Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer

We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.     

Mechanistic Evidence of a Ni(0/II/III) Cycle for Nickel Photoredox Amide Arylation

This work demonstrates the dominance of a Ni(0/II/III) cycle for Ni-photoredox amide arylation, which contrasts with other Ni-photoredox C-heteroatom couplings that operate via Ni(I/III) self-sustained cycles. The kinetic data gathered when using different Ni precatalysts supports an initial Ni(0)-mediated oxidative addition into the aryl bromide. Using NiCl₂ as the precatalyst resulted in an observable induction period, which was found to arise from a photochemical activation event to generate Ni(0) and to be prolonged by unproductive comproportionation between the Ni(II) precatalyst and the in situ generated Ni(0) active species. Ligand exchange after oxidative addition yields a Ni(II) aryl amido complex, which was identified as the catalyst resting state for the reaction. Stoichiometric experiments showed that oxidation of this Ni(II) aryl amido intermediate was required to yield functionalized amide products. The kinetic data presented supports a rate-limiting photochemically-mediated Ni(II/III) oxidation to enable C−N reductive elimination. An alternative Ni(I/III) self-sustained manifold was discarded based on EPR and kinetic measurements. The mechanistic insights uncovered herein will inform the community on how subtle changes in Ni-photoredox reaction conditions may impact the reaction pathway, and have enabled us to include aryl chlorides as coupling partners and to reduce the Ni loading by 20-fold without any reactivity loss.     

Synthesis,Characterisation and Reactivity of Copper(I) Amide Complexes and Studies on Their Role in the Modified Ullmann Amination Reaction

A series of copper(I) alkylamide complexes have been synthesised; copper(I) dicyclohexylamide ( 1 ), copper(I) 2,2,6,6‐tetramethylpiperidide ( 2 ), copper(I) pyrrolidide ( 3 ), copper(I) piperidide ( 4 ), and copper(I) benzylamide ( 5 ). Their solid‐state structures and structures in [D₆]benzene solution are characterised, with the aggregation state in solution determined by a combination of DOSY NMR spectroscopy and DFT calculations. Complexes 1 , 2 and 4 are shown to exist as tetramers in the solid state by X‐ray crystallography. In [D₆]benzene solution, complexes 1 , 2 and 5 were found by using ¹H DOSY NMR to exist in rapid equilibrium between aggregates with average aggregation numbers of 2.5, 2.4 and 3.3, respectively, at 0.05 M concentration. Conversely, distinct trimeric, tetrameric and pentameric forms of 3 and 4 were distinguishable by one‐dimensional ¹H and ¹H DOSY NMR spectroscopy. Complexes 3 – 5 are found to react stoichiometrically with iodobenzene, in the presence or absence of 1,10‐phenanthroline as an ancillary ligand, to give arylamine products indicative of their role as potential intermediates in the modified Ullmann reaction. The role of phenanthroline has also been explored both in the stoichiometric reaction and in the catalytic Ullmann protocol.     

Biosensing by Tandem Reactions of Structure Switching,Nucleolytic Digestion,and DNA Amplification of a DNA Assembly

ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3′–5′ digestion of single‐stranded but not double‐stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure‐switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre‐primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure‐switching event that causes nucleolytic conversion of the pre‐primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.     

Can a Six‐Letter Alphabet Increase the Likelihood of Photochemical Assault to the Genetic Code?

In 2014, two unnatural nucleosides, d5SICS and dNaM, were shown to selectively base pair and replicate with high fidelity in a modified strain of E. coli, thus effectively expanding its genetic alphabet from four to six letters. More recently, a significant reduction in cell proliferation was reported in cells cultured with d5SICS, and putatively with dNaM, upon exposure to brief periods of near‐visible radiation. The photosensitizing properties of the lowest‐energy excited triplet state of both d5SICS and dNaM were implicated in their cytotoxicity. Importantly, however, the excited‐state mechanisms by which near‐visible excitation populates the triplet states of d5SICS and dNaM are currently unknown. In this study, steady‐state and time‐resolved spectroscopies are combined with quantum‐chemical calculations in order to reveal the excited‐state relaxation mechanisms leading to efficient population of the triplet states in these unnatural nucleosides in solution. It is shown that excitation of d5SICS or dNaM with near‐visible light leads overwhelmingly to ultrafast population of their triplet states on the femtosecond time scale. The results presented in this work lend strong support to the proposal that photoexcitation of these unnatural nucleosides can accelerate oxidatively generated damage to DNA and other biomolecules within the cellular environment.     

Pullulan Encapsulation of Labile Biomolecules to Give Stable Bioassay Tablets

A simple and inexpensive method is reported for the long‐term stabilization of enzymes and other unstable reagents in premeasured quantities in water‐soluble tablets (cast, not compressed) made with pullulan, a nonionic polysaccharide that forms an oxygen impermeable solid upon drying. The pullulan tablets dissolve in aqueous solutions in seconds, thereby facilitating the easy execution of bioassays at remote sites with no need for special reagent handling and liquid pipetting. This approach is modular in nature, thus allowing the creation of individual tablets for enzymes and their substrates. Proof‐of‐principle demonstrations include a Taq polymerase tablet for DNA amplification through PCR and a pesticide assay kit consisting of separate tablets for acetylcholinesterase and its chromogenic substrate, indoxyl acetate, both of which are highly unstable. The encapsulated reagents remain stable at room temperature for months, thus enabling the room‐temperature shipping and storage of bioassay components.     

Control of flexural waves on a beam using distributed vibration neutralisers

This paper is concerned with the use of distributed vibration neutralisers to control the transmission of flexural waves on a beam. Of particular interest is an array of beam-like neutralisers and a continuous plate-like neutraliser. General expressions for wave transmission and reflection metrics either side of the distributed neutralisers are derived. Based on transmission efficiency, the characteristics of multiple neutralisers are investigated in terms of the minimum transmission efficiency, the normalised bandwidth and the shape factor, allowing optimisation of their performance. Analytical results show that the band-stop property of the neutraliser array depends on various factors, including the neutraliser damping, mass, separation distance in the array and the moment arm of each neutraliser. Moreover, it is found that the particular attachment configuration of an uncoupled force-moment-type neutraliser can be used to improve their overall performance. It is also shown that in the limit of many neutralisers in the array, the performance tends to that of a continuous neutraliser.     

Adsorption and diffusion of argon in disordered nanoporous carbons

Application-specific optimization of disordered nanoporous carbons remains a formidable challenge due to the difficulty in accurately characterizing their microstructures with current empirical methods. Using molecular simulation techniques, we investigated the adsorptive and diffusive behavior of argon in three models of disordered nanoporous carbons. We found that the structural and morphological differences between these models gave rise to distinct phenomenological properties. The adsorptive behavior of argon in both the low and high pressure regimes was enhanced dramatically in the models with more crystalline microstructures. As for dynamic properties, we found that the adsorbent’s structure and energetic topology significantly alters the rates of diffusion as well as the characteristics of the underlying diffusion mechanisms.     

Potential benefits of a non-linear stiffness in an energy harvesting device

The benefits of using a non-linear stiffness in an energy harvesting device comprising a mass–spring–damper system are investigated. Analysis based on the principle of conservation of energy reveals a fundamental limit of the effectiveness of any non-linear device over a tuned linear device for such an application. Two types of non-linear stiffness are considered. The first system has a non-linear bi-stable snap-through mechanism. This mechanism has the effect of steepening the displacement response of the mass as a function of time, resulting in a higher velocity for a given input excitation. Numerical results show that more power is harvested by the mechanism if the excitation frequency is much less than the natural frequency. The other non-linear system studied has a hardening spring, which has the effect of shifting the resonance frequency. Numerical and analytical studies show that the device with a hardening spring has a larger bandwidth over which the power can be harvested due to the shift in the resonance frequency.