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Abstract: This paper focuses on investigating the structure parameters of antibiotics which have decisive influence on the interactive mode between antibiotics and DNAs. The analytical results of Best Prediction Set Support Vector Machine Method (BPSSVM) show that the number of N atoms, the number of double bonds, the number of lone-pair electrons, the molar refractivity and the molecular radius are the main structure parameters which functionally decide their reactive modes. It is clear that the BPSSVM is potent in predicting the interactive modes between antibiotics and DNAs. [Copyright &y& Elsevier]

Abstract: In this paper, 24 parameters (descriptors) that can influence the interaction of selected antibiotic compound (antibiotics) and DNA have been investigated. Principal components analysis (PCA) and hierarchical cluster analysis (HCA) were employed in order to reduce dimensionality and investigate which subset of variables could be more effective for classifying the antibiotics according to their binding mode with DNA. Results of the PCA and HCA study showed that there are 12 descriptors closely related to the interaction. Based on these descriptors, multiple linear regression (MLR) and artificial neutral network (ANN) allowed us to propose three models which can predict binding constant and binding mode. For the prediction of binding constant, the minimal relative error is only 0.17% (MLR) and 0.72% (ANN); for the prediction of binding mode (ANN), five test molecules are all consistent with experimental results. [Copyright &y& Elsevier]

The electrochemical characteristics of kanamycin onto self-assembled monolayer (SAM) modified gold electrode (SAM/Au) is investigated by cyclic voltammetry. In the potential range 0–0.6 V, Cu(II) yields a pair of stable redox waves at the bare gold electrode. Epa is located at 0.189 V and Epc at 0.254 V. In contrast, Cu(II) is reduced at a more positive potential and a decreasing current at the kanamycin SAM/Au electrode. Cu(II) and kanamycin can form a stoichiometry complex with chemical ratio of 2:1. The interaction of Cu(II)–kanamycin complex with calf thymus DNA is also studied in the solution. And the interactive mode between Cu(II)–kanamycin complex and DNA is verified by the fluorescence method. Binding constants (K) of the Cu(II)–kanamycin complex to DNA and binding site size (s) are calculated from voltammetric data and equal to 1.5 × 107 l/mol and 4 bp, respectively. [Copyright &y& Elsevier]

The interaction of the two new synthesized transition-metal complexes, ML2 (M=Co, Cu, L=1,8-dihydroxyethyl-1, 3,8,10,13-hexa-azacyclotetradecane) with calf thymus DNA was probed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Adding deoxyribonucleic acid (DNA) into [CoL]2+ and [CuL]2+ solution, the ip value of all the peaks of [CoL]2+ and [CuL]2+ significantly decreased in proportion to concentration of DNA. Glassy carbon electrodes (GCEs) were modified with DNA by adsorption, and it was electrochemically characterized with transition-metal complexes, [ML]2+. The DNA modification layer on the GCE is unstable to alkali and to heat, but stable to acid solutions and very stable in long stock in a dry state. It could be seen that peak potential shifted positively and the peak current increased significantly. The electrochemical parameters, binding constant (kn+) and binding sites(s) were calculated by a nonlinear regression method. [Copyright &y& Elsevier]

The electrochemical behavior of complex EuMo2 (Mo = Morin, 2′,3,4′5,7-pentahydroxyflavone) and its interactions with calf thymus DNA were studied using cyclic voltammetry (CV) and double potential step chronocoulometry (DPSCC) at glass carbon electrode (GCE) and DNA modified GCE, respectively. Information such as diffusion coefficient (D), rate constant (ks) of EuMo2 and intrinsic binding constant (K), binding numbers (n) of bound species per DNA (bp) were obtained. EuMo2 can bind to DNA, and the binding mode is intercalation. By nonlinear fitting with Langmuir equation, a K of 1.02 × 106 M-1 and an n of 1 were obtained. [ABSTRACT FROM AUTHOR]

Abstract: Voltammetric behavior of Morin was studied in 0.1M HAc–NaAc+50mM KCl (pH 3.4) solution at glassy carbon electrode (GCE) using cyclic voltammetry (CV). Morin showed an irreversible anodic peak at 0.720V in CV which was involving two electrons and two protons. Also, the interaction of Morin with double-stranded calf thymus DNA (ctDNA) was studied by CV at GCE with an irreversible electrochemical equation. As a result of reaction with ctDNA, the voltammetric peak of Morin was a position shift and the peak current decreased. The diffusion coefficients of both free and binding Morin (D f =1.1086×10−7 cm2 s−1 and D b =8.2544×10−9 cm2 s−1), binding constant (K =1.7765×107 cm3 mol−1), and binding site size (s =0.8510) of the Morin–DNA complex were obtained simultaneously by non-linear fit analysis. The results demonstrate that Morin can bind to ctDNA in 0.1M HAc–NaAc+50mM KCl (pH 3.4) solution and the ring B of Morin intercalates between the DNA base pairs. [Copyright &y& Elsevier]

The Hexaaza macrocyclic copper(II) complex (Cu(II)L-1,8-Dihydroxyethyl-1,3,6,8,10,13-hexaazacyclotetradecane copper(II) perchlorate monohydrate) was synthesized and purified. The interaction of this complex with calf thymus DNA has been explored by using absorption, emission, viscosity measurements, electrochemical studies and DNA cleavage. All of the experimental results indicate that the complex bind to DNA by non-classical or partial intercalative interaction. The complex has also been found to promote the cleavage plasmid pBR 322, in the presence of H 2 O 2 and ascorbic acid. The cleaving mechanism for the Cu(II)L complex has been proposed. [ABSTRACT FROM AUTHOR]

Abstract: A porphyrin meso-tetrakis{[4-(1-pyridyl)propoxy]phenyl}porphyrin (TPyPP) and its Ni complex (TPyPP(Ni)) have been synthesized and characterized by 1H NMR, UV–vis spectra. The interaction of two porphyrins with calf thymus-DNA (CT-DNA) has been explored by UV–vis, fluorescence and circular dichroic spectroscopy and viscosity measurements. The results suggest that these porphyrins can bind to DNA by the same binding mode. TPyPP outside binds by self-stack with DNA both at low drug load r (=[porphyrin]/[DNA]) and high drug load. Though TPyPP(Ni) has center metal nickel, binding mode with DNA has little difference compared with TPyPP, dominating out-binding mode with different direction along DNA. The binding constants of the TPyPP and TPyPP(Ni) to DNA were 4.65 × 105 M−1 and 3.2 × 105 M−1, respectively. A colored precipitate was found after time in two porphyrin''s viscosity measurement. The reasonable interpretation is the porphyrins with alkyl connected N-position of pyridine can strongly interact with the anionic phosphates of DNA and lead to hydrophobic complex. [Copyright &y& Elsevier]

The interactions of quercetin (Qu) and Eu–Qu3 complex with calf thymus DNA were studied using cyclic voltammetry (CV) and double potential step chronocoulometry (DPSCC) at glass carbon electrode (GCE) for the surface method. The method is simple, convenient, reliable, reagent saving. Information such as intrinsic binding constant (K), and binding numbers (n) of bound species per DNA (bp), ratio (KOx/KRed) of the binding constants for the oxidized and reduced forms of a bound species and interaction mode was obtained using dsDNA-modified GCE. Quercetin and Eu–Qu3 can both bind to DNA, but quercetin binds to DNA mainly by electrostatic attraction and the complex bind to DNA by both intercalation and electrostatic attraction. For the quercetin/dsDNA-modified GCE systems, a K of (3.80 ± 0.3) × 104 M−1, saturation coverage value (Γs) of (2.28 ± 0.2) × 10−10 mol/cm2 and n of 1.2 were obtained. For the complex system, a saturation coverage value (Γs) of 1.65 × 10−10 mol/cm2 and n of 1.8 were obtained. [Copyright &y& Elsevier]

Checkpoint kinase 1 (Chk1) is a serine/threonine kinase that plays a key role in the response to DNA-mediated cell injury. In this paper, the quantitative structure–activity relationship (QSAR) models were constructed to predict the activity of pyrazolo[1,5-a]pyrimidine derivatives of Checkpoint kinase 1 (Chk1) by using SVM and PSO-SVM methods. The root-mean-square errors ( RMSE ) of the training set and the test set for the PSO-SVM model were 0.0886 and 0.1803, respectively. For the SVM model, the values were 0.2185 and 0.4023, respectively. The results showed that the performance of the PSO-SVM model was better than the corresponding SVM model. Thus, it can be inferred that the PSO-SVM analysis will be a promising method and be spread to apply in the QSAR studies. [ABSTRACT FROM AUTHOR]

MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Rapid, sensitive, and quantitative microRNAs detection methods with high specificity are imperative. Here, we for the first time developed a DNA-functionalized metal-organic framework (MOF)-based ratiometric fluorescent probe using the interaction between Thiazole Orange (TO) dye and Rhodamine B(RhB) dye molecules, and achieved sensitive detection and imaging of miRNA-21 in living cells. Among them, DNA was successfully conjugated with MOF through the Zr-O-P bond in a single step with high efficiency. Based on this ratiometric fluorescent probe, picomolar limit detection (57 pM) for miRNA-21 can be obtained without signal amplification. After penetration into the cell, intracellular miRNA-21 can also be imaged by strand-displacement reaction, even distinguishing cancer cells from normal cells was achieved. This work paves the way for the development of DNA-functionalized MOF for intracellular molecules analysis and is of great significance for the early disease diagnosis. [Display omitted] • Ratiometric fluorescent probe was constructed based on the interaction between Thiazole Orange and Rhodamine B molecules. • DNA molecules were efficiently linked to the metal-organic frameworks (MOFs) surface through Zr-O-P bonds in one step. • The developed probe demonstrated a detection limit down to 57 pM was achieved without signal amplification strategy. • The developed probe can be used for miRNA-21 imaging in different types of cells. [ABSTRACT FROM AUTHOR]

Abstract: DNA hybridization on the Aunano–DNA modified glassy carbon electrode (GCE) was investigated. The thiol modified probe oligonucleotides (SH–ssDNA) at the 5′ phosphate end were assembled on the Aunano–DNA modified GCE surface. The electrochemical response of the probe immobilization and hybridization with target DNA was measured by differential pulse voltammetry (DPV) using methylene blue (MB) as the electroactive indicator. Gold nanoparticles can be dispersed effectively on the GCE surface in the presence of calf thymus DNA. Aunano–DNA modified GCE could greatly increase the active sites and enhance the response signal during immobilization and hybridization. The hybridization amount of target DNA could be greatly increased. The linear detection range of Aunano–DNA electrode for the complementary 21-mer oligonucleotide (cDNA) was achieved from 1.52×10−10 to 4.05×10−8 molL−1. The detection limit could reach the concentration of 10−10 mol/L. [Copyright &y& Elsevier]

Absorption, fluorescence spectral and viscometric studies have been carried out on the interaction of Morin (2′,3,4′,5,7-pentahydroxyflavone, ) and its Cu complex, CuL2·2H2O [L=Morin (2′-OH group deprotonated), ] with calf thymus DNA. CuL2 shows different spectral characteristics from that of Morin in the presence of DNA. Increasing fluorescence is seen for CuL2 with DNA addition whereas decreased fluorescence is observed for Morin. Quenching fluorescence is observed for the DNA–EB system when CuL2 is added whereas slightly quenched fluorescence is seen for the DNA–EB system with Morin addition. The relative viscosity of DNA and the DNA–EB system increases with the addition of CuL2. Hypochromism and a smaller shift are observed in the UV–visible spectra of CuL2 in the presence of DNA and the denatured temperature of DNA is decreased in the presence of CuL2. The above results suggested that Morin and CuL2 can both bind to DNA, but the binding mode is different. The complex binds to DNA mainly by intercalation, while Morin binds in a nonintercalating mode. [Copyright &y& Elsevier]

Based on electrochemiluminescence resonance energy transfer (ERET) from Ru(bpy) 3 2+ to graphene oxide (GO), a novel label-free solid-state ECL sensor for sensitive detection of DNA was proposed. First, Ru(bpy) 3 2+/AuNPs was successfully prepared by using a simple and green method and characterized by transmission electron microscopy (TEM), Energy Dispersive X-ray (EDX), and UV–vis spectroscopy. Then, the Ru(bpy) 3 2+/AuNPs colloid was assembled on the gold electrode surface for solid-state ECL film which also later could be used to immobilize thiol-derivatized, single-stranded DNA (HS-ssDNA) via Au–S interactions. The stepwise modification procedure was characterized by cyclic voltammetry(CV), electrochemical impedance spectroscopy (EIS), probe approach curves (PAC) and ECL, respectively. The resulting modified electrode was tested as ECL biosensor for DNA detection. Upon addition of GO, the strong noncovalent interaction between HS-ssDNA and GO led to ECL quenching because of ERET. When in the presence of target ssDNA (t-ssDNA), the distance between the HS-ssDNA and GO increased, which significantly hindered the ERET and, thus, resulted in the restoration of ECL. The ECL intensity of the biosensor increased linearly with t-ssDNA concentration in the range of 50–1000pM, and the detection limit is 20pM. To the best of our knowledge, this is the first application of solid-state ERET from Ru(bpy) 3 2+ to GO and opens new opportunities for sensitive detection of biorecognition events. First, Ru(bpy) 3 2+/AuNPs was successfully prepared by using a facile and green method. Then, directly coating the as-prepared colloid on the surface of Au electrode surface produces a solid-state ECL film which later was used to label HS-ssDNA indirectly. Upon addition of GO, due to the strong noncovalent interaction between the HS-ssDNA and GO, the ECL of Ru(bpy) 3 2+ was efficiently quenched because of ERET. In the presence of target ssDNA (t-ssDNA), the binding between the HS-ssDNA and t-ssDNA disturbed the interaction between the HS-ssDNA and GO, the distance between the HS-ssDNA and GO increased, which significantly hindered the ERET and, thus, resulted in the restoration of Ru(bpy) 3 2+ ECL. Image 1 • A novel label-free solid-state ERET platform for detection of DNA was proposed. • A facile and green method to synthetize Ru(bpy) 3 2+/AuNPs was proposed for the first time. • Probe DNA and target DNA both do not require prior labeling. • The method has high quenching efficiency, stablity, and good specificity. [ABSTRACT FROM AUTHOR]