Synthesis, structure and interactions with DNA of novel tetranuclear, [Mn4(II/II/II/IV)] mixed valence complexes

Reaction of Mn(II) with phenoxyalkanoic acids and di-2-pyridyl ketone oxime (Hpko) leads to neutral tetranuclear complexes of the general formula Mn(4)(O)(pko)(4)(phenoxyalkanoato)(4) (phenoxyalkanoic acids: H-mcpa=2-methyl-4-chloro-phenoxy-acetic acid, H-2,4,5-T=2,4,5-trichloro-phenoxy-acetic acid or H3,4-D=3,4-dichloro-phenoxy-acetic acid). The compounds were synthesized by adding di-2-pyridyl ketone oxime to MnCl(2) in the presence of the sodium salts of the alkanoic acids in methanol. The crystal structure of Mn(4)(II/II/II/IV)(O)(pko)(4)(2,4,5-T)(4).2.5CH(3)OH.0.25H(2)O 1 shows that the complex consists of a [Mn(4)(mu(4)-O)](8+) core with a Mn(IV) and 3 Mn(II) ions in octahedral environment and a mu(4)-O atom bridging the four manganese ions. Spectroscopic studies of the interaction of these tetranuclear clusters with DNA showed that these compounds bind to dsDNA. The binding strength of the Mn(4)(II/II/II/IV)(O)(pko)(4)(2,4,5-T)(4) complex for calf thymus DNA is equal to 1.1x10(4)M(-1). Among the deoxyribonucleotides they bind preferentially to deoxyguanylic acid (dGMP). Competitive studies with ethidium bromide (EthBr) showed that the Mn(4)(II/II/II/IV)(O)(pko)(4)(2,4,5-T)(4) complex exhibited the ability to displace the DNA-bound EthBr indicating that the complex binds to DNA via intercalation in strong competition with EthBr for the intercalative binding site. Additionally, DNA electrophoretic mobility experiments showed that all three complexes, at low cluster concentration, are obviously capable of binding to pDNA causing its cleavage (relaxation) at physiological pH and temperature. At higher cluster concentration, catenated dimer forms of pDNA was formed.     

High nuclearity nickel compounds with three,four or five metal atoms showing antibacterial activity

The effect on DNA and the antibacterial activity of a series of high nuclearity nickel compounds with three, four and five metal atoms were examined. The compounds have a mixed ligand composition with salicylhydroxamic acid and di-2-pyridyl-ketonoxime as chelate agents. In the trinuclear compound Ni(3)(shi)(2)(Hpko)(2)(py)(2)(1), two metal ions show a square planar geometry while the third one is in an octahedral environment. The compounds with four and five nickel atoms construct metallacrown cores with two distinct connectivities. The tetranuclear vacant metallacrown [12-MC(Ni(II)N(Hshi)2(pko)2)-4](2+) shows the connectivity pattern [-O-Ni-O-N-Ni-N-](2), while the pentanuclear ([Ni(II)][12-MC(Ni(II)N(shi)2(pko)2)-4])(2+) follows the pattern [-Ni-O-N-](4). Two distinct arrangements of the chelates around the ring metal ions were observed; a 6-5-6-5-6-5-6-5 arrangement for the [12-MC(Ni(II)N(Hshi)2(pko)2)-4] core and a 6-6-5-5-6-6-5-5 arrangement for the [12-MC(Ni(II)N(shi)2(pko)2)-4] core. Magnetic variable temperature susceptibility study of the trinuclear compound revealed the presence of one paramagnetic nickel(II) ion with strong crystal field dependence, with D=5.0(4) cm(-1), g(xy)=2.7(3) and g(z)=2.3(3). The effect of the synthesized Ni(II) complexes on the integrity and electrophoretic mobility of nucleic acids was examined. Only compounds 2, 3 and 4 altered the mobility of pDNA, forming high molecular weight concatamers at low concentrations or precipitates at higher concentrations. Antibacterial activity screening of the above compounds suggests that nickel compounds 2, 3 and 4 were the most active and can act as potent antibacterial agents.     

Genetic heterogeneity of HIV-1 in Greece

The aim of this study was to detect and determine the genetic variation of HIV-1 in Greece and to analyze the phylogenetic relationships and transmission dynamics of identified variants. Eighty-six blood samples from HIV-1 seroconverted patients of different risk groups were collected from the AIDS clinic, AHEPA Hospital, Thessaloniki, Greece. Retroviral DNA was extracted from uncultured peripheral blood mononuclear cells. HIV-1 DNA sequences encoding a 500-bp fragment of the gp120 C2-C3 region were amplified from each study subject, and they were genetically subtyped by heteroduplex mobility assay and DNA sequencing. Genetic distances and phylogenetic relationships of DNA sequences were estimated using PHYLIP software. Our results revealed that 82 out of 86 (95.3%) subjects carried subtype B sequences, while four (4.7%) carried subtype A sequences. Subtype A in Greek individuals not having traveled abroad was documented. An average of intrasubtype B genetic divergence of 15% was noted. Our findings demonstrate the presence of at least two genetic subtypes of HIV-1 in northern Greece--subtype B and subtype A. The predominant subtype is subtype B, which was transmitted into Greece by multiple sources. Our observations lend support to the argument that the distribution of HIV-1 subtypes is determined by founder effects or other processes rather than any tropism for particular cell types or mode of transmission.     

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

Background  

To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive.     

An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR

To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically relevant fungi to physical, chemical and enzymatic cell wall disruption methods which constitutes the first step in extracting DNA. Examination by light microscopy showed that grinding with mortar and pestle was the most efficient means of disrupting the rigid fungal cell walls of hyphae and conidia. We then trialled several published DNA isolation protocols to ascertain the most efficient method of extraction. Optimal extraction was achieved by incorporating a lyticase and proteinase K enzymatic digestion step and adapting a DNA extraction procedure from a commercial kit (MO BIO) to generate high yields of high quality DNA from all 16 species. DNA quality was confirmed by the successful PCR amplification of the conserved region of the fungal 18S small-subunit rRNA multicopy gene.     

Targeting cancer cells: magnetic nanoparticles as drug carriers

Magnetic drug targeting employing nanoparticles as carriers is a promising cancer treatment avoiding side effects of conventional chemotherapy. We used iron oxide nanoparticles covered by starch derivatives with phosphate groups which bound mitoxantrone as chemotherapeutikum. In this letter we show that a strong magnetic field gradient at the tumour location accumulates the nanoparticles. Electron microscope investigations show that the ferrofluids can be enriched in tumour tissue and tumour cells.     

A nitric oxide releaser based on the μ-oxo-hexaacetate-bis(4-methylpyridine)triruthenium nitrosyl complex

The properties of the trinuclear cluster [Ru₃OAc₆(pic)₂(NO)]PF₆ (pic = 4-methyl pyridine, Ac = acetate ion) and the photochemical behavior of the corresponding molecular films are reported in this paper. In this compound, the unpaired π* electron from NO and the unpaired electron from the π-orbitals of the Ru₃O unity are strongly coupled; as a consequence, the changes in electronic distribution associated with the several successive redox states promote dramatic effects in the spectroscopic and electrochemical properties of the nitric oxide ligand and the entire complex. NO release has been observed by light irradiation (? = 0.038 at 365 nm and ? = 0.019 at 468 nm, in acetonitrile solution), changing the original violet color into deep blue. The same behavior has been observed in solid state and in PVA films incorporating this compound, revealing its potential usefulness as NO photoreleaser, as well as for the monitoration of light exposure intensities.     

A third variant of glucose phosphate isomerase in pigs

A new variant of glucose phosphate isomerase (GPI), also known as phosphohexose isomerase (PHI), was detected in a primitive pig population.