HMBC; [1H-13C] HMQC and [1H-15N] HMBC. Furthermore, the binding characteristics of the synthesized 2,3-dihydrothiazole derivatives were assessed with double-stranded calf-thymus DNA duplex (ct-DNA) and bovine serum albumin (BSA). Initial screening of all the synthesized 2,3-dihydrothiazole derivatives using various in silico techniques including molecular reactivity analysis, Lipinski rule and molecular docking, concluded 5-(4'-chlorobenzoyl)-3-((4''-methoxybenzylidene)amino)-2-(4'''-methoxybenzylidene)hydrazono)-4-methyl-2,3-dihydrothiazole derivative 6a as the most suitable compound for studying binding interaction with DNA and BSA. Additionally, to illustrate the ex vivo binding mode of 6a with DNA and BSA, several spectroscopic techniques viz. UV-visible, circular dichroism (CD), steady-state fluorescence and competitive displacement assays were carried out.

Theoretical design, synthesis, third-order nonlinear optical properties and DNA binding studies of benzothiadiazole based conjugated polymer

Benzothiadiazole based copolymer P(BTZ-BT) was theoretically designed by density functional theory methods employing B3LYP/6–31 G (d,p) and HSE06/6–31 G (d,p) basis sets. A low band gap of 1.31 eV was observed for the copolymer by HSE06/6–31 G (d,p) basis set. TG analysis of the polymer showed high thermal stability at 500 °C. Experimentally observed band gap for the copolymer was 1.66 eV by cyclic voltammetry. Fluorescence lifetime of the polymer P(BTZ-BT) was studied and it exhibited an average lifetime of 2.59 ns. The copolymer exhibited positive solvatochromism with a Stoke's shift value ranging from 3082 cm−1 to 4569 cm−1. Open-aperture Z-scan traces of the copolymer in DMSO at 91µJ, 165 µJ, 285 µJ and 450 µJ showed positive NLO absorption coefficient β in the range of 10−10m/W and exhibited optical threshold value of 0.03 GW/cm2, 0.05 GW/cm2 and 0.12 GW/cm2 respectively. No linear transmission was observed at 450 µJ for the copolymer during the study of optical limiting property. DNA binding studies of the copolymer with double stranded calfthymus DNA was carried out. Fluorescence observed for the copolymer was quenched by 85% on interaction with the ct-DNA and gradual decrease was observed in the lifetime of the copolymer from 2.59 ns to 1.8 ns.

ZnO nanoflowers modified pencil graphite electrode for voltammetric DNA detection and investigation of Gemcitabine–DNA interaction

In this study, ZnO nanoflowers (ZnONFs) were synthesized using sonochemical method, which is a simple, environmentally friendly, low-cost and rapid method. ZnONFs was characterized by using FE-SEM, EDS, elemental mapping, FTIR and XRD techniques. Single use pencil graphite electrode (PGE) modified with ZnONFs was characterized using FE-SEM, EDS, elemental mapping, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods. This developed electrode was used for the first time for the determination of calf thymus double-stranded DNA (dsDNA) and the chemotherapeutic drug Gemcitabine (GEM) using differential pulse voltammetry (DPV). The detection limits (DLs) of dsDNA and GEM were calculated as 1.91 μg/mL and 2.47 μg/mL, respectively. The interaction of GEM and dsDNA at different times was investigated by measuring the changes in both GEM and guanine oxidation signals by DPV technique. The developed nanoflower-based biosensor responded in as short as 5 min in the DNA-anticancer drug interaction study. The study provides advantages such as low cost, biocompatibility, and easy synthesis of the used nanomaterial synthesis, as well as low detection limit and short interaction time at the sensor stage.

Elucidating the interaction of antidepressant drug paroxetine with ct-dsDNA: A comparative study by electrochemical, spectroscopic, and molecular docking approaches

This study is designed to investigate the interaction of phenylpiperidine derivative drug paroxetine, which is an effective serotonin reuptake inhibitor and biomolecules through electrochemical, fluorescence spectroscopy, and molecular docking methods. The interaction between paroxetine and biomolecules was investigated by differential pulse voltammetry according to the decrease in deoxyguanosine anodic oxidation signal of double-stranded calf thymus DNA. Fluorescence spectroscopy studies were performed by titrating paroxetine against double-stranded calf thymus DNA solution at four different temperatures. The fluorescent results showed that paroxetine had a great affinity to bind with double-stranded calf thymus DNA. Interaction studies demonstrate that paroxetine binds to double-stranded calf thymus DNA via intercalation binding mode, and the binding constant values ​​were calculated as 7.24 × 104 M−1 and 1.52 × 104 M−1 at 25 °C, based on voltammetric and spectroscopic results, respectively. Moreover, with the aim of elucidating the interaction mechanism between paroxetine and double-stranded calf thymus DNA, electrochemical and fluorescence spectroscopy studies along with molecular docking analysis were made.

Cysteine 106 Controls HMGB1 Nucleocytoplasmic Distribution and Function: Role of Sex and Implication to Pulmonary Hypertension

IntroductionHigh mobility group box protein 1 (HMGB1) is a nuclear protein that gets released during cell damage and stimulates inflammatory and proliferative pathways in the survived neighboring cells. Our previous research discovered a significant sex difference in HMGB1 release and downstream signaling and confirmed its critical importance in the pathobiology of pulmonary hypertension (PH).HypothesisHMGB1 contains three cysteine residues (23/45/106) involved in the extracellular HMGB1 oligomerization and receptor binding, with Cys106 being especially critical for HMGB1 signaling. However, the role of cysteines in the intracellular HMGB1 activity is less established. We hypothesize that Cys106 regulates intracellular HMGB1 homeostasis and function and contributes to the pathogenic mechanisms relevant to PH.MethodsTo study the activities of HMGB1 cysteines, we designed peptides that bind to the specific regions of HMGB1 and, by shielding either Cys106 or Cys23/45, prevent their interaction with the downstream targets. The peptides with cell‐penetrating TAT sequences were used to study the intracellular role of HMGB1 cysteines, while peptides without TAT served as extracellular controls. Fractionating of pulmonary artery smooth muscle cells (PASMC) allowed the evaluation of HMGB1 cytosol/nuclear distribution. Calf thymus double‐stranded DNA cellulose was used to study the binding of recombinant fully reduced HMGB1 in the presence or absence of shielding peptide. The protective role of peptide in vivo was estimated using the rat Sugen/Hypoxia model of PH. Given the discovered sex difference in the HMGB1‐mediated signaling, the in vitro and in vivo studies were replicated in male and female animals and cells.ResultsThe cytosol and nuclear levels of HMGB1 were affected by cell‐penetrating peptide designed to shield Cys106 (TAT‐α‐HMGB1Cys106, or α‐Cys106) and not any other peptide. Further investigation revealed that α‐Cys106 peptide produced ~ 5.9 fold decrease in HMGB1 binding to DNA, enhanced the exit of nuclear HMGB1 to the cytosol, which was especially evident in male cells, and induced its proteasomal degradation (1±0.097 vs. 0.428±0.045 vs. 0.885±0.049 in untreated, α‐Cys106 and α‐Cys106/proteasome inhibitor (MG132, 10μM, 1hr) treated PASMC, p<0.001 and p<0.003, N=6). The peptide‐mediated decrease in HMGB1/DNA binding negatively affected the expression of TLR4 and p53 and reduced cell apoptosis. In females, treatment with α‐Cys106 (2.5 mg/kg/day, i.p during the wks 1‐2 or wks 3‐5) produced an anti‐apoptotic effect and reduced plasma HMGB1 levels, which corresponded to a decreased right ventricle (RV) systolic pressure at the early stage of PH and protected the RV at the later stage. In contrast, male PH rats showed no apoptosis activation in the lungs, and α‐Cys106 treatment produced no changes in plasma HMGB1 or hemodynamic parameters.ConclusionHMGB1Cys106 is the critical regulator of intracellular HMGB1 function, including HMGB1/DNA binding, regulation of p53 expression and apoptosis activation, the intracellular distribution of HMGB1, and its extracellular release. This study also confirms the significant sex difference in the levels of pulmonary apoptosis, HMGB1 release, and its contribution to the pathobiology of PH.

Probing the interaction of ciprofloxacin with dsDNA: Electrochemical, spectro-electrochemical and AFM investigation

Abstract The interaction of double strand calf thymus DNA (dsDNA) with the antibiotic, Ciprofloxacin (Cf) has been investigated using differential pulse voltammetry, impedance spectroscopy, UV–Vis spectroscopy, spectroelectrochemistry and atomic force microscopy (AFM) measurements. Investigation revealed good interaction between Cf and dsDNA, with formation constant of 2.65 × 104 M−1. Electrochemical measurements established the mechanism of interaction to be the intercalative in nature, which has been supported by the spectroscopic findings. The zeta potential analysis reveals that the Cf-dsDNA complex is stable enough to remain in the solution and is stabilized through electrostatic interaction as well as the intercalative binding. The AFM images of dsDNA (at 47 µM concentration) with various concentrations of Cf (0.1, 0.2, 0.5, 1, 5, 10 mM) reveal the condensation of DNA in the presence of the antibiotic drug. The mechanism of the dsDNA condensation by the presence of Cf is ascertained to be through the electrostatic interaction between the –NH– group of Cf and the phosphate group of DNA and also through the carboxylic acid group of Cf with the amine groups of the nucleotides present in the DNA strands.

Interaction of citalopram and escitalopram with calf Thymus DNA: A spectrofluorometric, voltammetric, and liquid chromatographic approach

Citalopram (CIT) and its S-enantiomer, escitalopram (ESC), are antidepressants belonging to the class called selective serotonin reuptake inhibitors and have many different pharmacological and biological properties. Understanding the interaction mechanism of small drug molecules with DNA both helps in the development of new DNA-targeted drugs and provides more in-depth knowledge for controlling gene expression. In this study, the interaction of CIT and ESC with double-stranded calf thymus DNA (ct-dsDNA) was investigated for the first time. Spectrofluorometric, liquid chromatographic, and voltammetric response profiles of drugs and ct-dsDNA at different concentrations showed DNA-drug complex formation. Calculated binding constants were greater with all three techniques for ESC compared to CIT and were of the order of 103-104, which is in accordance with those of well-known groove binders. The results also showed the significant effect of chirality on complex formation. The thermodynamic parameters, including free energy change (ΔG < 0) and enthalpy change (ΔH < 0) obtained at different temperatures, indicated that complex formation was mainly driven by hydrogen bonding and van der Waals forces for both drugs. The results of this study may enhance the understanding of the interaction between CIT or ESC and ct-dsDNA and can be considered as the pioneer for future studies to uncover possible hidden phenotypes of these compounds.

Synthesis, characterization, electrochemistry, biological and molecular docking studies of the novel Co(II), Ni(II) and Cu(II) complexes derived from methanethiol bridged (2-((1H-benzo[d]imidazol-2-yl)methylthio)-1H-benzo[d]imidazol-6-yl)(phenyl)methanone

The bio-active Co(II), Ni(II) and Cu(II) complexes derived from new (2-((1H-benzo[d]imidazol-2-yl)methylthio)-1H-benzo[d]imidazol-5-yl)(phenyl)methanone were synthesized in good yield. The structure of these metal complexes have been characterized using IR, Uv–visible, mass spectra,1H NMR, TGA and powder XRD techniques. The spectral data of the Co(II) and Ni(II) complex indicated the tri-dentate bonding mode with the ligand and that of the Cu(II) complex is in bi-dentate bonding mode. The electrocatalytic activity of the Co(II) complex was studied by cyclic voltammeter using modified GCE towards various concentration of dopamine (DA, 3,4-dihydroxyphenethylamine). The obtained Ip value linearly increased with increasing scan rates, indicating the oxidation process of dopamine (DA) which occurred by modified Co(II) complex/GCE through diffusion controlled process. The antimicrobial, antioxidant and cytotoxicity studies of the ligand and its metal complexes were performed, the obtained results showed that the complexes are more potent bio-active as compared with uncoordinated ligand. The DNA binding property of the metal complexes were performed on double strand calf thymus DNA using electronic absorption and fluorescence emission methods, in addition, photo induced DNA cleavage activity also studied on pBR322 DNA. The molecular docking of the Co(II) complex on 6-bp DNA (PDB code: 1Z3F) and C-KIT Tyrosive kinases (TRKs) (PDB code: 1t46), further confirms the inhibition ability of the metal complex. The experimental results and the drug likeness property of the metal complexes suggest the possible applications of metal complex which, could be developed as a potent drug in the near future.

ELECTROCHEMICAL DETERMINATION OF THE INTERACTION BETWEEN ANTICANCER DRUG CAPECITABINE AND DNA BY CARBON PASTE ELECTRODE

In this study, the interaction of an anticancer drug, Capecitabine with DNA was investigated by electrochemical methods using carbon paste electrode (CPE). The interaction of Capecitabine with single-stranded Calf thymus DNA (ss DNA) and double-stranded Calf thymus DNA (ds DNA) at electrode surface, or in solution phase was investigated by monitoring the changes at the oxidation signal of guanin base of DNA measured by differential pulse voltammetry (DPV) technique. Impedimetric measurements were performed by electrochemical impedance spectroscopy technique that also confirmed that ds DNA was immobilized onto the electrode surface. The detection limit (DL) in the case of interaction of Capecitabine with dsDNA and ssDNA interaction was calculated and found to be 17.35µg/mL and 17.12µg/mL, respectively.

Novel DNA Biosensor for Direct Determination of Carrageenan

A novel disposable electrochemical biosensor based on immobilized calf thymus double-stranded DNA (dsDNA) on the carbon-based screen-printed electrode (SPE) is developed for rapid biorecognition of carrageenan by using methylene blue (MB) redox indicator. The biosensor protocol for the detection of carrageenan is based on the concept of competitive binding of positively charged MB to the negatively charged dsDNA and carrageenan. The decrement in the MB cathodic peak current (ipc) signal as a result of the released MB from the immobilized dsDNA, and attracted to the carrageenan can be monitored via differential pulse voltammetry (DPV). The biosensor showed high sensitivity and selectivity to carrageenan at low concentration without interference from other polyanions such as alginate, gum arabic and starch. Calibration of the biosensor with carrageenan exhibited an excellent linear dependence from 1–10 mg L−1 (R2 = 0.98) with a detection limit of 0.08 mg L−1. The DNA-based carrageenan biosensor showed satisfactory reproducibility with 5.6–6.9% (n = 3) relative standard deviations (RSD), and possessing several advantages such as simplicity, fast and direct application to real sample analysis without any prior extensive sample treatments, particularly for seaweeds and food analyses.

Facile core-shell nanoparticles with controllable antibacterial activity assembled by chemical and biological molecules.

Antibiotic residues can induce the production of bacterial variability and increase the variety of resistant bacterial strains. In order to cope up with the global crisis, there is an urgent need to develop alternative drugs and strategies to effectively kill the bacteria and inhibit the emergence of superbugs. Herein, we developed an antibacterial strategy based on the conjugated polymer nanoparticles (CPNs) and the biomolecule-mediated regulation for the controllable antibacterial treatment. Upon being modified with Hoechst 33258 (H33258), the biocompatible CPNs tend to be effective antibacterial agents, with the antibacterial activity being regulated through the binding and separation of H33258 and calf thymus double-stranded DNA (dsDNA) with the aid of deoxyribonuclease I (DNase I). This eco-friendly antibacterial system not only provides a simple and controllable antibacterial strategy but also inspires the design of biomolecule-mediated antibacterial activity regulation.

Metallacarboranes on the Road to Anticancer Therapies: Cellular Uptake, DNA Interaction, and Biological Evaluation of Cobaltabisdicarbollide [COSAN

After uptake by U87 MG and A375 cancer cells, cobaltabisdicarbollide [COSAN]- distributes between membrane and nucleus and presents no relevant cytotoxicity against both cell lines even for long incubation times. The cytotoxicity of Na[COSAN] was also tested towards one normal cell line, the V79 fibroblasts, in order to ascertain the noncytotoxic profile of the compound. As the cell's nucleus contains DNA, the interaction between [COSAN]- and double-stranded calf thymus DNA (CT-dsDNA) has been investigated. There is a strong interaction between both molecules forming a nanohybrid CT-dsDNA-[COSAN] biomaterial, which was fully characterized. Moreover, Na[COSAN] shows characteristic redox peaks ascribed to the oxidation/reduction of Co3+/2+ at a formal potential of -1.444 V and it can be accumulated at a surface-immobilized DNA layer of glassy carbon electrodes. The equilibrium surface-binding constants (Kox /Kred ), which confirm that [COSAN]- interacts with DNA by an intercalative or electrostatic mode, depending on the ionic strength of the solution, were estimated. In addition, high binding affinity of Na[COSAN] to proteins was observed by 11 B{1 H} NMR and confirmed in vivo. Finally, biodistribution studies of [COSAN]- in normal mice were run. After administration, Na[COSAN] was distributed into many organs but mainly accumulated in the reticuloendothelial system (RES), including liver and spleen. After 1 h, the formation of aggregates by plasma protein interaction plays a role in the biodistribution profile; the aggregates accumulate mostly in the lungs. Na[COSAN], which displays low toxicity and high uptake by relevant cancer cells accumulating boron within the nucleus, could act as a suitable compound for further developments as boron neutron capture therapy (BNCT) agents.

Synthesis, characterization, DNA binding, topoisomerase I inhibition, and antiproliferation activities of (di-tert-butylbipyridine) platinum(II) complexes

Two mononuclear Pt(II) complexes, Pt(dbbpy)Cl2 (1) and [Pt(dbbpy)2](PF6)2 (2) (dbbpy = 4,4′-ditertbutyl-2,2′-biyridine) were synthesized and characterized by single-crystal X-ray diffraction analysis, elemental analysis, 1H NMR, and ESI–MS. Their binding affinities for both double-stranded (DS) calf thymus DNA (ct-DNA) and G-quadruplex DNA (HT21 and BCL-2) were investigated. In addition to structural differences, complex 1 displayed higher binding affinity for DS ct-DNA, whereas positively charged complex 2 was selective for binding to G-quadruplex DNA over DS DNA. The time-dependent cleavage of supercoiled circular plasmid pBR322 DNA by 1 was observed using agarose gel electrophoresis, whereas complex 2 hardly cleaved DS DNA. Stabilization of G-quadruplex HT21 DNA by both complexes was assessed by PCR stop assays. Both complexes exhibited moderate activities for inhibition of topoisomerase I as well as modest antiproliferation activities toward cancer cells in CKK-8 assays.

Binding affinity and in vitro cytotoxicity of harmaline targeting different motifs of nucleic acids: An ultimate drug designing approach

The work focuses towards interaction of harmaline, with nucleic acids of different motifs by multispectroscopic and calorimetric techniques. Findings of this study suggest that binding constant varied in the order single-stranded (ss) poly(A)>double-stranded calf thymus (CT) DNA>double-stranded poly(G)·poly(C)>clover leaf tRNAPhe . Prominent structural changes of ss poly(A), CT DNA, and poly(G)· poly(C) with concomitant induction of optical activity in the bound achiral alkaloid molecule was observed, while with tRNAPhe , very weak induced circular dichroism perturbation was seen. The interaction was predominantly exothermic, enthalpy driven, and entropy favored with CT DNA and poly(G)·poly(C), while it was entropy driven with poly(A) and tRNAPhe . Intercalated state of harmaline inside poly(A), CT DNA, and poly(G)·poly(C) was shown by viscometry, ferrocyanide quenching, and molecular docking. All these findings unequivocally pointed out preference of harmaline towards ss poly(A) inducing self-structure formation. Furthermore, harmaline administration caused a significant decrease in proliferation of HeLa and HepG2 cells with GI50 of 28μM and 11.2μM, respectively. Nucleic acid fragmentation, cellular ultramorphological changes, decreased mitochondrial membrane potential, upregulation of p53 and caspase 3, generation of reactive oxygen species, and a significant increase in the G2 /M population made HepG2 more prone to apoptosis than are HeLa cells.

Label-free detection of histone based on cationic conjugated polymer-mediated fluorescence resonance energy transfer

A simple and homogeneous histone assay is developed based on histone-induced DNA compressing coupled with cationic conjugated polymer (CCP)-mediated fluorescence resonance energy transfer (FRET). In this strategy, the CCP serves as the FRET donor and SYBR Green I (SG), which can strongly fluoresce not at its free state but after intercalated into the double stranded calf thymus DNA (dsDNA), serves as the acceptor of FRET. In the absence of histone, the dsDNA-SG and CCP combine with each other through electrostatic interaction and the strong FRET from CCP to SG occurs due to the overlapping between the fluorescent emitting spectrum of the CCP and the absorption spectrum of SG. Upon the introduction of histone, the formed compact complex of histone/dsDNA will lead to the compression of dsDNA structure and prevent SG binding to dsDNA and fluorescing, which gives rise to a significant decrease of FRET efficiency between CCP and SG. Thus, the quantitative analysis of histone is realized by monitoring the change of FRET ratio, namely, the intensity ratio of the two emission bands of CCP and SG. Due to the light harvesting and fluorescence amplification properties of CCP, high sensitivity is achieved with a low detection limit of 0.74ng/mL histone. This strategy provides a simple, homogeneous and sensitive strategy for histone analysis in the study of histone-related biological processes.

A spectroscopic investigation into the binding of novel platinum(IV) and platium(II) anticancer drugs with DNA

Platinum(II) complexes have had enormous success in cancer chemotherapy and novel PtIV complexes show potential for reduced toxic side effects and different mechanisms of action. While the action of PtII anticancer drugs with DNA has been well characterized with X-ray and many spectroscopic modalities, the mechanisms of binding PtIV complexes to DNA require further fundamental studies. In the present work using ATR-FTIR spectroscopy, we have extensively analyzed conformational changes in both single-stranded (ss) and double-stranded (ds) calf-thymus DNA, after binding to the PtIV anticancer complex, [Pt{((p-HC6F4)NCH2)2}(py)2(OH)2] (py=pyridine) (Pt103(OH)2), and its PtII analogue, [Pt{((p-HC6F4)NCH2)2}(py)2] (Pt103) in buffered aqueous acetone (55% water), under which conditions no hydrolysis of drugs occurs. To aid in band assignments of the Pt derivatives, DFT calculations using the M062X/cc-pVDZ level of theory were performed. The ssDNA is distorted and its conformation changes more towards the A-like DNA of dsDNA upon binding to both Pt103 and Pt103(OH)2. This conclusion is derived from the changes in the PO2− symmetric stretching vibrations (1086 to 1093cm−1) and CO (1055 to 1062cm−1) and CC (968 to 965cm−1) stretching vibrations of the phosphodiester backbone. Unlike ssDNA, only Pt103 binding to dsDNA induces distortions along with a conformational change in dsDNA from a more B-DNA like form to the more compact and distorted A-DNA form. The results show that there is no apparent reduction of Pt103(OH)2. Moreover, we demonstrate that Pt103(OH)2 can directly bind to ssDNA without any prior reduction. This study provides new insights into how these novel PtII and PtIV complexes interact with DNA. These results may have implications relevant to the development of new anti-cancer agents.