H. Holden Thorp

Cutting out the middleman: DNA biosensors based on electrochemical oxidation

There is considerable enthusiasm over electrochemical techniques in biotechnology, including the development of electrochemical biosensors for DNA hybridisation. The development of assay techniques that have the convenience of solid-phase hybridisation and are rapid, sensitive and readily multiplexed will have a significant impact on diagnostics and genomics. Because electrochemistry requires a solid electrode, there is a natural marriage between electrode detection and surface hybridisation. Modern electrochemical approaches include the detection of hybridisation at electrode surfaces using duplex-specific indicators and the shuttling of electrons from surface-bound nucleic acids to solid electrodes using soluble mediators with polentials matched to that of guanine.

Atomic Force Microscopy Studies of DNA-Wrapped Carbon Nanotube Structure and Binding to Quantum Dots

Single-stranded DNA is an effective noncovalent dispersant for individual single-walled carbon nanotubes (CNTs) in aqueous solution, forming a CNT-DNA hybrid material that has advantages for CNT separations and applications. Atomic force microscopy (AFM) reveals a regular pattern on the surface of CNT-DNA. We found this pattern to be independent of the length and sequence of the wrapping DNA, yet different from the structures observed for CNTs dispersed with sodium dodecyl sulfate in the absence of DNA. We wrapped CNTs with thiol-modified DNA to form stable conjugates of CNT-DNA and core/shell CdSe/ZnS quantum dots; AFM imaging of these conjugates identified for the first time the location of DNA on the CNT-DNA nanomaterial. Our results suggest that the AFM pattern of CNT-DNA is formed by helical turns (approximately 14-nm pitch) of wrapped DNA strands that are closely arranged end-to-end in a single layer along the CNT. This work demonstrates the useful functionalization of CNTs with quantum dots in a manner that avoids direct, destructive modification of the CNT surface and suggests nearly complete surface coverage of the nanotubes with DNA.

Alkyl hydroperoxide oxidation of alkanes and alkenes with a highly active Mn catalyst.

The system ROOH/[Mn3O4(dipy)4(OH2)2](ClO4)4 hydroxylates alkanes and converts ArCRCH2 to ArCRO with extremely high activity and good conversions and yields.

Electron-, Energy-, and Atom-Transfer Reactions Between Metal Complexes and Dna

Publisher Summary The reactivity of DNA towards both redox chemistry and hydrolysis is important in nucleotide biosynthesis and metabolism. Nucleic acids are excellent targets for anticancer and antiviral therapies, and nucleotide reactivity plays an important role in the design of specific nucleic acid damage agents and the understanding of natural products that cleave nucleic acid polymers. Ionizing radiation treatment leads to nucleic acid oxidation. There is a great deal of interest in using redox and hydrolytic chemistry to probe structures and manipulate sequences of complex nucleic acid polymers using targeted cleavage agents. The spectroscopic and electrochemical signatures of metal complexes can be used to understand DNA reactivity and to detect DNA structures. This chapter reviews researches that exploit the redox and photophysical properties of metal complexes to understand DNA reactivity. Metal complexes provide a special opportunity for these researches because they exhibit well-defined redox states that can be correlated with redox changes in nucleic acids and nucleotides. In metal complexes, changes in these redox states are coupled to changes in the optical spectroscopy of the metal center, which can be used to track the redox state of DNA. In addition, these spectroscopic signatures can also be used to determine DNA binding.

Ring-Opening Metathesis Polymerizations in Carbon Dioxide

Abstract The polymerization of norbornene was successfully initiated with Ru(H2O)6(tos)2 in a carbon dioxide medium. The resultant poly(norbornene) was prepared with yields and molecular weights comparable to those obtained in other solvent systems. It was also found that the cis/trans ratio of the polymer microstructure could be controlled by the addition of various amounts of methanol to the reaction mixture. A detailed account of the polymerizations is described and believed to be the first example of a ring-opening metathesis polymerization in carbon dioxide.

Concerted electron-proton transfer (EPT) in the oxidation of tryptophan with hydroxide as a base.

Tryptophan is unique among the redox-active amino acids owing to its weakly acidic indolic proton (pK(a) ≈ 16) compared to the -O-H proton of tyrosine (pK(a) = 10.1) or the -S-H proton of cysteine (pK(a) = 8.2). Stopped-flow and electrochemical measurements have been used to explore the roles of proton-coupled electron transfer and concerted electron-proton transfer (EPT) in tryptophan oxidation. The results of these studies have revealed a role for OH(-) as a proton acceptor base in EPT oxidation of N-acetyl-tryptophan but not for other common bases. The reorganizational barrier for (N-acetyl-tryptophan)(+/•) self-exchange is also estimated.

Bioinorganic chemistry and drug design: here comes zinc again

The structures and reactions of metal ions in proteins are of tremendous interest in bioinorganic chemistry, as is the potential for metals in creating novel medicines. New results combine these aspects in describing an unexpected mode for metal-mediated drug efficacy that relies on well-established principles of metalloprotein structure.

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

BACKGROUND The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms. RESULTS Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern. CONCLUSIONS The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

Application of the electrocatalytic reduction of nitric oxide mediated by ferrioxamine B to the determination of nitric oxide concentrations in solution

Abstract The electrocatalytic reduction of nitric oxide to nitrous oxide by the iron siderophore ferrioxamine B was used as a basis for an electrochemical NO sensor. Evaporation of a Nafion film onto a glassy carbon electrode produced modified surfaces into which the ferric complex of ferrioxamine B could be exchanged. Cyclic voltammetry of this modified electrode in aqueous solution produced two peaks, one of which (−0.73 V versus SSCE) corresponded to the quasi-reversible reduction of solution-bound ferrioxamine B and the other of which (−0.42 V) corresponded to an adsorbed species. Greater catalytic enhancement was observed in the presence of NO for the solution wave than for the adsorption pre-peak. The catalytic enhancement, expressed as the ratio of peak current in the presence of NO ( i cat ) to the current in the absence of NO ( i d ) was a linear function of the solution NO concentration down to 1 μ M. Better sensitivity was precluded by decomposition of the reduced form of the catalyst in the absence of NO.

New mechanisms in DNA cleavage by metal complexes

The chemistry of new families of DNA cleavage agents based on oxoruthenium(IV) or diplatinum pyrophosphite complexes is reviewed. The ruthenium complexes derived from Ru(tpy)(bpy)O2+ (tpy, 2, 2, 2′-terpyridine; bpy, 2, 2′-bipyridine) are effective DNA cleavage agents both electrocatalytically or thermally. The stoichiometric reaction quantitatively produces Ru(II), which also binds to DNA covalently in a slow, follow-up reaction. The cleavage by Pt2(pop)44− (pop, P2O5H2) is photoactivated and proceeds via H-atom abstraction by the platinum complex.