A wide-range, low-cost 150 bp ladder for sizing DNA fragments between 150 and 4500 bp

Agarose gel electrophoresis, a very routine procedure, requires molecular weight standards; these are usually manufactured from plasmid or viral DNA fragments, or more recently, from PCR products of defined sizes. We describe here the preparation of a molecular weight standard from a completely different DNA source - the uniquely organized genome of the beetle Tenebrio molitor. The standard can be used to accurately size DNAs between 150 and 4500 bp, a useful range of sizes for many agarose gel electrophoresis applications, including separation of PCR products and plasmid cloning targets. In addition, it is easy to prepare, inexpensive, and rivals the best of the commercial ladders.     

Corrole-based applications

Despite of the many similarities between corroles and porphyrins, the chemistry of the former remained undeveloped for decades because of severe synthetic obstacles. The recent discoveries of facile methodologies for the synthesis of triarylcorroles and the corresponding metal complexes allowed for their utilization in various fields. This survey reveals many examples where corroles were used as the key components in catalysis, sensing of gaseous molecules and medicine-oriented research. The focus in all these cases was on the special features of corroles: stabilization of high valent transition metal ions, unique photophysical properties, large NH acidity, facile synthetic manipulation and distinct catalytic properties. The latter aspect includes several examples of reactions that are not catalyzed by any non-corrole metal complex, such as the iron-based aziridination by Chloramine-T, the clean disproportionation of peroxynitrite, and the very facile N-H activation of amines.     

Listing minimal edge-covers of intersecting families with applications to connectivity problems

Let G=(V,E) be a directed/undirected graph, let s,t∈V, and let F be an intersecting family on V (that is, X∩Y,X∪Y∈F for any intersecting X,Y∈F) so that s∈X and t∉X for every X∈F. An edge set I⊆E is an edge-cover of F if for every X∈F there is an edge in I from X to V−X. We show that minimal edge-covers of F can be listed with polynomial delay, provided that, for any I⊆E the minimal member of the residual family F_I of the sets in F not covered by I can be computed in polynomial time. As an application, we show that minimal undirected Steiner networks, and minimal k-connected and k-outconnected spanning subgraphs of a given directed/undirected graph, can be listed in incremental polynomial time.     

Stable radicals formation in coals undergoing weathering: effect of coal rank

Once coal is excavated it comes into contact with atmospheric oxygen and begins to undergo low temperature oxidation. The mechanism by which the molecular oxygen interacts with the coal macromolecule is suggested to occur in several steps. These steps primarily involve O(2) diffusion to the surface where physical adsorption followed by chemical adsorption takes place. The chemical adsorption forms several types of oxides that can subsequently react to form several products, primarily CO(2). It has also been suggested that some of these oxidation mechanisms might involve radical reactions. As the previous studies were conducted under conditions where significant structural changes occur it is possible that in the low temperature range (T < 100 °C) the oxidation mechanism is different. Several different rank (lignite-subbituminous-bituminous) coals were isothermally heated at 95 °C in an air atmosphere for a period of up to 6 months and samples were collected at two week intervals. The radical concentration of each sample was measured by Continuous Wave Electron Paramagnetic Resonance (CW-EPR). It is apparent that there are distinct differences between the lower rank (lignite) and the higher rank (subbituminous, bituminous) coals. The lower rank coals exhibited only carbon centered radicals with an adjacent oxygen atom and the higher rank coals exhibited only carbon centered radicals. Interestingly, the lower rank coals exhibited no change in radical concentration due to the long term oxidation treatment while the higher rank coals showed a distinct increase in the radical concentration. These findings shed new light on the complex heterogeneous low temperature oxidation reactions occurring at the coal surface.     

Chlorinated corroles

Fully β-pyrrole chlorinated corrole was obtained via reaction of the cobalt(iii) complex of 5,10,15-tris(pentafluorophenyl)corrole with chlorine. The structural and electronic effects of chlorination are reported, together with the coordination chemistry of this complex.     

Fine tuning the reactivity of corrole-based catalytic antioxidants

In order to determine the electronic factors that may affect the catalytic antioxidant activity of water-soluble metallocorroles a series of 10-aryl-5,15-pyridinium manganese(III) corroles was prepared. These complexes were examined regarding the effect of the C(10) substituent on the Mn(IV)/Mn(III) redox potentials, catalytic rate constants for decomposition of HOONO, prevention of tyrosine nitration, and superoxide dismutase activity. This structure-activity relationship investigation provides new insight regarding the mechanism by which manganese(III) corroles act as catalytic antioxidants. It also discloses the superiority of the C(10)-anysil-substituted complex in all examined aspects.     

A chromophore-supported structural and functional model of dinuclear copper enzymes,for facilitating mechanism of action studies

Type III dicopper centres are the heart of the reactive sites of enzymes that catalyze the oxidation of catechols. Numerous synthetic model complexes have been prepared to uncover the fundamental chemistry involved in these processes, but progress is still lagging much behind that for heme enzymes. One reason is that the latter gain very much from the informative spectroscopic features of their porphyrin-based metal-chelating ligand. We now introduce sapphyrin-chelated dicopper complexes and show that they may be isolated in different oxidation states and coordination geometries, with distinctive colors and electronic spectra due to the heme-like ligands. The dicopper(i) complex 1-Cu2 was characterized by ¹H and ¹⁹F NMR spectroscopy of the metal-chelating sapphyrin, the oxygenated dicopper(ii) complex 1-Cu2O2 by EPR, and crystallographic data was obtained for the tetracopper(ii)-bis-sapphyrin complex [1-Cu2O2]2. This uncovered a non-heme [Cu₄(OH)₄]⁴⁻ cluster, held together with the aid of two sapphyrin ligands, with structural features reminiscent of those of catechol oxidase. Biomimetic activity was demonstrated by the 1-Cu2O2 catalyzed aerobic oxidation of catechol to quinone; the sapphyrin ligand aided very much in gaining information about reactive intermediates and the rate-limiting step of the reaction.

Di-copper chelation by sapphyrin facilitates reaction mechanism investigations and characterization of reactive intermediates regarding biomimetic catechol oxidation.     

Liposome-Based Optochemical Nanosensors

 This paper describes the optochemical pH and oxygen sensing properties of dye-encapsulating and fluorescently labeled nano-sized unilamellar liposomes. To prepare the oxygen sensitive liposomes a lipid mixture consisting of dimyristoylphospatidylcholine, cholesterol, and dihexadecyl phosphate (molar ratio 5:4:1) all dissolved in dry isopropyl alcohol is injected into a sensing dye solution. The mixture is then sonicated with a liposome maker to form dye-encapsulating liposomes. A lipid mixture consisting of dimyristoylphospatidylcholine, N-(fluorescein-5-thiocarbamoyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine triethylammonium salt (fluorescein DHPE), cholesterol, and dihexadecyl phosphate (molar ratio 20:1:16:4) is used to prepare the pH sensitive liposomes by the same sonication technique. Fluorescein labeled DHPE phospholipids are combined with DMPC phospholipids in a 1:20 ratio to incorporate the sensing dye directly into the bilayer membrane, virtually eliminating any instability due to dye leakage. Oxygen sensing liposomes are created by encapsulating the oxygen sensitive ruthenium tris(1,10)-phenanthroline complex [Ru(phen)₃]. The dye is believed to exist both in free solution within the liposome, and as an adherent on the inner membrane of the liposome. High uniformity of the liposomes is realized by extruding them back and forth through a 100 nm pore-size polycarbonate membrane. TEM images of the liposomes, stained with uranyl acetate, show that the liposomes are unilamellar, spherical in shape, maintain high structural integrity, and average 70 nm in diameter. The liposomes show high stability with respect to dye leaking at room temperature for 8 days, and high photostability when exposed to the excitation light. Individual liposomes are used to monitor the pH and oxygen level in their vicinity during the enzymatic oxidation of glucose by the enzyme glucose oxidase. The newly prepared environmentally sensitive liposomes can be applied for non-invasive pH and oxygen determination in tissues and single biological cells. Received June 8, 1998. Revision November 10, 1998.     

The First Direct Synthesis of Corroles from Pyrrole

The solvent-free, catalyst-free condensation of pyrrole and aldehydes provides an extremely facile synthetic pathway to novel corroles [Eq. (1); Ar=C₆F₅, 2,6-F₂C₆H₃, 2,6-Cl₂C₆H₃]. The product containing pentafluorophenyl groups is an excellent precursor of other derivatives, including an ionic, water-soluble corrole.