Isoelectric characteristics and the secondary structure of some nucleic acids

Fabrication of electrospun ion exchanger adsorbents with morphologies designed for the separation of proteins and plasmid DNA

Electrospun cellulose adsorbents are an emergent class of materials applied to a variety of bioprocess separations as an analogue to conventional packed bed chromatography. Electrospun adsorbents have proven to be effective as rapid cycling media, enabling high throughput separation of proteins and viral vectors without compromising selectivity and recovery. However, there is a current lack of knowledge in relation to the manipulation and control of electrospun adsorbent structure with function and performance to cater to the separation needs of emerging, diverse biological products. In this study, a series of electrospun cellulose adsorbents were fabricated by adjusting their manufacturing conditions. A range of fiber diameters (400 to 600 nm) was created by changing the electrospinning polymer solution. Additionally, a range of porosities (0.4 to 0.7 v/v) was achieved by varying the laminating pressures on the electrospun sheets. The adsorbents were functionalized with different degrees of quaternary amine ligand density to create 18 prototype anion exchangers. Their morphology was characterized by BET nitrogen adsorption surface area, X-ray computed tomography, capillary flow porometry and scanning electron microscopy measurements. The physical characteristics of the adsorbents were used in an adapted semi-empirical model and compared to measured permeability data. Permeabilities of prototypes ranged from 10-2 to 10-4 mDarcy. The measured data showed good adherence to modelled data with possible improvements in acquiring wet adsorbent characteristics instead of dried material. Finally, the electrospun adsorbents were characterized for their binding capacity of model proteins of different sizes (diameters of 3.5 nm and 8.9 nm) and plasmid DNA. Static binding capacities ranged from 5 mg/ml to 25 mg/ml for the proteins and plasmid DNA and showed <20 % deviation from monolayer coverage based on BET surface area. Therefore, it was concluded that the electrospun adsorbents most likely adsorb monolayers of proteins and plasmid DNA on the surface with minimal steric hindrance.

Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation

The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.

Electrochemically-gated graphene broadband microwave waveguides for ultrasensitive biosensing

Identification of non-amplified DNA sequences and single-base mutations is essential for molecular biology and genetic diagnostics. This paper reports a novel sensor consisting of electrochemically-gated graphene coplanar waveguides coupled with a microfluidic channel. Upon exposure to analytes, propagation of electromagnetic waves in the waveguides is modified as a result of interactions with the fringing field and modulation of graphene dynamic conductivity resulting from electrostatic gating. Probe DNA sequences are immobilised on the graphene surface, and the sensor is exposed to DNA sequences which either perfectly match the probe, contain a single-base mismatch or are unrelated. By monitoring the scattering parameters at frequencies between 50 MHz and 50 GHz, unambiguous and reproducible discrimination of the different strands is achieved at concentrations as low as one attomole per litre (1 aM). By controlling and synchronising frequency sweeps, electrochemical gating, and liquid flow in the microfluidic channel, the sensor generates multidimensional datasets. Advanced data analysis techniques are utilised to take full advantage of the richness of the dataset. A classification accuracy >97% between all three sequences is achieved using different Machine Learning models, even in the presence of simulated noise and low signal-to-noise ratios. The sensor exceeds state-of-the-art sensitivity of field-effect transistors and microwave sensors for the identification of single-base mismatches.

Exploiting endocytosis for transfection of mRNA for cytoplasmatic delivery using cationic gold nanoparticles

Introduction

Gene therapy holds promise to cure various diseases at the fundamental level. For that, efficient carriers are needed for successful gene delivery. Synthetic 'non-viral' vectors, as cationic polymers, are quickly gaining popularity as efficient vectors for transmitting genes. However, they suffer from high toxicity associated with the permeation and poration of the cell membrane. This toxic aspect can be eliminated by nanoconjugation. Still, results suggest that optimising the oligonucleotide complexation, ultimately determined by the size and charge of the nanovector, is not the only barrier to efficient gene delivery.

Methods

We herein develop a comprehensive nanovector catalogue comprising different sizes of Au NPs functionalized with two different cationic molecules and further loaded with mRNA for its delivery inside the cell.

Results and Discussion

Tested nanovectors showed safe and sustained transfection efficiencies over 7 days, where 50 nm Au NPs displayed the highest transfection rates. Remarkably, protein expression was increased when nanovector transfection was performed combined with chloroquine. Cytotoxicity and risk assessment demonstrated that nanovectors are safe, ascribed to lesser cellular damage due to their internalization and delivery via endocytosis. Obtained results may pave the way to design advanced and efficient gene therapies for safely transferring oligonucleotides.

Effect of DNA Aptamer Concentration on the Conductivity of a Water-Gated Al:ZnO Thin-Film Transistor-Based Biosensor

Field-effect transistor-based biosensors (bio-FETs) are promising candidates for the rapid high-sensitivity and high-selectivity sensing of various analytes in healthcare, clinical diagnostics, and the food industry. However, bio-FETs still have several unresolved problems that hinder their technological transfer, such as electrical stability. Therefore, it is important to develop reliable, efficient devices and establish facile electrochemical characterization methods. In this work, we have fabricated a flexible biosensor based on an Al:ZnO thin-film transistor (TFT) gated through an aqueous electrolyte on a polyimide substrate. In addition, we demonstrated techniques for establishing the operating range of such devices. The Al:ZnO-based devices with a channel length/width ratio of 12.35 and a channel thickness of 50 nm were produced at room temperature via magnetron sputtering. These Al:ZnO-based devices exhibited high field-effect mobility (μ = 6.85 cm2/Vs) and threshold voltage (Vth = 654 mV), thus showing promise for application on temperature-sensitive substrates. X-ray photoelectron spectroscopy was used to verify the chemical composition of the deposited films, while the morphological aspects of the films were assessed using scanning electron and atomic force microscopies. The gate-channel electric capacitance of 40 nF/cm2 was determined using electrochemical impedance spectroscopy, while the electrochemical window of the gate-channel system was determined as 1.8 V (from -0.6 V to +1.2 V) using cyclic voltammetry. A deionized water solution of 10 mer (CCC AAG GTC C) DNA aptamer (molar weight -2972.9 g/mol) in a concentration ranging from 1-1000 pM/μL was used as an analyte. An increase in aptamer concentration caused a proportional decrease in the TFT channel conductivity. The techniques demonstrated in this work can be applied to optimize the operating parameters of various semiconductor materials in order to create a universal detection platform for biosensing applications, such as multi-element FET sensor arrays based on various composition nanostructured films, which use advanced neural network signal processing.

Adsorption of double-stranded ribonucleic acids (dsRNA) to iron (oxyhydr-)oxide surfaces: comparative analysis of model dsRNA molecules and deoxyribonucleic acids (DNA)

Double-stranded ribonucleic acid (dsRNA) molecules are novel plant-incorporated protectants expressed in genetically modified RNA interference (RNAi) crops. Ecological risk assessment (ERA) of RNAi crops requires a heretofore-missing detailed understanding of dsRNA adsorption in soils, a key fate process. Herein, we systematically study the adsorption of a model dsRNA molecule and of two double-stranded deoxyribonucleic acid (DNA) molecules of varying lengths to three soil iron (oxyhydr-)oxides - goethite, lepidocrocite, and hematite - over a range of solution pH (4.5-10), ionic strength (I = 10-100 mM NaCl) and composition (0.5, 1, and 3 mM MgCl2) and in the absence and presence of phosphate (0.05-5 mM) as co-adsorbate. We hypothesized comparable adsorption characteristics of dsRNA and DNA based on their structural similarities. Consistently, the three nucleic acids (NAs) showed high adsorption affinities to the iron (oxyhydr-)oxides with decreasing adsorption in the order goethite, lepidocrocite, and hematite, likely reflecting a decrease in the hydroxyl group density and positive charges of the oxide surfaces in the same order. NA adsorption also decreased with increasing solution pH, consistent with weakening of NA electrostatic attraction to and inner-sphere complex formation with the iron (oxyhydr-)oxides surfaces as pH increased. Adsorbed NA concentrations increased with increasing I and in the presence of Mg2+, consistent with adsorbed NA molecules adopting more compact conformations. Strong NA-phosphate adsorption competition demonstrates that co-adsorbates need consideration in assessing dsRNA fate in soils. Comparable adsorption characteristics of dsRNA and DNA molecules to iron (oxyhydr-)oxides imply that information on DNA adsorption to soil particle surfaces can inform dsRNA ERA.

Assessment of 1/f noise associated with nanopores fabricated through chemically tuned controlled dielectric breakdown

Recently, we developed a fabrication method-chemically-tuned controlled dielectric breakdown (CT-CDB)-that produces nanopores (through thin silicon nitride membranes) surpassing legacy drawbacks associated with solid-state nanopores (SSNs). However, the noise characteristics of CT-CDB nanopores are largely unexplored. In this work, we investigated the 1/f noise of CT-CDB nanopores of varying solution pH, electrolyte type, electrolyte concentration, applied voltage, and pore diameter. Our findings indicate that the bulk Hooge parameter (α_b ) is about an order of magnitude greater than SSNs fabricated by transmission electron microscopy (TEM) while the surface Hooge parameter (α_s ) is ∼3 order magnitude greater. Theα_s of CT-CDB nanopores was ∼5 orders of magnitude greater than theirα_b , which suggests that the surface contribution plays a dominant role in 1/f noise. Experiments with DNA exhibited increasing capture rates with pH up to pH ∼8 followed by a drop at pH ∼9 perhaps due to the onset of electroosmotic force acting against the electrophoretic force. The1/f noise was also measured for several electrolytes and LiCl was found to outperform NaCl, KCl, RbCl, and CsCl. The 1/f noise was found to increase with the increasing electrolyte concentration and pore diameter. Taken together, the findings of this work suggest the pH approximate 7-8 range to be optimal for DNA sensing with CT-CDB nanopores.

Aptamer-Based Affinity Chromatography for Protein Extraction and Purification

Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.

Reversibly pH-responsive gold nanoparticles and their applications for photothermal cancer therapy

Microenvironment responsive nanomaterials are attractive for therapeutic applications with regional specificity. Here we report pH responsive gold nanoparticles which are designed to aggregate in acidic condition similar to cancer environment and returned to its original disassembled states in a physiological pH. The pH responsive behavior of the particles is derived by change of electrostatic interaction among the particles where attraction and repulsion play a major role in low and high pH of the environment, respectively. Since different electrostatic interaction behavior of the particles in varied pH is induced not by irreversible chemical change but by simple protonation differences, the pH responsive process of assembly and disassembly is totally reversible. The low pH specific aggregation of gold nanoparticles resulted in red shift of plasmonic absorption peak and showed higher photothermal efficacy in acidic pH than in normal physiological pH. The low pH specific photothermal effect with long wave laser irradiation was directly applied to cancer specific photothermal therapy and resulted higher therapeutic effect for melanoma cancer cells than non-pH responsive gold nanoparticles.

Citrate-assisted efficient local delivery of naked oligonucleotide into live mouse brain cells

Objectives

Synthetic oligonucleotides have shown promise in brain imaging. However, delivery of oligonucleotides into live brain cells remains challenging. In this study, we aim to develop a facile yet efficient strategy for local delivery of oligodeoxynucleotide (ODN) to neural cells in live adult mouse brain.

Materials and methods

A fluorescence‐labelled ODN was diluted with sodium citrate buffer (100 mmol/L, pH = 3). One microlitre of the mixture was injected into a live adult mouse brain. Six hours later, we sacrificed the mouse and prepared brain slices for microscopic imaging.

Results

We find that the use of sodium citrate buffer in the one‐shot local delivery can improve the diffusion and cell entry efficiency of the unmodified ODN for dozens of times. Only 1 pmol ODN leads to hundreds of positively transferred brain cells. We reason that this promotion is due to the local acidic condition created by the citrate buffer, which leads to the protonation of the ODN and some membrane proteins, thus reduces the Coulomb repulsion between the ODN and the cell membrane. Based on this strategy, we demonstrate fluorescent microscopic imaging of brain cells in different brain regions including striatum, cortex, hippocampus and midbrain.

Conclusions

The citrate buffer can be used as an adjuvant for facile and effective local injection delivery of ODNs, which may provide a new tool for brain imaging.

Attomolar Label-Free Detection of DNA Hybridization with Electrolyte-Gated Graphene Field-Effect Transistors

In this work, we develop a field-effect transistor with a two-dimensional channel made of a single graphene layer to achieve label-free detection of DNA hybridization down to attomolar concentration, while being able to discriminate a single nucleotide polymorphism (SNP). The SNP-level target specificity is achieved by immobilization of probe DNA on the graphene surface through a pyrene-derivative heterobifunctional linker. Biorecognition events result in a positive gate voltage shift of the graphene charge neutrality point. The graphene transistor biosensor displays a sensitivity of 24 mV/dec with a detection limit of 25 aM: the lowest target DNA concentration for which the sensor can discriminate between a perfect-match target sequence and SNP-containing one.

Solid lipid nanoparticles release DNA upon endosomal acidification in human embryonic kidney cells

Nanotechnology can produce materials with unique features compared to their bulk counterparts, which can be useful for medical applications (i.e. nanomedicine). Among the therapeutic agents used in nanomedicine, small molecules or biomacromolecules, such as proteins or genetic materials, can be designed for disease diagnostics and treatment. To transport these biomacromolecules to the target cells, nanomedicine requires nanocarriers. Solid lipid nanoparticles (SLNs) are among the promising nanocarriers available, because they can be made from biocompatible materials and present high stability (over one year). In addition, upon the binding genetic material, SLNs form SLNplexes. However, little is yet known about how cells process these SLNplexes-in particular, how internalization and endosome acidification affects the transfection mediated by SLNplexes. Therefore, we aim to investigate how these processes affect SLNplex transfection in HEK293T cells. We find that the SLNplex is mainly internalized by clathrin-mediated endocytosis, which is a fast and reliable pathway to transfection, leading to approximately 60% transfection efficiency. Interestingly, upon acidification (below pH 5.0), the SLN seems to release its DNA content, which can be an essential step for SLNplex transfection. The underlying mechanisms described in this work may help improve SLNplex formulations and transfection efficiency. Moreover, these advances can improve the field of nanomedical research and bring new ways to cure diseases.

Assembly and Immunological Processing of Polyelectrolyte Multilayers Composed of Antigens and Adjuvants

While biomaterials provide a platform to control the delivery of vaccines, the recently discovered intrinsic inflammatory characteristics of many polymeric carriers can also complicate rational design because the carrier itself can alter the response to other vaccine components. To address this challenge, we recently developed immune-polyelectrolyte multilayer (iPEMs) capsules electrostatically assembled entirely from peptide antigen and molecular adjuvants. Here, we use iPEMs built from SIINFEKL model antigen and polyIC, a stimulatory toll-like receptor agonist, to investigate the impact of pH on iPEM assembly, the processing and interactions of each iPEM component with primary immune cells, and the role of these interactions during antigen-specific T cell responses in coculture and mice. We discovered that iPEM assembly is pH dependent with respect to both the antigen and adjuvant component. Controlling the pH also allows tuning of the relative loading of SIINFEKL and polyIC in iPEM capsules. During in vitro studies with primary dendritic cells (DCs), iPEM capsules ensure that greater than 95% of cells containing at least one signal (i.e., antigen, adjuvant) also contained the other signal. This codelivery leads to DC maturation and SIINFEKL presentation via the MHC-I antigen presentation pathway, resulting in antigen-specific T cell proliferation and pro-inflammatory cytokine secretion. In mice, iPEM capsules potently expand antigen-specific T cells compared with equivalent admixed formulations. Of note, these enhancements become more pronounced with successive booster injections, suggesting that iPEMs functionally improve memory recall response. Together our results reveal some of the features that can be tuned to modulate the properties of iPEM capsules, and how these modular vaccine structures can be used to enhance interactions with immune cells in vitro and in mice.

Interfacial biomimetic synthesis of silica nanocapsules using a recombinant catalytic modular protein

This paper reports interfacially driven synthesis of oil-core silica-shell nanocapsules using a rationally designed recombinant catalytic modular protein (ReCaMoP), in lieu of a conventional chemical surfactant. A 116-residue protein, D4S2, was designed by modularizing a surface-active protein module having four-helix bundle structure in bulk and a biosilicification-active peptide module rich in cationic residues. This modular combination design allowed the protein to be produced via the industrially relevant cell factory Escherichia coli with simplified purification conferred by thermostability engineered in design. Dynamic interfacial tension and thin film pressure balance were used to gain an overview of the protein behavior at macroscopic interfaces. Functionalities of D4S2 to make silica nanocapsules were demonstrated by facilitating formation and stabilization of pharmaceutically grade oil droplets through its surface-active module and then by directing nucleation and growth of a silica shell at the oil-water interface through its biosilicification-active module. Through these synergistic activities in D4S2, silica nanocapsules could be formed at near-neutral pH and ambient temperature without using any organic solvents that might have negative environmental and sustainability impacts. This work introduces parallelization of biomolecular, scale-up and interfacial catalytic design strategies for the ultimate development of sustainable and scalable production of a recombinant modular protein that is able to catalyze synthesis of oil-filled silica nanocapsules under environmentally friendly conditions, suitable for use as controlled-release nanocarriers of various actives in biomedical and agricultural applications.

Cotranslational protein folding within the ribosome tunnel influences trigger-factor recruitment

In recent years, various folding zones within the ribosome tunnel have been identified and explored through x-ray, cryo-electron microscopy (cryo-EM), and molecular biology studies. Here, we generated ribosome-bound nascent polypeptide complexes (RNCs) with different polyalanine (poly-A) inserts or signal peptides from membrane/secretory proteins to explore the influence of nascent chain compaction in the Escherichia coli ribosome tunnel on chaperone recruitment. By employing time-resolved fluorescence resonance energy transfer and immunoblotting, we were able to show that the poly-A inserts embedded in the passage tunnel can form a compacted structure (presumably helix) and reduce the recruitment of Trigger Factor (TF) when the helical motif is located in the region near the tunnel exit. Similar experiments on nascent chains containing signal sequences that may form compacted structural motifs within the ribosome tunnel and lure the signal recognition particle (SRP) to the ribosome, provided additional evidence that short, compacted nascent chains interfere with TF binding. These findings shed light on the possible controlling mechanism of nascent chains within the tunnel that leads to chaperone recruitment, as well as the function of L23, the ribosomal protein that serves as docking sites for both TF and SRP, in cotranslational protein targeting.