DNA-PEG-DNA triblock macromolecules for reagentless DNA detection

The sandwich assay is the most common design for electrochemical DNA sensors. This assay consists of three individual DNA components: an immobilized capture strand, a target strand, and a probe strand containing a redox-active reporter group. We report a simplified DNA assay where two strands of ssDNA, the capture and probe strands, are linked together via a flexible poly(ethylene glycol) (PEG) spacer forming an ABA triblock macromolecule. We have developed an electrochemical assay where the detection signal arises as a consequence of a large structural change induced upon hybridization with target DNA. In this system, the DNA-PEG-DNA macromolecule folds or wraps around the target DNA, bringing the ferrocene probe in close proximity to the electrode, affording an electrochemical response.     

High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2

The crystal structure of [d(CGCAAATTTGCG)]2 has been determined to 1.5 A resolution, representing the first high-resolution structure of this DNA fragment. The ion interactions are novel. A spermine molecule replaces a Mg2+ observed in analogous structures. Unlike lower-resolution structures, the minor groove is narrow and the major groove lacks extra Watson-Crick hydrogen bonds. In addition, a monolayer of solvent sites, including a "spine of hydration", is visible in the minor groove. The crystal of [d(CGCAAATTTGCG)]2 was grown from a solution containing spermine, magnesium, and lithium. The conformation recapitulates that of "monovalent-minus" DNA.     

Comparison of C-H...pi and hydrophobic interactions in a beta-hairpin peptide: impact on stability and specificity

We have examined the impact of C-H...pi and hydrophobic interactions in the diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe, Trp, or Cha (cyclohexylalanine) with Lys or Nle (norleucine). NMR studies, including NOESY and chemical shift perturbation studies, of the Lys side chain indicates that Lys interacts in a specific geometry with Phe or Trp through the polarized C epsilon. In contrast, Nle does not interact in a specific manner with the diagonal aromatic residue. Thermal denaturation provides additional support that Lys and Nle interact in fundamentally different manners. Folding of the peptide with a diagonal Trp...Lys interaction was found to be enthalpically driven, whereas the peptide with a diagonal Trp...Nle interaction displayed cold denaturation, as did the control peptide with a diagonal Cha...Nle interaction, indicating different driving forces for interaction of Lys and Nle with Trp. These findings have significant implications for specificity in protein folding and de novo protein design.     

Visualising mouse neuroanatomy and function by metal distribution using laser ablation-inductively coupled plasma-mass spectrometry imaging

Metals have a number of important roles within the brain. We used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to map the three-dimensional concentrations and distributions of transition metals, in particular iron (Fe), copper (Cu) and zinc (Zn) within the murine brain. LA-ICP-MS is one of the leading analytical tools for measuring metals in tissue samples. Here, we present a complete data reduction protocol for measuring metals in biological samples, including the application of a pyramidal voxel registration technique to reproducibly align tissue sections. We used gold (Au) nanoparticle and ytterbium (Yb)-tagged tyrosine hydroxylase antibodies to assess the co-localisation of Fe and dopamine throughout the entire mouse brain. We also examined the natural clustering of metal concentrations within the murine brain to elucidate areas of similar composition. This clustering technique uses a mathematical approach to identify multiple ‘elemental clusters’, avoiding user bias and showing that metal composition follows a hierarchical organisation of neuroanatomical structures. This work provides new insight into the distinct compartmentalisation of metals in the brain, and presents new avenues of exploration with regard to region-specific, metal-associated neurodegeneration observed in several chronic neurodegenerative diseases.     

n‐Dopants Based on Dimers of Benzimidazoline Radicals: Structures and Mechanism of Redox Reactions

Dimers of 2‐substituted N,N′‐dimethylbenzimidazoline radicals, (2‐Y‐DMBI)₂ (Y=cyclohexyl (Cyc), ferrocenyl (Fc), ruthenocenyl (Rc)), have recently been reported as n‐dopants for organic semiconductors. Here their structural and energetic characteristics are reported, along with the mechanisms by which they react with acceptors, A (PCBM, TIPS‐pentacene), in solution. X‐ray data and DFT calculations both indicate a longer C?C bond for (2‐Cyc‐DMBI)₂ than (2‐Fc‐DMBI)₂, yet DFT and ESR data show that the latter dissociates more readily due to stabilization of the radical by Fc. Depending on the energetics of dimer (D₂) dissociation and of D₂‐to‐A electron transfer, D₂ reacts with A to form D⁺ and A^? by either of two mechanisms, differing in whether the first step is endergonic dissociation or endergonic electron transfer. However, the D⁺/0.5 D₂ redox potentials—the effective reducing strengths of the dimers—vary little within the series (ca. ?1.9 V vs. FeCp₂^+/0) (Cp=cyclopentadienyl) due to cancelation of trends in the D^+/0 potential and D₂ dissociation energy. The implications of these findings for use of these dimers as n‐dopants, and for future dopant design, are discussed.     

On‐Tip Photo‐Modulated Molecular Printing

The concept of using cantilever‐free scanning probe arrays as structures that can modulate nanoscale ink flow and composition with light is introduced and evaluated. By utilizing polymer pen arrays with an opaque gold layer surrounding the base of the transparent polymer pyramids, we show that inks with photopolymerizable or isomerizable constituents can be used in conjunction with light channelled through the pyramids to control ink viscosity or composition in a dynamic manner. This on‐tip photo‐modulated molecular printing provides novel chemically and mechanically controlled approaches to regulating ink transport and composition in real time and could be useful not only for rapidly adjusting feature size but also for studying processes including photoreactions and mass transport at the nanoscale, self‐assembly, and cell–material interactions.     

Raman dye-labeled nanoparticle probes for proteins

In this paper, we demonstrate how one can chemically design Raman dye-functionalized nanoparticle probes with specific protein-binding affinities and use these probes, coupled with surface-enhanced Raman scattering (SERS) spectroscopy, to perform multiplexed screening of protein-small molecule interactions and protein-protein interactions in a protein microarray format.     

Total synthesis of (+/-)-cameroonan-7alpha-ol and biomimetic rearrangements to related nopsane sesquiterpenes

A total synthesis of the novel silphinane sesquiterpene alcohol (+/-)-cameroonanol (6-OH) from bicyclic enone 10 was accomplished by conjugate addition of crotylsilane, photochemical hydrobromination, intramolecular alkylation, and hydride reduction. The stereoisomers cameroonan-7beta-ol (18-OH) and 9-epicamerooonanols (19 and 20) were separated from isomer mixtures and the 9-desmethylcameroonanols (21-OH and 22-OH) were obtained by similar means. Solvolysis of 6-OMs and 18-OMs effected skeletal rearrangements to (+/-)-silphiperfol-6-ene (5), (+/-)-prenopsanol (7) and (+/-)-nopsanol (8), and (+/-)-silphiperfolan-7beta-ol (9) in parallel with biogenetic schemes proposed for these naturally occurring sesquiterpenes. The nor analogues 21-OMs and 22-OMs underwent solvolytic rearrangments to a similar set of nor products. The increase in solvolytic rates for the 7beta-mesylates 18-OMs and 22-OMs in comparison to the 7alpha epimers is attributed to concerted antiperiplanar Wagner-Meerwein rearrangements to the prenopsyl and norprenopsyl carbocations. Further analysis of the kinetic data and comparisons with solvolysis rates for the structurally related silphin-1beta-yl and silphin-1alpha-yl mesylates (28 and 29) are presented. The rearrangements observed afford chemical precedent for the biogenetic pathways in the literature for these silphinane sesquiterpenes.     

Vertical agarose gel electrophoresis and electroblotting of high-molecular-weight proteins

The electrophoretic separation of high-molecular-weight proteins (> 500 kDa) using polyacrylamide is difficult because gels with a large enough pore size for adequate protein mobility are mechanically unstable. A 1% vertical sodium dodecyl sulfate (SDS)-agarose gel electrophoresis (VAGE) system has been developed that allows titin (a protein with the largest known SDS subunit size of 3000-4000 kDa) to migrate over 10 cm in a approximately 13 cm resolving gel. Such migration gives clear and reproducible separation of titin isoforms. Proteins ranging in size from myosin heavy chain ( approximately 220 kDa) up to titin can be resolved on this gel system. Electroblotting of these very large proteins was nearly 100% efficient. This VAGE system has revealed two titin size variants in rabbit psoas muscle, two N2BA bands in rabbit cardiac muscle, and species differences between titins from rat and rabbit muscle. Agarose electrophoresis should be the method of choice for separation and blotting of proteins with very large subunit sizes.     

Defining rules for the shape evolution of gold nanoparticles

The roles of silver ions and halides (chloride, bromide, and iodide) in the seed-mediated synthesis of gold nanostructures have been investigated, and their influence on the growth of 10 classes of nanoparticles that differ in shape has been determined. We systematically studied the effects that each chemical component has on the particle shape, on the rate of particle formation, and on the chemical composition of the particle surface. We demonstrate that halides can be used to (1) adjust the reduction potential of the gold ion species in solution and (2) passivate the gold nanoparticle surface, both of which control the reaction kinetics and thus enable the selective synthesis of a series of different particle shapes. We also show that silver ions can be used as an underpotential deposition agent to access a different set of particle shapes by controlling growth of the resulting gold nanoparticles through surface passivation (more so than kinetic effects). Importantly, we show that the density of silver coverage can be controlled by the amount and type of halide present in solution. This behavior arises from the decreasing stability of the underpotentially deposited silver layer in the presence of larger halides due to the relative strengths of the Ag(+)/Ag(0)-halide and Au(+)/Au(0)-halide interactions, as well as the passivation effects of the halides on the gold particle surface. We summarize this work by proposing a set of design considerations for controlling the growth and final shape of gold nanoparticles prepared by seed-mediated syntheses through the judicious use of halides and silver ions.