Enhancement of DNAzymatic activity using iterative in silico maturation.

DNAzyme-based (catalytic nucleic acid) biosensing technology is recognised as a valuable biosensing tool in diagnostic medicine and seen as a cheaper, more stable alternative to antibodies or enzymes. However, like enzyme discovery, no method exists to predict DNAzyme sequences that result in high catalytic activity using computer software (in silico). In this work, iterative in silico maturation and in vitro evaluation were applied to a DNAzyme oligodeoxynucleotide (ODN) sequence to elucidate novel synthetic sequences with enhanced DNAzyme activity. An already well-known model DNAzyme, the G-quadruplex/hemin complex, was iterated over eight generations to elucidate synthetic sequences that were up to five times faster than the original parent sequence. By combining molecular dynamics simulations, we found that the POD-mimicking activities were largely affected by docking modes and the tightness of locking between complexes. Ultimately, the theoretical models showed significant sequence-dependencies.

Spatially isolated redox processes enabled by ambipolar charge transport in multi-walled carbon nanotube mats.

This work demonstrates a simple dual-well device which enables spatially isolated solutions to undergo complementary redox reactions. The device functions by the ambipolar transport of charge carriers between two spatially isolated poly(dimethylsiloxane) (PDMS) microwells through an underlying multi-walled carbon nanotube (MWCNT) mat. This MWCNT mat enables charge carriers, produced from the decomposition of an analyte in one solution, to drive a redox reaction in a spatially isolated second colorimetric read-out solution via a potential difference between the wells. As proof-of-concept a visible colorimetric read-out was shown using an enzyme, cytochrome c (reduced in 16 h), and the visualizing reagent 3,3',5,5'-tetramethylbenzidine (TMB) (oxidized in 2.5 h) for the detection of dithionite and hydrogen peroxide, respectively, without any external energy input. We discuss the origin of this phenomenon and highlight the ability of MWCNTs to accept and transport both electrons and holes efficiently between spatially isolated solutions giving rise to a highly versatile sensor suitable for use in simple, low-cost point-of-care diagnostics.

Probing Contact Electrification: A Cohesively Sticky Problem.

Contact electrification and the triboelectric effect are complex processes for mechanical-to-electrical energy conversion, particularly for highly deformable polymers. While generating relatively low power density, contact electrification can occur at the contact-separation interface between nearly any two polymer surfaces. This ubiquitousness of surfaces enables contact electrification to be an important phenomenon to understand energy conversion and harvesting applications. The mechanism of charge generation between polymeric materials remains ambiguous, with electron transfer, material (also known as mass) transfer, and adsorbed chemical species transfer (including induced ionization of water and other molecules) all being proposed as the primary source of the measured charge. Often, all sources of charge, except electron transfer, are dismissed in the case of triboelectric energy harvesters, leading to the generation of the "triboelectric series", governed by the ability of a polymer to lose, or accept, an electron. Here, this sole focus on electron transfer is challenged through rigorous experiments, measuring charge density in polymer-polymer (196 polymer combinations), polymer-glass (14 polymers), and polymer-liquid metal (14 polymers) systems. Through the investigation of these interfaces, clear evidence of material transfer via heterolytic bond cleavage is provided. Based on these results, a generalized model considering the cohesive energy density of polymers as the critical parameter for polymer contact electrification is discussed. This discussion clearly shows that material transfer must be accounted for when discussing the source of charge generated by polymeric mechanical energy harvesters. Thus, a correlated physical property to understand the triboelectric series is provided.

Oxacillin Coupled G-Quadruplexes as a Novel Biofilm-Specific Antibiotic for Staphylococcus aureus Biofilms.

One of the most important traits of pathogenic microbial biofilms is their high tolerance to conventional antimicrobial agents, which is partially due to the presence of metabolically inactive and transiently resistant persister cells. Here, we use guanine-rich DNA structures known as G-quadruplexes (G4s) coupled with the ß-lactam antibiotic, oxacillin (OX), and loaded with an iron-containing protoporphyrin IX (hemin), as OXG4/hemin complex biofilm-specific antibiotic agents. By coupling the OX to the G4, to form an OXG4/hemin complex, the diffusion of the OX was facilitated into the biofilm. Further, by utilizing the known oxidizing behavior (peroxidase-mimicking) of the G4/hemin complex, the entire system was found to be highly effectively against Staphylococcus aureus biofilms. By using G4 structures to penetrate biofilms, this work paves the way for an entirely new DNA-based therapy for biofilm eradication.

Hi-fidelity discrimination of isomiRs using G-quadruplex gatekeepers.

Core microRNA (miRNA) sequences exist as populations of variants called isomiRs made up of different lengths and nucleotide compositions. In particular, the short sequences of miRNA make single-base isomiR mismatches very difficult to be discriminated. Non-specific hybridizations often arise when DNA probe-miRNA target hybridization is the primary, or initial, mode of detection. These errors then become exacerbated through subsequent amplification steps. Here, we present the design of DNA probes modified with poly-guanine (PG) tracts that were induced to form G-quadruplexes (G4) for hi-fidelity discrimination of miRNA core target sequence from single-base mismatched isomiRs. We demonstrate that, when compared to unmodified probes, this G4 'gate-keeping' function within the G4-modified probes enables more stringent hybridization of complementary core miRNA target transcripts while limiting non-specific hybridizations. This increased discriminatory power of the G4-modified probes over unmodified probes is maintained even after further reverse transcriptase extension of probe-target hybrids. Enzymatic extension also enhanced the clarity and sensitivity of readouts and allows different isomiRs to be distinguished from one another via the relative positions of the mismatches.

Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator.

Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded-DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP-Cytosine > TPP-Thymine > TPP-Adenine ≥ TPP-Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80-90% quenching), compared to 25-30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs.