An Electropolymerized Membrane Biosensor for Specific DNA Recognition

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A Palladium-mediated DNA Base Pair of a β-C-Nucleoside Possessing a 2-Aminophenol as the Nucleobase

Abstract

An approach we have used in this study for the incorporation of metal ions into DNA, is the direct modification of a DNA base itself, turning it into a metal-chelating nucleobase wherein two nucleobases are paired through metal coordination. Herein we report the X-ray crystal structure of a synthetic intermediate 6 for the aminophenol bearing nucleoside 3 and its metal coordination properties with Pd²⁺. The anomeric configuration of the nucleoside was unequivocally determined to be β-form by the X-ray analysis of 6; the structure has been resolved by direct methods (S1R97) and expanded using Fourier techniques (DIRDIF94) using 2628 independent reflections with I>2.00 [sgrave](I) and 425 parameters. Final R (R_w) was 0.037 (0.043): orthorhombic, space group P2₁2₁2₁ (#19) with a=16.562(1) Å, b=16.933(1) Å, c=11.205(1) Å, and V=3142.2(4) ų; D_c =1.369g/cm³ for Z=4, and molecular weight 647.65. This result is consistent with the tentative assignment by our previous ¹H NOE differentiation experiments. Detailed ¹H NMR studies showed that the nucleoside forms a stable 2:1 complex with Pd²⁺ with concomitant deprotonation of its phenolic proton. Although there are two possible structures (cis or trans) for the square-planar Pd²⁺ complex, the ratio of cis to trans was approximately 1:1. The electrospray ionization time-of-flight mass spectrum of the complex also provided clear evidence for the 2:1 complexation.     

Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution： A Molecular Dynamics Study

Quinolones,a series of nalidixic acid analogues,represent a class of extremely potent antibacterial drugs.Although the functional target of these agents such as norfloxacin has been identified as the enzyme DNA gyrase,the direct binding site of the drug is the DNA itself1.Interactions between quinolones and diversified DNA have been studied by several biochemical,spectroscopic and computational methods2-8.Shen et al.proposed a cooperative drug-DNA binding model.The essential feature of th…     

Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A–U Base Pairs in Double-Stranded RNA

Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases ( I _o ) were designed for binding A–U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A–U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.     

Organomagnesium Compounds as Promoters for Increasing the Catalytic Efficiency in the Polymerization of Ethylene

It wasstudied that organomagnesium compounds can promote the catalytic efficiencyof catalysts of Ti system with MgCl2 as the carrier for polymerization of ethylene.     

Electrochemical Studies of the Recognition Interaction of Rhodamine B with DNA

The recognition interaction of rhodamine B (RB) with DNA was studied in pH 7.5 Britton-Robinson (B-R) buffer solution by electrochemical techniques. An irreversible oxidation peak at glassy carbon electrode was obtained at 0.92V (vs. SCE). After the addition of DNA into the RB solution, the peak current of RB decreased apparently without the shift of peak potential. The electrochemical parameters such as the charge transfer coefficient α and the electrode reaction standard rate constant ks of RB in the absence and presence of DNA were determined, which did not change, indicating that a non-electroactive complex was formed, so the concentration of RB in the solution decreased and the peak current decreased correspondingly.     

Anomeric and Enantiomeric 2’-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

Dodecamer duplex DNA containing anomeric (α/β-d ) and enantiomeric (β-l /β-d ) 2’-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine–cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d -dC with enantiomeric β-l -dC is superior to the well-noted β-d /β-d -dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.     

Hydration of DNA Bases and Compounds Containing Small Rings—A Model for Interactions of the Ricin Toxin A-Chain. A Theoretical Ab Initio Study

Ab initio quantum chemical calculations were performed for four neutral gas phase adenine and four pterin tautomers along with guanine and formycin bases. The water complexes of the lowest energy tautomers of these bases have been studied to mimic their interaction with the ricin toxin A chain (RTA). The water molecules create a full first hydration shell around the bases. Full geometry optimizations without any constraints on the planarity of these hydrated complexes were carried out at the HF/6-31G(d,p) level. Single point calculations were also performed at the correlated MP2/6-31G(d,p)//HF/6-31G(d,p) level of theory. Hydration energies were corrected for the basis set superposition error. Hydration energies of adenine and formycin are predicted to be lower (in magnitude) than those for the pterin and guanine. Due to these properties, two pterin tautomers can be considered as potentially useful inhibitors of RTA.     

Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.     

CH-π Multi-Interaction-Driven Recognition and Isolation of Planar Compounds in a Spheroidal Polyaromatic Cavity

π-π Interactions are established as a powerful supramolecular tool, whereas the usability of CH-π interactions has been rather limited so far. Here we present (i) selective binding of planar polyaromatics and (ii) effective isolation of planar metal complexes by a polyaromatic capsule, utilizing multiple CH-π interactions. In the spheroidal cavity, one molecule of large and medium-sized polyaromatic molecules (i. e., coronene and pyrene) is exclusively bound from mixtures bearing the same number of aromatic CH groups. Theoretical studies reveal that multiple host-guest CH-π interactions (up to 32 interactions) are the predominant driving force for the observed selectivity. In addition, one molecule of planar metal complexes (i. e., porphine and bis(acetylacetonato) Cu(II) complexes) is quantitatively bound by the capsule through aromatic and aliphatic CH-π multi-interactions, respectively. The ESR and theoretical studies demonstrate the isolation capability of the capsular framework and an unusual polar environment in the polyaromatic cavity.     

Specific Proteins in the Indirect Somatic Embryogenesis of Freesia

Using the young inflorescence segments of Freesia refracta as explants, indirect somatic embryogenesis of somatic cells was induced in a N6 medium supplemented with some exogenous hormones. SDS-polyacrylamide gel electrophoresis（SDS-PAGE） was used for the analysis of soluble proteins produced during the somatic embryogenesis of this plant. There are six polypeptides, which might play some roles in the process of somatic embryo development. Tltree polypeptides（45, 53 and 55 kD） were detected in the stages of embryogenic callus, globular embryoid, and embryoid with coleoptiles, except the embryoid with leaf. One polypeptide（ 83 kD） was specific for the stages of embryoid with eoleoptiles and embryoid with leaf. One polypeptide（37 kD） was detected in the first two stages, namely, embryogenic callus and globular embryoid. One polypeptide（35 kD） was regularly synthesized in each stage, from embryogenic callus to embryoid with leaf.     

Thermodynamic Model for the Solubility of TcO2⋅xH2O in Aqueous Oxalate Systems

The room temperature solubility of amorphous, hydrous technetium(IV) oxide (TcO₂⋅xH₂O) was studied across a broad range of pH values extending from 1.5 to 12 and in oxalate concentrations from dilute (10⁻⁶ mol⋅kg⁻¹) to complete saturation with respect to sodium bioxalate at lower pH values, and to saturation with respect to sodium oxalate at higher pH values. The solubility was measured to very long equilibration times (i.e., as long a 1000 days or longer). The thermodynamic modeling results show that the dominant species in solution must have at least one more hydroxyl moiety present in the complex than proposed by previous investigators (e.g., TcO(OH)Ox⁻ rather than TcO(Ox)(aq)). Inclusion of the single previously unidentified species TcO(OH)Ox⁻ in our aqueous thermodynamic model explains a wider range of observed solubility data for TcO₂⋅xH₂O(am) in the presence of oxalate and over a broad range of pH values. Inclusion of this species is also supported by the recently proposed thermodynamic data for the TcO(OH)⁺ hydrolysis species that indicates that this species is stable at pH values as low as one.     

Dried–Reswollen Immobilized Biocatalysts for Detoxification of Organophosphorous Compounds in the Flow Systems

New immobilized biocatalysts based on polypeptides containing N- or C-terminal polyhistidine sequences and possessing organophosphorus hydrolase activity were investigated for detoxification of organophosphorous neurotoxic compounds in the flow systems. The biocatalysts were revealed to have a high catalytic activity within wide pH and temperature ranges 7.5–12.5 °C and 15–65 °C, respectively. The immobilized biocatalysts can be dried and reswollen before use with 92–93% catalytic activity remaining after drying and rehydration procedures. The half-lives of the biocatalysts under wet and dry storage conditions were 420 and 540 days, respectively.     

The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine–Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration

Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2′-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA–dT base pair. T_m data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2′-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2′-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.     

Polyurethane Molecular Stamps for the in situ Synthesis of DNA Microarray

Fabrication of polyurethane molecular stamps (PU stamps) based on polypropylene glycol (PPG) and toluene dissocyanate (TDI), using 3,3′-dichloro-4,4′-methylenedianiline (MOCA) as the crosslinker ,is reported. It was shown from the contact angle measurement that PU stamps surface has good affinity with acetonitrile,guaranteeing the well distribution of DNA monomers on patterned stamps. Laser confocal fluorescence microscopy images of oligonucleotide arrays after hybridization confirmed polyurethane is an excellent material for molecular stamps when ransferring polar chemicals and conducting rections on interfaces by stamping.     

A New Reagent for the Reduction of Aromatic Nitro Compounds

Reagentsforthereductionofaromaticnitrocompoundstothecorrespondinganilineshavebeensupplementedb}'selenoPheno1'andtransitionmetalhydrides.'ReactionwithtyPicalhydridereagentssuchasLinlffi.'Lotl(OR),H,'andNaBffi4areusuallysluggish.Sodiumselenatedborohydride(NaBH2Se3)andpotaSsiurnselenatedborohydride(KBH2Se3)hadbeenpreparedfromthereactionofsodiumborohydridewithseleniuminglyInebyLalancetteetal5.However,thebehavesasreducerstowardsmanyorganicfunctionalgroupsandtheirapplicationstoorganicsynthes…     

Violation of Environmental Standards for Inorganic Nitrogen Compounds in Glacial Rivers of the Central Caucasus in 2017‒2019

Russian Journal of General Chemistry - The results of monitoring of the concentrations of nitrates, nitrites, and ammonium nitrogen in glacial rivers of the Central Caucasus during the winter...     

Recognition of DNA based on changes in the fluorescence intensity of CdSe/CD QDs–phenanthroline systems

The CdSe quantum dots (QDs) modified by mercapto-β-cyclodextrin (CD) were synthesized and characterized by transmission electron microscopy, powder X-ray diffraction, excitation and emission spectra, and fluorescence lifetime. When λ_ex = 370 nm, the fluorescence peak of CdSe/CD QDs is at 525 nm. Phenanthroline (Phen) is able to quench their fluorescence, which can be recovered by the addition of DNA. The quenching and restoration of fluorescence intensity were found to be linearly proportional to the amount of Phen and DNA, respectively. The variation of the fluorescence intensity of the CdSe/CD QDs–Phen system was studied, and it was demonstrated to result from a static mechanism due to the formation of a Phen inclusion complex with the CdSe QDs modified by mercapto-β-cyclodextrin. The fluorescence recovery was due to the binding of DNA with Phen in the inclusion complex, leading to the freeing of the CdSe/CD QDs. The binding constants and sizes of the binding sites of the Phen–DNA interaction were calculated to be 1.33 × 10⁷ mol^?1 L and 10.79 bp.     

Modulating Electrostatic Interactions in Ion Pair Intermediates To Alter Site Selectivity in the C−O Deoxygenation of Sugars

Controlling which products one can access from the predefined biomass-derived sugars is challenging. Changing from CH₂Cl₂ to the greener alternative toluene alters which C−O bonds in a sugar are cleaved by the tris(pentafluorophenyl)borane/HSiR₃ catalyst system. This increases the diversity of high-value products that can be obtained through one-step, high-yielding, catalytic transformations of the mono-, di-, and oligosaccharides. Computational methods helped identify this non-intuitive outcome in low dielectric solvents to non-isotropic electrostatic enhancements in the key ion pair intermediates, which influence the reaction coordinate in the reactivity-/selectivity-determining step. Molecular-level models for these effects have far-reaching consequences in stereoselective ion pair catalysis.     

Development and Validation of a HPLC Method for the Determination of Five Bioactive Compounds in the “Xuebijing” Injection

A reversed phase high performance liquid chromatographic (RP-HPLC) method with ultraviolet (UV) detector was developed for simultaneously determining five bioactive components (i.e., hydroxysafflor yellow A: HSYA; paeoniflorin, ferulic acid, benzoic acid, and danshensu) in “Xuebijing” (XBJ) injection, a widely used traditional Chinese medicine (TCM) for treating sepsis and multiple organ dysfunction syndrome. A Zorbox SB C₁₈ column was used with 0.2% phosphoric acid (V/V)-acetonitrile as the mobile phase under the condition of gradient elution. The five components were analyzed by using a timed wavelength measure according to their maximum absorption wavelength. The intraday and interday precisions of the five investigated compounds were less than 1.17% and the average recoveries ranged from 97.3% to 103.2%. There were good linear correlations between the concentrations of the five components and their chromatographic peak areas (R² ≥ 0.9998), the proposed method was successfully applied to determine the five components in different batches of XBJ injection products, the results indicated that the proposed method is simple, stable, and accurate and could be readily utilized as a quality control method for manufacturing process of XBJ injection.