Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods

The binding of transcription factors to DNA is one of the main mechanisms in gene regulation. While transcription factors frequently bind to unwrapped long DNA sequences known as open chromatin structures, most bioassays that study protein–DNA binding rely on short oligonucleotide probes. In this work, we develop a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After the determination of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance and compared it to other established techniques

Sensing of circulating cancer biomarkers with metal nanoparticles

The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future

Growth of anisotropic gold nanoparticles in photoresponsive fluid for UV sensing and erythema prediction

Aim: To develop a novel plasmonic nanosensing technique to monitor the exposure levels of UV light for sunlight disease prevention. Methods: Anisotropic gold nanoparticles were grown inside a UV photoresponsive fluid, which was previously exposed to UV radiation from different sources. The morphology and optical properties of the obtained nanoparticles were monitored by spectroscopy and microscopy. Results: The morphological and optical properties of the nanoparticles were dependent on the UV dose. The UV exposure levels were accurately correlated to the UV minimal doses to produce erythema to different skin types. Conclusion: This plasmonic nanosensing technique can be employed as novel sunlight-indexing tool for monitoring the dangerous level of skin exposure

Tunable plasmonic colorimetric assay with inverse sensitivity for extracellular DNA quantification

Extracellular DNA (eDNA) is a biomolecule commonly used to characterize microorganism communities in soil and aqueous environments. In this work we developed a gold nanorod (AuNR)-based colorimetric assay with inverse sensitivity and tunable dynamic range for eDNA. The effects of three key parameters, such as AuNR aspect ratio, DNA length and structure, have been identified allowing the assay to reach the detection levels necessary for the quantification of environmental eDNA

Characterization techniques for nanoparticles: comparison and complementarity upon studying nanoparticle properties

Nanostructures have attracted huge interest as a rapidly growing class of materials for many applications. Several techniques have been used to characterize the size, crystal structure, elemental composition and a variety of other physical properties of nanoparticles. In several cases, there are physical properties that can be evaluated by more than one technique. Different strengths and limitations of each technique complicate the choice of the most suitable method, while often a combinatorial characterization approach is needed. In addition, given that the significance of nanoparticles in basic research and applications is constantly increasing, it is necessary that researchers from separate fields overcome the challenges in the reproducible and reliable characterization of nanomaterials, after their synthesis and further process (e.g. annealing) stages. The principal objective of this review is to summarize the present knowledge on the use, advances, advantages and weaknesses of a large number of experimental techniques that are available for the characterization of nanoparticles. Different characterization techniques are classified according to the concept/group of the technique used, the information they can provide, or the materials that they are destined for. We describe the main characteristics of the techniques and their operation principles and we give various examples of their use, presenting them in a comparative mode, when possible, in relation to the property studied in each case

A plasmonic nanosensor with inverse sensitivity for circulating cell-free DNA quantification

A plasmonic nanosensor (using gold nanorods) with inverse sensitivity is presented for circulating cell-free DNA quantification. The inverse sensitivity (i.e. the lower the analyte concentration, the higher the response intensity) is achieved by the unusual DNA concentration-dependent gold nanorod aggregation. This assay method can adjust the dynamic range by controlling the concentration of nanoparticles in solution. Graphical abstract: A plasmonic nanosensor with inverse sensitivity for circulating cell-free DNA quantificatio

Fluorescence sensing of protein-DNA interactions using conjugated polyelectrolytes and graphene oxide

© 2018 Protein-DNA binding, particularly transcription factor-DNA binding, is one of the main molecular interactions involved in gene regulation. These interactions are sequence-specific, play a key role in many fundamental biological processes, and are deregulated in the pathogenesis of several diseases. In this study, a robust analytical bioassay to characterize protein-DNA binding was built by combining the optical properties of water soluble conjugated polyelectrolytes, and graphene oxide's superquenching capabilities. Cationic conjugated polyelectrolytes bind strongly to double stranded DNA through electrostatic interactions, and provide fluorescent signals to track the DNA without any chemical modification. In addition, the labeled DNA retains its protein binding ability. An important oncogenic transcription factor (i.e. estrogen receptor α) was used to demonstrate the concept, and two collaborative factors involved in the estrogen gene transcription (i.e. forkhead box A1 and activating enhancer binding protein 2 gamma) were employed as controls. This method overcame the main limitations of previous nanomaterial-based bioassays, while keeping the sensitivity and precision of the gold standard techniques. These benefits, combined with the high versatility and low-costs, could lead this bioassay to be used in several fundamental biomedical research lines, such as large scale protein-DNA binding studies and drug discovery

Fine-Tuning Gold Nanorods Dimensions and Plasmonic Properties Using the Hofmeister Salt Effects

Gold nanorods (Au NRs) present unique optical and electronic properties that depend on their morphology. Their applications in sensing and therapeutics require easy synthesis with precise control over their dimensions. Here, we report a method for the synthesis of highly pure and monodisperse Au NRs with fine-tuneable dimensions and longitudinal localised surface plasmon resonance by addition of Hofmeister salts into the growth medium. The control of Au NR formation relies on the double interaction between salt–gold and salt–surfactant (cetyl trimethylammonium bromide, CTAB). With the addition of Hofmeister salts (i.e. NaNO3, NaBr, NaCl and NaHSO4) we can fine-tune the aspect ratio of Au NRs in the range of 3.3 to 4.8 with a precision of 0.1 and the longitudinal absorption band from 777 to 960 nm. In addition, we have studied the physical changes in the CTAB micelles induced by the salts using rheology, electron microscopy and light-scattering techniques. We report for the first time cryo-electron microscopy imaging of the micelles under Au NR growth conditions. With the comprehensive characterization of CTAB micelles in the growth solution, this study provides a deeper understanding of the anisotropic growth of metallic crystals

Involvement of PPAR-γ in the neuroprotective and anti-inflammatory effects of angiotensin type 1 receptor inhibition: effects of the receptor antagonist telmisartan and receptor deletion in a mouse MPTP model of Parkinson's disease

<p>Abstract</p> <p>Background</p> <p>Several recent studies have shown that angiotensin type 1 receptor (AT1) antagonists such as candesartan inhibit the microglial inflammatory response and dopaminergic cell loss in animal models of Parkinson's disease. However, the mechanisms involved in the neuroprotective and anti-inflammatory effects of AT1 blockers in the brain have not been clarified. A number of studies have reported that AT1 blockers activate peroxisome proliferator-activated receptor gamma (PPAR γ). PPAR-γ activation inhibits inflammation, and may be responsible for neuroprotective effects, independently of AT1 blocking actions.</p> <p>Methods</p> <p>We have investigated whether oral treatment with telmisartan (the most potent PPAR-γ activator among AT1 blockers) provides neuroprotection against dopaminergic cell death and neuroinflammation, and the possible role of PPAR-γ activation in any such neuroprotection. We used a mouse model of parkinsonism induced by the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and co-administration of the PPAR-γ antagonist GW9662 to study the role of PPAR-γ activation. In addition, we used AT1a-null mice lesioned with MPTP to study whether deletion of AT1 in the absence of any pharmacological effect of AT1 blockers provides neuroprotection, and investigated whether PPAR-γ activation may also be involved in any such effect of AT1 deletion by co-administration of the PPAR-γ antagonist GW9662.</p> <p>Results</p> <p>We observed that telmisartan protects mouse dopaminergic neurons and inhibits the microglial response induced by administration of MPTP. The protective effects of telmisartan on dopaminergic cell death and microglial activation were inhibited by co-administration of GW9662. Dopaminergic cell death and microglial activation were significantly lower in AT1a-null mice treated with MPTP than in mice not subjected to AT1a deletion. Interestingly, the protective effects of AT1 deletion were also inhibited by co-administration of GW9662.</p> <p>Conclusion</p> <p>The results suggest that telmisartan provides effective neuroprotection against dopaminergic cell death and that the neuroprotective effect is mediated by PPAR-γ activation. However, the results in AT1-deficient mice show that blockage of AT1, unrelated to the pharmacological properties of AT1 blockers, also protects against dopaminergic cell death and neuroinflammation. Furthermore, the results show that PPAR-γ activation is involved in the anti-inflammatory and neuroprotective effects of AT1 deletion.</p

Deep Brain Stimulation of Nucleus Accumbens Region in Alcoholism Affects Reward Processing

The influence of bilateral deep brain stimulation (DBS) of the nucleus nucleus (NAcc) on the processing of reward in a gambling paradigm was investigated using H2[15O]-PET (positron emission tomography) in a 38-year-old man treated for severe alcohol addiction. Behavioral data analysis revealed a less risky, more careful choice behavior under active DBS compared to DBS switched off. PET showed win- and loss-related activations in the paracingulate cortex, temporal poles, precuneus and hippocampus under active DBS, brain areas that have been implicated in action monitoring and behavioral control. Except for the temporal pole these activations were not seen when DBS was deactivated. These findings suggest that DBS of the NAcc may act partially by improving behavioral control