Ionic liquids: prospects for nucleic acid handling and delivery

Operations with nucleic acids are among the main means of studying the mechanisms of gene function and developing novel methods of molecular medicine and gene therapy. These endeavours usually imply the necessity of nucleic acid storage and delivery into eukaryotic cells. In spite of diversity of the existing dedicated techniques, all of them have their limitations. Thus, a recent notion of using ionic liquids in manipulations of nucleic acids has been attracting significant attention lately. Due to their unique physicochemical properties, in particular, their micro-structuring impact and tunability, ionic liquids are currently applied as solvents and stabilizing media in chemical synthesis, electrochemistry, biotechnology, and other areas. Here, we review the current knowledge on interactions between nucleic acids and ionic liquids and discuss potential advantages of applying the latter in delivery of the former into eukaryotic cells.

Electrochemical biosensor for detection of MON89788 gene fragments with spiny trisoctahedron gold nanocrystal and target DNA recycling amplification

The shape-controlled synthesis of gold nanocrystals via shape induction of hexadecyltrimethylammonium chloride, potassium bromide, and potassium iodide and enantioselective direction of L-cysteine is reported. The resulting gold nanocrystals (STO-Au) offer spiny trisoctahedron nanostructures with good monodispersity and enhanced exposed high-index facets and high catalytic activity. Construction of the electrochemical sensing platform for MON89788 gene involves the modification of STO-Au, thionine (Thi), and labeled bipedal DNA probe 1 or 2 (P1 or P2) for target DNA-induced recycling amplification. In the detection, two surface DNA probes were immobilized on gold electrode via the Au-S bond. Then, hairpin DNA 1 (H1), Thi-STO-Au-P1, and Thi-STO-Au-P2 self-assemble into two-dimensional DNA nanopores (DNPs) on the electrode surface. Target DNA hybridizes with hairpin DNA 2 (H2) to open hairpin structure of H2. The opened H2 binds with H1 in the DNPs to release Thi-STO-Au-P1, Thi-STO-Au-P2, and target DNA by toehold-mediated strand-displacement. The utilization of target DNA-induced recycling allows one target DNA to release 2N STO-Au-labeled DNA strands, promoting significant signal amplification. The detection signal is further enhanced by the catalyzed redox reaction of Thi with STO-Au. The differential pulse voltammetric signal, best measured at - 0.18 V vs. Ag/AgCl, decreases linearly with increasing concentration of MON89788 in the range 0.02-8 × 104 fM, and the detection limit is 0.0048 fM (S/N = 3). The proposed method was successfully applied for electrochemical detection of MON89788 gene fragments in the PCR products from genetically modified soybean. Graphical Abstract We develop l-cysteine controlled synthesis of spiny trisoctahedron gold nanocrystals with good monodispersity and highly exposed high-index facets. The architecture achieves to ultrahigh catalytic activity. The electrochemical biosensor based on gold nanocrystals and target DNA recycling amplification provides advantage of sensitivity, repeatability, and regeneration-free.

Electrochemical sensory detection of Sus scrofa mtDNA for food adulteration using hybrid ferrocenylnaphthalene diimide intercalator as a hybridization indicator

In this study, an electrochemical DNA biosensor was developed based on the fabrication of silicon nanowires/platinum nanoparticles (SiNWs/PtNPs) on a screen-printed carbon electrode (SPCE) for the detection of Sus scrofa mitochondrial DNA (mtDNA) in food utilizing a new hybrid indicator, ferrocenylnaphthalene diimide (FND). The morphology and elemental composition of the SiNWs/PtNPs-modified SPCE was analyzed by field emission scanning electron microscopy (FESEM) combined with energy dispersive X-ray spectroscopy (EDX). Cyclic voltammetry (CV) was used to study the electrical contact between the PtNPs and the screen-printed working electrode through SiNWs, while electrochemical impedance spectroscopy (EIS) was used to measure the charge transfer resistance of the modified electrode. The results clearly showed that the SiNWs/PtNPs were successfully coated onto the electrode and the effective surface area for the SiNWs/PtNPs-modified SPCE was increased 16.8 times as compared with that of the bare SPCE. Differential pulse voltammetry used for the detection of porcine DNA with FND as an intercalator confirmed its specific binding to the double-stranded DNA (dsDNA) sequences. The developed biosensor showed a selective response towards complementary target DNA and was able to distinguish non-complementary and mismatched DNA oligonucleotides. The SiNWs/PtNPs-modified SPCE that was fortified with DNA hybridization demonstrated good linearity in the range of 3 × 10⁻⁹ M to 3 × 10⁻⁵ M (R² = 0.96) with a detection limit of 2.4 × 10⁻⁹ M. A cross-reactivity study against various types of meat and processed food showed good reliability for porcine samples.

An electrochemical DNA biosensor was developed based on the fabrication of silicon nanowires/platinum nanoparticles on a screen-printed carbon electrode for the detection of Sus scrofa mitochondrial DNA in food.

A novel electrochemical DNA biosensor for transgenic soybean detection based on triple signal amplification

A novel electrochemical DNA biosensor was developed and MON89788 of soybean transgenic gene sequence was detected based on a strategy of rolling circle amplification (RCA) and gold nanoparticle cube (AuNPC)-labeled multiple probes. First, the mercapto-modified capture DNA was immobilized on the surface of the Fe3O4@Au magnetic nanoparticles via an Au-S bond, and the capture DNA was opened and complementarily hybridized with the target DNA to form a double-stranded DNA. In the 10 × reaction buffer, Exonuclease III (ExoIII) specifically recognized and sheared the double-stranded DNA to release the target DNA, which led to the next round of reaction. Afterward, AuNP cube-loaded ssDNA (AuNPC/DNA) was added with the rolling circle reaction with the help of Phi29 DNA polymerase and T4 ligase. Finally, [Ru(NH3)6]3+ was attracted directly by the anionic phosphate of ssDNA via electrostatic interaction. The determination was carried out by using chronocoulometry (CC), and the CC signal was recorded. The mass amount of DNA strands extended infinitely on the AuNPs cube and numerous [Ru(NH3)6]3+ were absorbed, thus the detected signal was highly amplified. The corresponding CC signal showed a good linear relationship with the logarithm of the target DNA concentration in the range of 1 × 10-16 to 1 × 10-7 mol L-1, with a detection limit of 4.5 × 10-17 mol L-1. Specific gene sequence of MON89788 in soybean samples was determined, and the recoveries ranged from 97.3% to 102.0%. This sensor is one of the most sensitive sensors for genetic sequence assessment at present. Moreover, it demonstrates good selectivity, stability, and reproducibility.

Bimodal Porosity and Stability of a TiO2 Gig-Lox Sponge Infiltrated with Methyl-Ammonium Lead Iodide Perovskite

We created a blend between a TiO2 sponge with bimodal porosity and a Methyl-Ammonium Lead Iodide (MAPbI3) perovskite. The interpenetration of the two materials is effective thanks to the peculiar sponge structure. During the early stages of the growth of the TiO2 sponge, the formation of 5-10 nm-large TiO2 auto-seeds is observed which set the micro-porosity (<5 nm) of the layer, maintained during further growth. In a second stage, the auto-seeds aggregate into hundreds-of-nm-large meso-structures by their mutual shadowing of the grazing Ti flux for local oxidation. This process generates meso-pores (10-100 nm) treading across the growing layer, as accessed by tomographic synchrotron radiation coherent X-ray imaging and environmental ellipsometric porosimetry. The distributions of pore size are extracted before (>47% V) and after MAPbI3 loading, and after blend ageing, unfolding a starting pore filling above 80% in volume. The degradation of the perovskite in the blend follows a standard path towards PbI2 accompanied by the concomitant release of volatile species, with an activation energy of 0.87 eV under humid air. The use of dry nitrogen as environmental condition has a positive impact in increasing this energy by ~0.1 eV that extends the half-life of the material to 7 months under continuous operation at 60 °C.

Multi-Scale-Porosity TiO2 scaffolds grown by innovative sputtering methods for high throughput hybrid photovoltaics

We propose an up-scalable, reliable, contamination-free, rod-like TiO₂ material grown by a new method based on sputtering deposition concepts which offers a multi-scale porosity, namely: an intra-rods nano-porosity (1–5 nm) arising from the Thornton’s conditions and an extra-rods meso-porosity (10–50 nm) originating from the spatial separation of the Titanium and Oxygen sources combined with a grazing Ti flux. The procedure is simple, since it does not require any template layer to trigger the nano-structuring, and versatile, since porosity and layer thickness can be easily tuned; it is empowered by the lack of contaminations/solvents and by the structural stability of the material (at least) up to 500 °C. Our material gains porosity, stability and infiltration capability superior if compared to conventionally sputtered TiO₂ layers. Its competition level with chemically synthesized reference counterparts is doubly demonstrated: in Dye Sensitized Solar Cells, by the infiltration and chemisorption of N-719 dye (∼1 × 10²⁰ molecules/cm³); and in Perovskite Solar Cells, by the capillary infiltration of solution processed CH₃NH₃PbI₃ which allowed reaching efficiency of 11.7%. Based on the demonstrated attitude of the material to be functionalized, its surface activity could be differently tailored on other molecules or gas species or liquids to enlarge the range of application in different fields.

A homogeneous assay for highly sensitive detection of CaMV35S promoter in transgenic soybean by förster resonance energy transfer between nitrogen-doped graphene quantum dots and Ag nanoparticles

In this work, a novel homogeneous assay for DNA quantitative analysis based on förster resonance energy transfer (FRET) was developed for cauliflwer mosaic virus 35s (CaMV35S) promoter of transgenic soybean detection. The homogenous FRET of fluorescence signal was fabricated by DNA hybridization with probe modified nitrogen-doped graphene quantum dots (NGQDs) and silver nanoparticles (AgNPs), which acted the donor-acceptor pairs for the first time. The highly efficient FRET and unique properties of the NGQDs made the proposed FRET system as a functionalized detection platform for labelling of DNA. Upon the recognition of specific target DNA (tDNA), the FRET between NGQDs and AgNPs was triggered to produce fluorescence quenching, which could be used for tDNA detection. The fabricated homogeneous FRET assay displayed a wide linear range of 0.1-500.0 nM and a low limit of detection 0.03 nM for the detection of CaMV35S (S/N = 3). This proposed biosensor revealed high specificity to detect tDNA, with acceptable intra-assay precision and excellent stability. This method was successfully applied to identify the real sample of 0.5% containing transgenic soybean, which achieved the most of national law regulations. This assay was further validated by polymerase chain reaction as the genetically modified organisms, suggesting that the proposed FRET system is a feasible tool for the further daily genetically modified organism detection.

When biomolecules meet graphene: from molecular level interactions to material design and applications

Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses. The different interactions between graphene and biomolecules at the molecular level are demonstrated and discussed in detail. In addition, the potential applications of the created graphene-biomolecule nanohybrids in drug delivery, cancer treatment, tissue engineering, biosensors, bioimaging, energy materials, and other nanotechnological applications are presented. This review will be helpful to know the modification of graphene with biomolecules, understand the interactions between graphene and biomolecules at the molecular level, and design functional graphene-based nanomaterials with unique properties for various applications.

The graphene/nucleic acid nanobiointerface

In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.

Electrochemical biosensors on platforms of graphene

In recent years, graphene, the two-dimensional closely packed honeycomb carbon lattice, has been attracting much attention in the field of electrochemistry due to its intrinsic properties and merits. Efforts to create novel graphene based electrochemical biosensors have led to the establishment of effective strategies for diverse bioassays, from simple molecules to complex biotargets. In this Feature Article, we provide an overview of electrochemical biosensing with graphene related materials, and discuss the role of graphene in different sensing protocols.