Chiral salen ligands designed to form polymetallic complexes

Chiral salen ligands capable of forming polymetallic complexes have been designed. The ligands possess substituents in the 4,4′-positions, but have no substituent in the 3,3′-positions to allow a second metal ion access to the salen oxygen atoms. Ligands in which a polyether chain links the 4,4′-positions were prepared and complexed to copper. In addition, acyclic ligands with potential metal coordinating substituents in the 4,4′-positions were prepared and complexed to copper and cobalt. The crystal structure of one of the cobalt complexes shows it to be a trimetallic complex in which a Co(II)(OAc)₂ group coordinates to the salen oxygen atoms of two Co(III)(salen)(OAc) units. In contrast, the crystal structure of a Co(salen) complex with tert-butyl groups attached to the 3,3′-positions is found to be mononuclear. All of the complexes were tested as asymmetric phase transfer catalysts for the asymmetric alkylation of an alanine methyl ester, forming (R)-α-methyl phenylalanine methyl ester with up to 85% ee.     

Frontier orbitals of trivalent cages: (3,6) cages and (4,6) cages

A qualitative molecular-orbital treatment and group-theoretical analysis reveals the nature of the frontier orbitals of (3,6) and (4,6) polyhedral cages, consisting of a hexagonal network with triangular and square defects, respectively. Leapfrog (3,6) cages have two nonbonding filled orbitals. Leapfrog (4,6) cages have a high HOMO-LUMO gap, while nonleapfrog (4,6) cages with octahedral symmetry have a very small HOMO-LUMO gap. The symmetry of the frontier orbitals is determined.     

The first 1D twofold interpenetrating metal-organic network generated by 1D triple helical chains with nanosized cages

Reaction of AgPF(6) with the asymmetric ligand 1,6-dihydro-2-methyl-6-oxo-(3,4'-bipyridine)-5-carbonitrile (1), afforded a significant silver coordination polymer {[Ag(2)(1)(3)](2).(CH(3)OH)(3).(PF(6))(4)}(n) (2) with unique 1D twofold interpenetrating metal-organic frameworks constructed by 1D triple helical chains with nanosized cages hosting counterions as guests. This compound exhibits high thermal stability and blue-shift emission with large intensity enhancement compared with that of the free ligand.     

Polydipyrrole- and polydicarbazole-nanorods as new nanosized supports for DNA hybridization

Novel functional polydipyrrole- and polydicarbazole nanorods have been AAO template-synthesized from COOH-dipyrrole/-dicarbazole monomers using Vapor Deposition and Liquid Phase Polymerizations (VDP and LPP). They were tested as insoluble supports for covalent DNA attachment and hybridization.     

Isolation of microbial DNA by newly designed magnetic particles

Carboxyl group-containing magnetic nonporous poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) (P(HEMA-co-GMA)) microspheres and cobalt ferrite nanoparticles modified with alginic acid (natural carboxylic polysaccharide) were used for isolation of microbial DNA of lactic acid bacteria (LAB) from dairy products, lyophilised cell cultures, and bacterial colonies grown on hard media, and Trichophyton fungi DNA from lyophilised cells. DNA from the samples with lysed cells was reversibly adsorbed to the particles in the presence of high poly(ethylene glycol) (PEG 6000) and sodium chloride concentrations. The optimal final PEG and NaCl concentrations were 9.1 wt.% and 2.0 M, respectively. The adsorbed DNA was released from the particles in low ionic strength TE buffer. The quality of isolated DNA was checked by PCR amplification. Moreover, PCR amplicons were isolated on cobalt ferrite nanoparticles modified with alginic acid and checked by restriction analysis.     

Fluorescence relaxation dynamics of acridine orange in nanosized micellar systems and DNA

In this paper, we report a detailed study of the fluorescence relaxation dynamics of a well-known fluorescent DNA intercalator, acridine orange (AO), in reverse micelles (RM), micelles, and DNA using picosecond resolved fluorescence spectroscopy. Solvation studies of AO in AOT reverse micelles (RM) containing water indicate the locations of AO close to the interface and those in RM containing NaOH; there are two types of AO--one in the nonpolar oil phase and the other at the interface. The bound water at the reverse micellar interface is found to be much more rigid than that at the micellar interface of sodium dodecyl sulfate (SDS) micelles. Dynamic light scattering (DLS) studies allow for the determination of the hydrodynamic radius and the overall tumbling motion of the macromolecules. Wobbling-in-cone data analysis of the temporal fluorescence anisotropy decay allows for determination of restriction on the motion of fluorophores attached to the macromolecules. This model further applied to AO-intercalated genomic DNA and synthetic oligonucleotides within their structural integrity (as confirmed through circular dichroism (CD) studies) shows that AO experiences less restriction in genomic salmon sperm DNA compared with that in synthetic oligonucleotides, and among the oligonucleotides, the ones with AT base pairs are much more rigid. This study would invoke further research on the dynamical nature of AO in restricted environments.     

New designed DNA light switch Ruthenium complexes as DNA photocleavers and Topoisomerase I inhibitors

Two ruthenium complexes containing a new ligand phipz (phipz = 2‐(1,10‐phenanthroline)‐1H‐imidazo[4,5‐b]phenazine) were designed and synthesized. These complexes were found to inhibit the DNA supercoiled relaxation mediated by topoisomerase I (topo I), cleave DNA under irradiation and bind to calf thymus DNA through intercalative mode. Furthermore, complex 2 shows higher photocleavage activity, topo I inhibition activity and DNA affinity than complex 1 . Additionally, introduction of phenazine unit may be the reason that two complexes exhibit DNA ‘light switch’ behavior. The present work shows that two complexes might be potential as new DNA ‘light switches’, DNA photocleavers and topo I inhibitors.     

Chromium‐metformin ternary complexes: Thermal,DNA interaction and Docking studies

Three chromium ternary complexes with metformin (met) as a primary ligand and bipyridine (bipy) or ortho‐phenylenediamine (opda) or ortho‐phenanthroline (phen) as secondary ligand were synthesized. These complexes [Cr (Cl)₂(Hmet)(bipy)]‐( 1 ), [Cr (Cl)₂(Hmet)(opda)]‐( 2 ) and [Cr (Cl)₂(Hmet)(phen)]‐( 3 ) were characterized by LC–MS, elemental analysis, molar conductance, thermal analysis, infrared spectroscopy, electronic spectroscopy. The geometrical structures have been found to be octahedral. Degradation pattern of the compounds is shown by thermal studies. The Kinetic parameters‐ energy of activation (E_a), enthalpy (ΔH), entropy (ΔS) and free energy changes (ΔG) have been determined by thermogravimetric data. Coats‐Redfern integration method with thirteen kinetic models was used to calculate the kinetic and thermodynamic parameters for the degradation of all the complexes. The stabilities of the complexes were obtained from their molecular orbital structures from which the quantum chemical parameters were calculated using the HOMO‐LUMO energies. UV–Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV–Vis spectrum with DNA. The binding constants K_b from UV–Vis absorption studies were 3.1x10⁴, 4.4x10⁴, 5x10⁴ M^?1 for 1, 2, 3 respectively and Stern–Volmer quenching constants (K_sq) from fluorescence studies were 0.137, 0.532, 0.631 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT‐DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decrease in the order of 3 > 2 > 1.The light switching properties of the complexes were also evaluated. The complexes were docked in to B‐DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)‐3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.     

Molecular acrobatics: self-assembly of calixarene-porphyrin cages

Calix[4]arenes equipped with two and four zinc porphyrins have been prepared, and they show remarkable flexibility in their self-assembly properties with the bidentate ligand DABCO. The calix-bisporphyrin forms a 2:2 complex with DABCO, generating a large cavity that has the potential to act as a supramolecular host. The calix-tetraporphyrin, on the other hand, forms four different complexes with DABCO depending on the stoichiometry and concentration. During the course of a titration, all four complexes are populated, leading to large conformational changes and the formation of both intramolecular and intermolecular calix-tetraporphyrin-DABCO sandwich complexes. The system was fully characterized using a combination of UV-visible and (1)H NMR spectroscopy to identify the complexes. At a calix-tetraporphyrin:DABCO ratio of 2:4, the major species is dimeric cage assembly that features a large internal cavity for guest complexation.     

A high-performance multilane microdevice system designed for the DNA forensics laboratory

We report preliminary testing of "GeneTrack", an instrument designed for the specific application of multiplexed short tandem repeat (STR) DNA analysis. The system supports a glass microdevice with 16 lanes of 20 cm effective length and double-T cross injectors. A high-speed galvanometer-scanned four-color detector was specially designed to accommodate the high elution rates on the microdevice. All aspects of the system were carefully matched to practical crime lab requirements for rapid reproducible analysis of crime-scene DNA evidence in conjunction with the United States DNA database (CODIS). Statistically significant studies demonstrate that an absolute, three-sigma, peak accuracy of 0.4-0.9 base pair (bp) can be achieved for the CODIS 13-locus multiplex, utilizing a single channel per sample. Only 0.5 microL of PCR product is needed per lane, a significant reduction in the consumption of costly chemicals in comparison to commercial capillary machines. The instrument is also designed to address problems in temperature-dependent decalibration and environmental sensitivity, which are weaknesses of the commercial capillary machines for the forensics application.     

A DNA crystal designed to contain two molecules per asymmetric unit

We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal.     

A nucleobase-discriminating pyrrolo-dC click adduct designed for DNA fluorescence mismatch sensing

New pyrrolo-dC click adducts (4 and 5) tethered with a 1,2,3-triazole skeleton were synthesized and oligonucleotides were prepared. The triazole system was either directly linked to the pyrrolo moiety (5) or connected via an n-butyl linker (4). The quantum yield of nucleoside 5 (Φ=0.32), which is 10 times higher than those of 8-methylpyrrolo-dC (1?b, Φ=0.026) or the long linker derivative 4 (Φ=0.03), is maintained in oligonucleotides. Compound 5 was used as a nucleobase-discriminating fluorescence sensor in duplex DNA. Excellent mismatch discrimination was observed when 5 was positioned opposite the four canonical nucleosides. Compound 5 has the potential to be used for SNP detection in long DNA targets when conventional techniques such as high resolution melt analysis fail.     

Cholesterol and its fatty acid esters in native DNA preparations: lipid analysis,computer simulation of their interaction with DNA and cholesterol binding to immobilized oligodeoxyribonucleotides

Supramolecular DNA complexes were isolated from rat normal cells and murine tumors. The content of DNA-bound lipids (cholesterol and its esters) was determined. The content of cholesterol esters is higher than that of free cholesterol; the lipid content in tumor cells is higher than in normal cells. Using the molecular mechanics approach, it is demonstrated for the first time that cholesterol and its esters with stearic, oleic, linoleic, and linolenic acids bind to the DNA minor groove more strongly than with the major groove. The calculated DNA binding energies of cholesterol and its esters depend on both the number of double bonds in the fatty acid residue and on the DNA nucleotide composition. The formation of stable complexes between cholesterol molecules and d(AT)-rich oligonucleotides was demonstrated using biological microchip containing immobilized octadeoxyribonucleotides. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2138–2144, September, 2005.     

Octahydroxypyridine[4]arene self-assembles spontaneously to form hexameric capsules and dimeric aggregates

In recent years it has been observed that resorcin[4]arenes and pyrogallol[4]arenes form hydrogen-bonded hexameric capsules in nonpolar solvents. In the present study we have used NMR spectroscopy, with an emphasis on diffusion NMR, to investigate the self-assembly and the aggregation mode of solutions of octahydroxypyridine[4]arene (1 b) in chloroform. In spectroscopic studies, the hexameric capsule of C-undecylresorcin[4]arene (2 b) was used as a reference compound and in some cases also as an internal reference. The current diffusion NMR spectroscopy study shows, in contrast to a previous report, that compound 1 b self-assembles spontaneously into hexameric and dimeric aggregates in solutions in chloroform. The (1)H NMR and diffusion NMR spectroscopic studies on a solution of 1 b in CHCl(3) show the presence of new upfield-shifted peaks, which diffuse with the same diffusion coefficient as the hexameric peaks in the spectrum. Therefore, these new upfield-shifted peaks were attributed to encapsulated CHCl(3) molecules. Interestingly, diffusion NMR measurements showed that the addition of trifluoroacetic acid (6.7 equiv), which had no effect on the hexameric capsules of 2 b, led to the disassembly of the hexamer and the dimer of 1 b into its monomers. Therefore, we conclude that compound 1 b self-assembles spontaneously into hexameric capsules in nonpolar organic solvents, as do resorcin[4]arenes 2 b and 2 c and pyrogallol[4]arenes 3 a and 3 b.     

Alternant boron nitride cages: A theoretical study

Heteroatomic cages (B_N/2N_N/2) with borons and nitrogens fully replacing alternant sets of carbons in cages are built graph-theoretically and investigated via the semiempirical MNDO Hamiltonian. The comparison with their parent carbon cages C_N is made in terms both of electronic and of geometric changes. Infinite classes first of octahedral symmetry and second of hexagonal-bipyramidal symmetry fullerenoid cages are considered in detail. The difference in the electronegativities for boron and nitrogen implies the opening of HOMO-LUMO gaps for alternant BN clusters. In general, the borons prefer planar geometry (sp² hybridization) while the nitrogens prefer pyramidalization (sp³ hybridization). © 1997 John Wiley & Sons, Inc.     

DNA quantitation and degradation assessment: a quantitative PCR protocol designed for small forensic genetics laboratories

For over 10 years, quantitative PCR (qPCR) for DNA quantitation has been reported in forensics. However, assays have not been described for small qPCR platforms. Thus, technological advancement is not always implemented in small forensic genetics laboratories. A duplex qPCR assay is reported, using a StepOne instrument and targeting a short and a long human DNA region. This study was performed according to international validation guidelines, including sensitivity, repeatability, reproducibility, precision, accuracy, contamination assessment, known and case-type samples, and degradation studies. Characterization of the genetic markers, species specificity, and population studies had already been conducted. Moreover, case-type samples were quantified, amplified using commercial kits and the number of alleles detected was recorded. Sensitivity was shown to be 10 pg/µL. Standard curve replicates demonstrated the assay is accurate, precise, as well as fairly repeatable and reproducible. The NGM Detect kit was shown to yield higher peaks than Identifiler Plus and NGM Select for degraded samples. Moreover, quality sensors were always present and proved useful. The quantification values of the large target showed a correlation with the number of alleles detected in the STR profiles for known and casework samples. The degradation index was shown to be informative, with a value of 10 or higher indicating dropout. It is suggested that after quantitation, samples with low or degraded DNA be amplified using newer amplification kits containing quality sensors to confirm that the low-quality profile was not affected by inhibition.