Electrostatically directed visual fluorescence response of DNA-functionalized monolithic hydrogels for highly sensitive Hg²+ detection

A novel graphene-DNA biosensor for selective detection of mercury ions

A novel electrochemical biosensor for sensitive and selective detection of mercury (II) ions (Hg²⁺) based on a DNA grafted graphene is proposed. Graphene oxide (GO) was reduced by dopamine, and then the single-strand probe DNA modified at the 5'-end with an alkylamino modifier (NH₂-ssDNA) was grafted on the reduced graphene oxide (RGO) surface via Michael addition reaction. In the presence of Hg²⁺, the target DNA with four thymine-thymine (T-T) mismatches would hybridize with the probe DNA on the glassy carbon electrode (GCE) through T-Hg²⁺-T coordination chemistry. The hybridization of the two oligonucleotides leads to the increase in the peak currents of [Ru(NH₃)₆]³⁺, which could be used for electrochemical sensing of Hg²⁺. The difference in the value of the peak currents of [Ru(NH₃)₆]³⁺ before and after DNA hybridization was linear with the concentration of Hg²⁺ in the range from 8.0×10⁻⁹ to 1.0×10⁻⁷ M with a linear coefficiency of 0.996. The detection limit was 5.0×10⁻⁹ M (S/N=3). The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of Hg²⁺. Particularly, the proposed method was applied successfully to the determination of Hg²⁺ in real environmental samples.

Preferentially grown ultranano c-diamond and n-diamond grains on silicon nanoneedles from energetic species with enhanced field-emission properties

The design and fabrication of well-defined nanostructures have great importance in nanoelectronics. Here we report the precise growth of sub-2 nm (c-diamond) and above 5 nm (n-diamond) size diamond grains from energetic species (chemical vapor deposition process) at low growth temperature of about 460 °C. We demonstrate that a pre-nucleation induced interface can be accounted for the growth of c-diamond or n-diamond grains on Si-nanoneedles (Si-NN). These preferentially grown allotropic forms of diamond on Si-NN have shown high electron field-emission properties and signify their high potential towards diamond-based electronic applications.

Stabilizing structure-switching signaling RNA aptamers by entrapment in sol-gel derived materials for solid-phase assays

Structure-switching, fluorescence-signaling DNA and RNA aptamers have been reported as highly versatile molecular recognition elements for biosensor development. While structure-switching DNA aptamers have been utilized for solid-phase sensing, equivalent RNA aptamers have yet to be successfully utilized in solid-phase sensors due to their lack of chemical stability and susceptibility to nuclease attack. In this study, we examined entrapment into sol-gel derived organic-inorganic composite materials as a platform for immobilization of structure-switching fluorescence-signaling RNA aptamer reporters, using both the synthetic theophylline- and naturally occurring thiamine pyrophosphate-binding RNA aptamers as test cases. Structure-switching versions of both aptamers were entrapped into a series of sol-gel derived composites, ranging from highly polar silica to hydrophobic methylsilsesquioxane-based materials, and the target-binding and signaling capabilities of these immobilized aptamers were assessed relative to solution. Both immobilized aptamers demonstrated sensitivity and selectivity similar to that of free aptamers when entrapped in a composite material derived from 40% (v/v) methyltrimethoxysilane/tetramethoxysilane. Importantly, this material also conferred protection from nuclease degradation and imparted long-term chemical stability to the RNA reporter systems. Given the versatility of sol-gel entrapment for development of biosensors, microarrays, bioaffinity columns, and other devices, this entrapment method should provide a useful platform for numerous solid-phase RNA aptamer-based devices.

Aptamer-functionalized hydrogel microparticles for fast visual detection of mercury(II) and adenosine

With a low optical background, high loading capacity, and good biocompatibility, hydrogels are ideal materials for immobilization of biopolymers to develop optical biosensors. We recently immobilized mercury and lead binding DNAs within a monolithic gel and demonstrated ultrasensitive visual detection of these heavy metals. The high sensitivity was attributed to the enrichment of the analytes into the gels. The signaling kinetics was slow, however, taking about 1 h to obtain a stable optical signal because of a long diffusion distance. In this work, we aim to understand the analyte enrichment process and improve the signaling kinetics by preparing hydrogel microparticles. DNA-functionalized gel beads were synthesized using an emulsion polymerization technique and most of the beads were between 10 and 50 μm. Acrydite-modified DNA was incorporated by copolymerization. Visual detection of 10 nM Hg(2+) was still achieved and a stable signal was obtained in just 2 min. The gel beads could be spotted to form a microarray and dried for storage. A new visual sensor for adenosine was designed and immobilized within the gel beads. The adenosine aptamer binds its target about 1000-fold less tightly compared to the mercury binding DNA, allowing a comparison to be made on analyte enrichment by aptamer-functionalized hydrogels.

Metal-induced specific and nonspecific oligonucleotide folding studied by FRET and related biophysical and bioanalytical implications

Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, nonspecific folding induced by mono- or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg(II) binding DNA and monitored metal-induced folding in the presence of various cations. While nonspecific electrostatically mediated folding can be very significant, at each tested salt condition, Hg(II) induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signal the formation of double-stranded DNA showed a lower dependency on ionic strength.

Stimuli-responsive releasing of gold nanoparticles and liposomes from aptamer-functionalized hydrogels

Controlled release of therapeutic agents is important for improving drug efficacy and reducing toxicity. Recently, hydrogels have been used for controlled release applications. While the majority of the previous work focused on releasing the cargo in response to physical stimuli such as temperature, light, electric field, and pH, we aim to trigger cargo release in the presence of small metabolites. In our system a DNA aptamer that can bind to adenosine, AMP, and ATP was used as a linker to attach either DNA-functionalized gold nanoparticles or liposomes to DNA-functionalized hydrogels. In the presence of the metabolite, both the nanoparticle and liposome cargos were released. The effect of salt, temperature, target concentration, and drying has been systematically studied. Interestingly, we found that the gel can be completely dried while retaining the DNA linkages and adenosine induced release was still achieved after rehydration. Our work demonstrates that aptamers can be used to control the release of drugs and other materials attached to hydrogels.