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UV absorption spectra and circular dichroism spectra of aqueous solutions of cytosin- and thyminecontaining single-stranded Oligodeoxyribonucleotide 5′-CCTTTCCTTTTCCTTTCC-3′(ckit4) were measured at various pH in the range 3.3–8.9. The chemometric analysis of the multiinstrumental data matrix was carrie out. The diagrams of relative contents of complex forms of the DNA molecule absorbing in the studied wavelength range (220–320 nm) were constructed by the ALS-MCR soft simulation procedure without initial postulation of their chemical compositions. The model of equilibrium complex formation describing observed changes in the spectra depending on the solution acidity was developed on the basis of the matrix method. Intrinsic protonation constants of the oligonucleotide ckit4 were calculated. The formation of intramolecular complexes between cytosine C.C+ bases in the studied DNA molecule is of a cooperative nature, and thei subsequent protonation is an anticooperative process. [ABSTRACT FROM AUTHOR]

The presence of antibiotic residues in cow's milk entails high risk for consumers, the dairy industry, and the environment. Therefore, the development of highly specific and sensitive screening tools for the rapid and cost-effective identification of traces of these compounds is urgently needed. A multiplexed screening platform utilizing DNA-directed immobilization (DDI) was developed aiming to detect three classes of antibiotic residues (fluoroquinolones, sulfonamides, and tylosin) prevalently found in milk. Throughout this work, each oligonucleotide sequence was conjugated to a different hapten molecule, while the three complementary strands were immobilized in 24 independent microarray chips on a single glass slide. First, the array was incubated with the pool of hapten-oligonucleotide conjugate site encoded the signal through DNA hybridization. Next, commercial milk samples were incubated with the cocktail of monoclonal antibodies following a secondary fluorophore-labeled antibody which was required for fluorescent readout. Direct sample detection was achieved in milk diluting 20 times in assay buffer. The limits of detection (LODs) reached were 1.43 µg kg−1, 1.67 µg kg−1, and 0.89 µg kg−1 for TYLA, STZ, and CIP, respectively, which represented in raw milk 7.15 µg kg−1, 8.35 µg kg−1, and 4.45 µg kg−1 for TYLA, STZ, and CIP, respectively, that are below the EU regulatory limits. Cross-reactivity profiles were evaluated against the family of structurally related antibiotics in order to demonstrate the capability to detect antibiotics from the same family of compounds. A pre-validation study was performed by spiking 20 blind samples above and below the maximum residue limits established by the EU guidelines. The system was successfully implemented towards randomized sample classification as compliant or non-compliant. The proposed DDI-based immunoarray provides a fast and cost-effective alternative to obtain semi-quantitative information about the presence of three veterinary residues simultaneously in milk samples. Antibody fluorescent microarray based on DDI. The figure shows the main steps involved in the immunoassay. First, the printing of the oligo N4-6down probe over the glass slide, followed by an incubation with a complementary strand conjugated to the hapten and finally the selective recognition using monoclonal antibodies and fluorescent quantification. [ABSTRACT FROM AUTHOR]

The invasive mosquito Aedes ( Stegomyia) albopictus (Skuse) (Diptera: Culicidae) was detected for the first time in Spain, in Sant Cugat del Vallès, a city in the north-east of the country (41°28′ N, 2°4′ E, altitude 120 m), during August 2004. A male and one larva were collected in the backyard of a house and in a tree hole, respectively. Dense populations of adults and larvae were found in subsequent surveys, confirming the establishment of the species in the area. This is the first report of the establishment of this species in the Iberian Peninsula. [ABSTRACT FROM AUTHOR]

A correction to an author's affiliation published in a previous issue is presented.

Abstract: DNA testing requires the development of sensitive and fast devices to measure the presence of nucleic acid sequences by DNA hybridization. In this paper, a simple and label-free DNA-biosensor has been investigated based on the detection of DNA hybridization on layered double hydroxide (LDH) nanomaterials with special emphasis on targeting long single stranded DNA sequences. First, the immobilization of a 20 bases long DNA probe on a thin layer of Mg2AlCO3 and Mg3AlCO3 LDH was studied. Then, DNA hybridization reaction was detected by means of Electrochemical Impedance Spectroscopy. The resulting biosensor showed a high sensitivity for the detection of 80 bases long DNA complementary sequences. The dynamic range was 18–270ng/ml with a detection limit lower than 1.8ng/ml. [Copyright &y& Elsevier]

The interactions of actinomycin D (ACTD) with the oligonucleotides 5′-CAAAGCTTTG-3′, 5′-CATGGCCATG-3′ and 5′-TATGGCCATA-3′ were investigated by means of acid–base titrations and mole-ratio and melting experiments monitored by molecular absorption and circular dichroism (CD) spectroscopies. For each experiment, CD and molecular absorption spectra were recorded at each point in the experiment, and later analyzed via appropriate multivariate data analysis methods. The study of the interactions between these oligonucleotides and ACTD at 25 °C showed the formation of an interaction complex with a stoichiometry of 1:1 (ACTD:duplex) and values for the log(formation constant) of 5.1 ± 0.3, 6.4 ± 0.2, and 5.6 ± 0.2, respectively. An additional interaction complex at higher temperatures was also detected, which might be related to the single-stranded forms of the oligonucleotides. [ABSTRACT FROM AUTHOR]

• The interaction of fluorescent ligands with folded DNAs is studied. • Alkaloid berberine binds equally to folded and unfolded cytosine-rich DNA sequences. • Binding with i-motif structures is weak and electrostatics in nature. The alkaloid berberine presents many biological activities related to its potential to bind DNA structures, such as duplex or G-quadruplex. Recently, it has been proposed that berberine may interact with i-motif structures formed from the folding of cytosine-rich sequences. In the present work, the interaction of this alkaloid with the i-motif formed by the human telomere cytosine-rich sequence, as well as with several positive and negative controls, has been studied. Molecular fluorescence and circular dichroism spectroscopies, as well as nuclear magnetic resonance spectrometry and competitive dialysis, have been used with this purpose. The results shown here reveal that the interaction of berberine with this i-motif is weak, mostly electrostatics in nature and takes place with bases not involved in C·C+ base pairs. Moreover, this ligand is not selective for i-motif structures, as binds equally to both, folded structure, and unfolded strand, without producing any stabilization of the i-motif. As a conclusion, the development of analytical methods based on the interaction of fluorescent ligands, such as berberine, with i-motif structures should consider the thermodynamic aspects related with the interaction, as well as the selectivity of the proposed ligands with different DNA structures, including unfolded strands. [ABSTRACT FROM AUTHOR]

The photoactivatable modified oligonucleotides were used to investigate direct contacts formed by the type IIE EcoRII restriction endonuclease and the T/A bases of its recognition site (5'-CCT/AGG). EcoRII dimer consists of a central catalytic core, made of two C-terminal endonuclease-like domains (EcoRII-C) from different subunits, and two N-terminal effector DNA binding domains (EcoRII-N). According to co-crystal structure of isolated EcoRII-C with DNA catalytic dimer EcoRII-C flips nucleotides of the central T/A pair into the enzyme binding pockets. Нere, photocross-linking technique was used to investigate the direct contacts formed by extrahelical T/A bases in the protein pockets of full-length EcoRII within the pre-reactive EcoRII–DNA complex obtained in the presence of Ca2+ in solution. Photoreactive zero-length agent 5-iodo-2'-deoxyuridine (IdU) was introduced as single substituent into the central T/A position of EcoRII recognition site or into the flanking nucleotide sequences of 14-mer DNA substrate. The substitution of only dT or dA residues in EcoRII recognition site resulted in formation of photocross-links upon irradiation only in the presence of Ca2+. Proteolytic digestion of the enzyme-oligonucleotide conjugates followed by MALDI-MS analysis have allowed to identify the 224VEYD227 EcoRII region involved in the formation of the cross-links. This region belongs to the central part of H-10 α-helix. Y226 residue was suggested to form cross-link with T or A bases of EcoRII site replaced by IdU within the pre-reactive complex. The flipped base pair protein pockets of EcoRII seem to accommodate equally well both A and T bases of the DNA substrate. Altogether, IdU-containing photoactivatable DNA substrates have allowed to trap the flipped bases in complex with full-length EcoRII before DNA cleavage in the solution and to identify direct enzyme–DNA contacts important for high specificity of EcoRII for the Т/A nucleotides providing a highly specific cleavage reaction. [ABSTRACT FROM AUTHOR]

Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c - kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 10 5 M −1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies. [ABSTRACT FROM AUTHOR]

The development of novel non-viral delivery vehicles is essential in the search of more efficient strategies for retina and brain diseases. Herein, optimized niosome formulations prepared by oil-in water (o/w) and film-hydration techniques were characterized in terms of size, PDI, zeta potential, morphology and stability. Three ionizable glycerol-based cationic lipids containing a primary amine group (lipid 1 ), a triglycine group (lipid 2 ) and a dimethylamino ethyl pendent group (lipid 3 ) as polar head-groups were part of such niosomes. Upon the addition of pCMS-EGFP plasmid, nioplexes were obtained at different cationic lipid/DNA ratios (w/w). The resultant nioplexes were further physicochemically characterized and evaluated to condense, release and protect the DNA against enzymatic digestion. In vitro experiments were performed to evaluate transfection efficiency and cell viability in HEK-293, ARPE-19 and PECC cells. Interestingly, niosome formulations based on lipid 3 showed better transfection efficiencies in ARPE-19 and PECC cells than the rest of cationic lipids showed in this study. In vivo experiments in rat retina after intravitreal and subretinal injections together with in rat brain after cerebral cortex administration showed promising transfection efficiencies when niosome formulations based on lipid 3 were used. These results provide new insights for the development of non-viral vectors based on cationic lipids and their applications for efficient delivery of genetic material to the retina and brain. [ABSTRACT FROM AUTHOR]

Review: 200 refs. [ABSTRACT FROM AUTHOR]

Abstract: Niosomes represent a recent promising approach for gene delivery purposes. We elaborated on a novel niosome formulation based on the 2,3-di(tetradecyloxy)propan-1-amine cationic lipid, combined with squalene and polysorbate 80 to evaluate the transfection efficiency in rat retinas. Niosomes prepared by the solvent emulsification–evaporation technique were mixed with the pCMSEGFP plasmid to form lipoplexes which were characterized in terms of morphology, size, surface charge, and DNA condensation, protection and release. In vitro studies were conducted to evaluate transfection efficiency, viability and internalization mechanism in HEK-293 and ARPE-19 cells. The efficacy of the most promising formulation was evaluated in rat eyes by monitoring the expression of the EGFP after intravitreal and subretinal injections. Lipoplexes at 15/1 ratio were 200nm in size, 25mV in zeta potential and exhibited spherical morphology. At this ratio, niosomes condensed and protected the DNA from enzymatic digestion. Lipoplexes successfully transfected HEK-293 and specially ARPE-19 cells, without affecting the viability. Whereas lipoplexes entered mainly retinal cells by clathrin-mediated endocytosis, HEK-293 cells showed a higher caveolae-dependent entry. After ocular administration, the expression of EGFP was detected in different cells of the retina depending on the administration route. This novel niosome formulation represents a promising approach to deliver genetic material into the retina to treat inherited retinal diseases. [Copyright &y& Elsevier]

This article demonstrates a method for the fabrication of patterned surfaces using hairpin oligonucleotides carrying a novel photolabile group at the apex of the loop. Photolysis of surfaces carrying photolabile hairpin oligonucleotides results in the formation of areas carrying single-stranded DNA sequences that direct the deposition of the complementary sequence at the photolysed sites. The non-photolysed areas carrying the intact hairpin do not bind to complementary sequences due to the presence of the more stable intramolecular hairpin duplex. The photolithographic process was performed on silicon wafers and followed by atomic force microscopy and epi-fluorescent microscopy. The method described offers an attractive option for the fabrication of biologically interfaced patterned surfaces with specific recognition properties with potential uses in electronics and as biosensors. [ABSTRACT FROM AUTHOR]

The synthesis of parallel hairpins carrying 8-aminopurines is described. These hairpins have a high affinity for specific polypyrimidine sequences resulting in the formation of very stable triplexes. [ABSTRACT FROM AUTHOR]

The urinary elimination of thioethers urinary thioethers (UT) was studied in 83 schoolchildren living in two different areas of the city of Mataró, with special attention paid to the influence of a waste incinerator and of the smoking habits of their parents. The mean UT values were 8.79±3.23 and 7.52±3.23 mmol/mol creatinine in the area close to the incinerator (A1) and in the area far away from it (A2) respectively (statistically n.s.). Children exposed to environmental tobacco smoke (ETS) at home presented increased levels of UT (8.60±3.11 vs 5.93±3.22 mmol/mol creatinine; P=0.002). Considering the two exposures together (waste incinerator and ETS), no differences were found between the two areas studied (A1 and A2) in non-exposed (ETS) children, whereas slight differences were found when comparing highest ETS exposed children from the two areas (10.18±2.70 vs 8.00±3.42 mmol/mol creatinine; P=0.04). Exposure to ETS could affect health more than pollutants from a waste incinerator and may interfere with non-selective assays such as urinary thioethers. [ABSTRACT FROM AUTHOR]

• Ethylcellulose nanoparticles with positive zeta potential formed from nano-emulsion. • Nanoparticles non-toxic to HeLa cells up to 3 mM of cationic species. • Successful nanoparticle complexation with an antisense oligonucleotide. • Optimum transfection efficiency (40%) for the cationic/anionic ratio 28. Oil-in-water nano-emulsions have been obtained in the HEPES 20 mM buffer solution / [Alkylamidoammonium:Kolliphor EL = 1:1] / [6 wt% ethylcellulose in ethyl acetate] system over a wide oil-to-surfactant range and above 35 wt% aqueous component at 25 °C. The nano-emulsion with an oil-to-surfactant ratio of 70/30 and 95 wt% aqueous component was used for nanoparticles preparation. These nanoparticles (mean diameter around 90 nm and zeta potential of +22 mV) were non-toxic to HeLa cells up to a concentration of 3 mM of cationic species. Successful complexation with an antisense phosphorothioate oligonucleotide targeting Renilla luciferase mRNA was achieved at cationic/anionic charge ratios above 16, as confirmed by zeta potential measurements and an electrophoretic mobility shift assay, provided that no Fetal Bovine Serum is present in the cell culture medium. Importantly, Renilla luciferase gene inhibition shows an optimum efficiency (40%) for the cationic/anionic ratio 28, which makes these complexes promising for " in vitro " cell transfection. [ABSTRACT FROM AUTHOR]