Effects of the nature of counterions in solution on interactions of phenoxazones, xanthones, and carbazoles containing benzo-crown groups with DNA

The interactions of DNA with phenoxazones, xanthones, and carbazoles containing the (benzo-18-crown-6)-4′-yl and (benzo-15-crown-5)-4′-yl radicals bonded to the chromophore via spacers of different lengths in the presence of Na⁺ and K⁺ ions were studied by spectrophotometry, circular dichroism, and dynamic birefringence. The thermodynamic parameters of the binding of the compounds with DNA and changes in the macromolecular parameters of the DNA molecule during complexation were determined. Based on the results of these studies, we suggested the models of bonding of these compounds to the double helix of DNA. It is shown that the mode of DNA binding with a phenoxazone derivative containing two (benzo-15-crown-5)-4′-yl radicals bonded via a fragment of glycine to chromophore depends on the type of the counterion in solution. In the presence of Na⁺, the chromophore is intercalated into the double helix of DNA; in the presence of K⁺, it is bound to DNA in the form of a dimer outside the double helix. The type of the counterion does not affect the mode of binding of other crown-containing compounds of actinocin with DNA. For compounds containing the (benzo-18-crown-6)-4′-yl radical, the mode of binding to DNA adepends only on the spacer length.     

MP2 Study on the Stacking Interactions Between 2-Hydroxyadenine and Four DNA Bases

MP2 calculations were used to perform an energy scan of 2-hydroxyadenine (2-OH-A) stacked with four canonical DNA bases. The structures that were studied correspond to potential energy surface points of B-DNA. Eight stacking complexes were analyzed in detail: 5′-2-OH-A/A-3′, 5′-2-OH-A/C-3′, 5′-2-OH-A/G-3′, 5′-2-OH-A/T-3′, 5′-A/2-OH-A-3′, 5′-C/2-OH-A-3′, 5′-G/2-OH-A-3′, and 5′-T/2-OH-A-3′. The stabilization energy, including electron correlation terms, suggests that the 5′-G/2-OH-A-3′ pair is the most stable among all of the studied complexes. The dependence of the stacking energy on the vertical separation and on the twist angle between the two stacked bases were studied in great detail.     

Recognition determinants in a T4 ← G4 mutant derived from a 5′-GCGTGGGCGT-3′ oligomer in a zinc finger 268–DNA complex.

The 5′-GCGTGGGCGT-3′ (T4) oligomer found in the zinc finger 268–DNA complex was mutated into the sequence 5′-GCGGGGGCGT-3′ (G4). A 3D model was constructed from the T4 sequence using an X-ray structure as a template. Molecular dynamics simulations were used to test the thermal stability of the model. A 500-ps trajectory was obtained for the fully charged complex in water using GROMOS87. The complex and the G4 sequence are found to have dynamically stationary behavior. Comparisons made with a previous T4 sequence molecular dynamics simulation show both systems have similar thermal stability. The structure of DNA appears to be maintained by its global interactions with the protein although the mutated site does not contribute with its full potential for binding. The protein structure shows some small differences compared to the T4 simulation. The simulation provided evidence for the role of a chloride ion interacting with the protein and helping in the recognition process. Received: 21 June 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000     

Electrochromic properties of poly(alkoxy-terthiophenes): an experimental and theoretical investigation

Much effort has been made to synthesize novel compounds and enhance the optical properties of poly(terthiophenes). The electrochromic properties of poly(4,4′′-dimetoxy-3′-methyl-2′-5′,2′′-terthiophene) (PDMMT) and poly(4,4′′-dipentoxy-3′-methyl-2′-5′,2′′-terthiophene) (PDPMT) have been studied focusing on the differences in the alkoxy-group length. Theoretical calculations were employed to elucidate the structural and thermodynamic stability of the monomers and dimmers. The results showed that in this type of thiophenes large alkoxy chains assist positive charge dispersion through hyperconjugative effect. Thus, PDPMT is thermodynamically more stable than PDMMT in the oxidized state, leading to better electrochromic stability and optical memory.     

Energy basis of recognition of base pair for platinum-based antitumour drug ZD0473 and cisplatin

Platinum-based antitumour drug ZD0473 was designed to reduce the cisplatin resistance to the tumor cells. In this paper, the mixed method of molecular mechanics and quantum chemistry, HF/lanl2dz// MM/uff and B3LYP/lanl2dz//6-31G*, are used to investigate the differences between four types of GG, 3′AG5′, 3′GA5′, and AA complexes, which are formed from four discrete DNA fragments recognized by ZD0473 and cisplatin. The results show that the binding interaction of both ZD0473 and cisplatin drugs with the GG base pair is much stronger than with other base pairs, namely the recognition capability of such drugs to the GG base pair is more considerable. Moreover, the interaction of four complexes of ZD0473 with DNA fragments is stronger than that of cisplatin with corresponding DNA fragments, which indicates the stronger binding capability of ZD0473 with DNA fragments and high antitumour activity of ZD0473. The main reason for easier forming of 3′GA5′ complex than the 3′AG5′ one is that the drug molecule prefers to bind with a single G base to form a monoligand compound firstly; then the con- figuration transformation from such monoligand compound to the bi-ligand one is limited.     

Suppression of MDR1 gene expression by chemically modified siRNAs

The ability of chemically modified siRNAs targeted to MDR1 mRNA to inhibit P-glycoprotein expression and to restore sensitivity of cancer cells to antibiotic vinblastine was investigated. The effects of chemical modifications on RNA stability in cell culture medium and inhibition of MDR1 gene expression were tested. We found that siRNAs containing 2′-O-methyl ribonucleotides within either sense or/and antisense strands display high stability in serum but exhibit a significant reduction in the biological activity. The protection of 3′-ends of siRNA by introduction of 3′-3′-inverted phosphodiester bonds and two 2′-O-methyl ribonucleotides in protruding 3′-ends considerably increase their biological activity, which allows a 30-fold decrease in the cytostatic agent concentration required for cancer cell death. The data obtained demonstrate that the chemically modified siRNAs can be considered as potential therapeutics, which enhances the efficiency of cancer chemotherapy. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1227–1235, July, 2006.     

A new method for the detection of ATP using a quantum-dot-tagged aptamer

Fluorescence resonance energy transfer (FRET) between a quantum dot as donor and an organic fluorophore as acceptor has been widely used for detection of nucleic acids and proteins. In this paper, we developed a new method, characterized by 605-nm quantum dot (605QD) fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease, to detect adenosine triphosphate (ATP). The new method involved the use of three different oligonucleotides: 3′-biotin-modified DNA that binds to streptavidin-conjugated 605QD; 3′-Cy5-labelled DNA; and a capture DNA consisting of an ATP aptamer and a sequence which could hybridize with both 3′-biotin-modified DNA and 3′-Cy5-labelled DNA. In the absence of the target ATP, the capture DNA binds to 3′-biotin-modified DNA and 3′-Cy5-labelled DNA, bringing quantum dot and Cy5 into close proximity for greater FRET efficiency. When ATP is introduced, the release of the 3′-Cy5-labelled DNA from the hybridization complex took place, triggering 605QD fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease. Taken together, the virtue of FRET pair 605QD/Cy5 and the property of aptamer-specific conformation change caused by aptamer–ATP interaction, combined with the fluorescence intensity change of both 605QD and Cy5, provide prerequisites for simple and convenient ATP detection. Zhang Chen and Guang Li contributed equally to this work.     

Assignment of E/Z isomers in Schiff bases of 3-acyltetramic acids with ethylenediamine by 1H and 13C NMR spectroscopy

The reaction of ethylenediamine with an equivalent mixture of diversely substituted 3-acyltetramic acids leads to Z/Z, Z/E, E/Z and E/E isomers. The E/Z isomerisation is slow in the NMR time scale of the ¹H and ¹³C chemical shifts; therefore at room temperature and in deuterochloroform all isomers of the new synthesized asymmetric compounds N,N′-ethylene-(1-ethyl-5,5-dimethyl-1′,5′,5′-trimethyl-3,3′-acetyltetramic acid) a, N,N′-ethylene-(5,5-dimethyl-1′,5′,5′-trimethyl-3,3′-acetyltetramic acid) b and, N,N′-ethylene-(1,5,5-trimethyl-1′,5′,5′-trimethyl-3-acetyl-3′-formyl-tetramic acid) c could be found in the corresponding spectra. To assign the ¹³C NMR signals we used two-dimensional ¹³C-¹H one-bond (HMQC) and ¹³C-¹H multibond (HMBC) correlated spectroscopy and the empirical rule that CO signals involved in hydrogen bonds are shifted to a lower field. The relative stability of isomers depending on substitution pattern could be estimated from the composition of the equilibria. b crystallizes as Z/Z isomer from ethanolic solution. The X-ray structural analysis of b has shown two CH-O hydrogen bonds. Received: 31 May 1996 / Revised: 26 June 1996 / Accepted: 1 July 1996     

Study of cis-trans equilibrium of oxacarbocyanine dyes in solution and in a complex with DNA

Cis-trans equilibrium for a number of meso-substituted oxacarbocyanine dyes, 3,3′-diethyloxacarbocyanine iodide (K1), 3,3′-diethyl-9-methyloxacarbocyanine iodide (K2), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K3), 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K4), and 3,3′,9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), has been studied in solutions and in a complex with DNA by spectral and fluorescent methods. A shift of the cis-trans isomer equilibrium toward the formation of the trans-isomer was observed in the presence of DNA, which determined in many respects the spectral effects observed upon the complexation of the oxacarbocyanine dyes. A steep rise of fluorescence (due to binding of the trans-isomer) in a complex with DNA is favorable for using oxacarbocyanine dyes to determine DNA.     

Synthesis of 6′-carbamoylmethylthio-5′-cyano-1′,4′-dihydro-3,4′-bipyridine-3′-carboxylic and 6′-carbamoylmethylthio-5′-cyano-1′,4′-dihydro-4,4′-bipyridine-3′-carboxylic esters and investigation of their stability. 2. Esters of 6′-carbamoylmethyl-thio-5′-cyano-1′,4′-dihydro-4,4′-bipyridine-3-carboxylic acids

The stability of solutions of esters of 6′-carbamoylmethylthio-5′-cyano-2′-methyl-1′,4′-dihydro-4,4′-bipyridine-3′-carboxylic acids was investigated by HPLC. The corresponding esters of 6′-carbamoylmethylthio-5′-cyano-4,4′-bipyridine-3′-carboxylic acids,esters of 8-cyano-5-methyl-3-oxo-7-(4-pyridyl)-2,3-dihydro-7H-thiazolo-[3,2-a]pyridine-6-carboxylic acids, methyl 3-amino-2-carbamoyl-6-methyl-4-(4-pyridyl)-4,7-dihydrothieno[2,3-b]pyridine-5-carboxylate, and methyl 3-amino-2-carbamoyl-6-methyl-4-(4-pyridyl)-thieno[2,3-b]pyridine-5-carboxylate were synthesized as standard compounds (typical impurities). Analysis by HPLC was realized under the conditions of reverse-phase chromatography. It was established that solutions of the investigated compounds (with mixtures of acetonitrile with phosphate buffer, having pH values of not less than 3 and not more than 5, as solvents) are stable for one month when the solutions are stored in a place protected against light. It is also necessary to use chromatographic systems in which the aqueous components have pH 3–5 during determination of the purity of the esters of 6′-carbamoylmethylthio-5′-cyano-2′-methyl-1′,4′-dihydro-4, 4′-bipyridine-3′-carboxylic acid by HPLC in order to separate the analyzed sorbates and their typical impurities more completely. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 6, pp. 841–848, June, 2007.     

Microarray of DNA probes on carboxylate functional beads surface

The microarray of DNA probes with 5′-NH₂ and 5′-Tex/3′-NH₂ modified terminus on 10 μm carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.     

An unusual conformation of 1,1′-dimethyl-isoindigo in crystals

The crystal and molecular structure of 1,1′-dimethyl-isoindigo is studied by single crystal X-ray diffraction analysis. It is shown that the molecules of 1,1′-dimethyl-isoindigo are nonplanar due to the rotation of two oxindole rings relative to the double bond.     

Synthesis and investigation of the stability of esters of 6′-carbamoylmethylthio-5′-cyano-1′,4′-dihydro-3,4′-and-4,4′-bipyridine-3′-carboxylic acids 1. Esters of 6′-carbamoylmethylthio-5′-cyano-1′,4′-dihydro-3,4′-bipyridine-3′-carboxylic acids

Esters of 6′-carbamoylmethylthio-5′-cyano-1′,4′-dihydro-3,4′-bipyridine-3′-carboxylic acids are obtained by the alkylation of piperidinium 3′-alkoxycarbonyl-5′-cyano-1′,4′-dihydro-3,4′-bipyridine-6′-thiolates with iodoacetamide. For an HPLC study of the stability of solutions of the abovementioned 1,4-dihydrobipyridines (solution pH 2.3–9.0) the appropriate esters of 6′-carbamoylmethylthio-5′-cyano-3,4′-bipyridine-3′-carboxylic acids and esters of 8-cyano-5-methyl(or phenyl)-3-oxo-7-pyridin-3-yl-2,3-dihydro-7H-thiazolo[3,2-a]pyridine-6-carboxylic acids were synthesized as reference compounds. Analysis by HPLC was carried out under conditions of reverse-phase chromatography. It was shown that solutions of the investigated compounds in a mixture of acetonitrile and phosphate buffer (pH 3.0–5.0) were stable for 1 month on storage protected from light. Under the action of light in all the solutions investigated irrespective of pH the formation occurs of the corresponding esters of 6′-carbamoylmethylthio-5′-cyano-3,4′-bipyridine-3′-carboxylic acids. The presence of esters of 8-cyano-5-methyl(or phenyl)-3-oxo-7-pyridin-3-yl-2,3-dihydro-7H-thiazolo[3,2-a]pyridine-6-carboxylic acids (no more than 4%) was detected only in 0.1% solutions of phosphoric acid (pH 2.3) under conditions of storage of the latter protected from light. A series of as yet unidentified products was detected in solutions of pH 7.0–9.0. Dedicated to E. Lukevics on his 70th birthday __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 59–68, January, 2007.     

Differences in electrostatic potential around DNA fragments containing guanine and 8-oxo-guanine

Changes of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large-scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6–31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Aptasensor for ampicillin using gold nanoparticle based dual fluorescence–colorimetric methods

A gold nanoparticle based dual fluorescence–colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. The selected aptamers, AMP4 (5′-CACGGCATGGTGGGCGTCGTG-3′), AMP17 (5′-GCGGGCGGTTGTATAGCGG-3′), and AMP18 (5′-TTAGTTGGGGTTCAGTTGG-3′), were confirmed to have high sensitivity and specificity to ampicillin (K _d, AMP7 = 9.4 nM, AMP17 = 13.4 nM, and AMP18 = 9.8 nM, respectively). The 5′-fluorescein amidite (FAM)-modified aptamer was used as a dual probe for observing fluorescence differences and color changes simultaneously. The lower limits of detection for this dual method were a 2 ng/mL by fluorescence and a 10 ng/mL by colorimetry for ampicillin in the milk as well as in distilled water. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues. In addition, this dual aptasensor will be a more accurate method for antibiotics in food products as it concurrently uses two detection methods: fluorescence and colorimetry.     

Synthesis,characterization and DNA binding studies of two cyclopentadienyl ruthenium(II) complexes with amino acid ligands

Two new half-sandwich cyclopentadienyl ruthenium(II) complexes containing α-amino acids, [CpRu(PPh₃)₂(Ser)] (Ser = l-serine) and [CpRu(PPh₃)(Met)] (Met = l-methionine), were synthesized and characterized by physicochemical methods. Interactions of these two complexes with calf thymus DNA were investigated by UV–Vis absorption spectroscopy, emission spectroscopy and competitive binding studies. The results indicate that both complexes can interact with DNA, leading to the damage of the double helix. [CpRu(PPh₃)₂(Ser)] binds to DNA by intercalation, while the binding mode for [CpRu(PPh₃)(Met)] is more complicated due to the formation of an EB-DNA-complex (EB = ethidium bromide). The affinity of the Met complex for DNA is stronger than that of the Ser complex, which could be due to groove–surface combination or electrostatic interaction in addition to intercalative binding.     

Asymmetric syntheses with BINOL-based imidoyl azide

Thermal decomposition of 2,4,6-trimethylphenyl and (+)-2′-methoxy-1,1′-binaphthalen-2-yl (4-methylphenylsulfonyl)azidimidocarbonates in the presence of norbornene, methyl acrylate, and camphene was studied. (+)-2′-Methoxy-1,1′-binaphthalen-2-yl (4-methylphenylsulfonyl)azidimidocarbonate reacted with norbornene to give (+)-exo-2′-methoxy-1,1′-binaphthalen-2-yl N-(4-methylphenylsulfonyl)-3-azatricyclo-[3.2.1.0^2,4]octane-3-carboximidoate, while in the reaction with methyl acrylate a mixture of stereoisomeric methyl 1-[(2′-methoxy-1,1′-binaphthalen-2-yloxy)(4-methylphenylsulfonylimino)methyl]aziridine-2-carboxylates was obtained. The reaction of 2,4,6-trimethylphenyl (4-methylphenylsulfonyl)azidimidocarbonate with (−)-camphene involved insertion of intermediate nitrene into the exocyclic double bond with formation of 2,4,6-trimethylphenyl N-(3,3-dimethylbicyclo[2.2.1]heptan-2-ylidenemethyl)-N′-(4-methylphenylsulfonyl)-imidocarbamate as a 3: 1 mixture of E,E and E,Z diastereoisomers in good yield. Published in Russian in Zhurnal Organicheskoi Khimii, 2008, Vol. 44, No. 10, pp. 1495–1500. The text was submitted by the authors in English.     

Synthesis,DNA-binding and photocleavage studies of cobalt(III) complexes [Co(bpy)<Subscript>2</Subscript>(dpta)]<Superscript>3+</Superscript> and [Co(bpy)<Subscript>2</Subscript>(amtp)]<Superscript>3+</Superscript>

Two novel cobalt(III) mixed-polypyridyl complexes [Co(bpy)₂(dpta)]³⁺ and [Co(bpy)₂(amtp)]³⁺ (bpy = 2,2′-bipyridine, dpta = dipyrido-[3,2-a;2′,3′-c]-thien-[3,4-c]azine, amtp = 3-amino-1,2,4-triazino[5,6-f]-1,10-phenanthroline) have been synthesized and characterized. The interaction of Co^III complexes with calf thymus DNA was investigated by spectroscopic and viscosity measurements. Results suggest that the two complexes bind to DNA via an intercalative mode. Moreover, Co^III complexes have been found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365 nm. The mechanism studies reveal that hydroxyl radical (OH^•) is likely to be the reactive species responsible for the cleavage of plasmid DNA by [Co(bpy)₂(dpta)]³⁺ and superoxide anion radical (O ₂ ^•− ) acts as the key role in the cleavage reaction of plasmid DNA by [Co(bpy)₂(amtp)]³⁺.     

Structures of oxidation products of 4,6-di-tert-butylpyrogallol

Oxidation of 4,6-di-tert-butylpyrogallol gave two dimeric products instead of the expected 4,6-di-tert-butyl-3-hydroxy-1,2-benzoquinone (2). It was established by X-ray diffraction analysis that the first product has the structure of tetra-tert-butyl-6, 10a-dihydroxy-1,2-dioxo-3,4a,7,9-1,2,4a, 10a-tetrahydrodibenzo-1,4-dioxine. From this it follows that compound 2 undergoes regio- and stereospecific dimerization according to the [2π+4π]-cycloaddition mechanism,viz, the hetero Diels—Alder reaction. The double intensities of the signals in the¹H NMR spectrum are indicative of a symmetrical structure of the second product, 2,6,4′, 6′-tetra-tert-butyl-4,4′-dihyroxy-3,5,3′,5′-tetraoxo-4,4′-bi(cyclohexene), which is a racemate of enantiomers formed upon recombination (r+r orl+l) of the intermediate of oxidation of pyrogallol, namely, of ther,l-stereogenic 3,5-di-tert-butyl-1-hydroxy-2,6-dioxocyclohex-3-enyl radical. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 139–146, January, 1999.