Poly(D,L-lactide-co-glycolide acid) nanoparticles for DNA delivery: waiving preparation complexity and increasing efficiency

When designing a nonviral gene delivery system based on polymeric nanoparticles (NPs), it is important to keep in mind obstacles associated with future clinical applications. Simplifying the procedure of NPs production and taking toxicity into account are the most important issues that need to be addressed. Toxicity concerns in clinical trials may be raised when using additives such as cationic polymers/lipids, buffering reagents, and proteins. Therefore, the aim of this study was to simplify the formulation of poly (lactide-co-glycolide) acid NPs by shortening steps such as sonication time and by avoiding the use of additives while preserving its efficiency. NPs (300 nm) were formulated using a modified w/o/w technique with DNA entrapment efficiency of 80%. Once achieving such NPs, formulation parameters such as DNA loading, release kinetics, DNA integrity and bioactivity, uptake by cells, and toxicity were addressed. The NPs were readily taken by several cell lines and were localized mostly in their endo-lysosomal compartments. The NPs did not affect cells viability. Most importantly, transfection studies in COS-7 and Cf2th cells resulted with a 250-fold protein expression levels when compared with the control. These expression levels are higher than ones achieved with more complicated NPs systems, demonstrating the efficiency of our simplified NPs for gene delivery.     

Molecular interaction studies of zinc sulphide nanoparticles with DNA and its consequence: a multitechnique approach

Molecular interaction studies between nanoparticles (NPs) and biomolecules are of great importance in the field of nanomedicine as they affect many physiological processes. Therefore, the interaction of zinc sulphide nanoparticles (ZnS NPs) with calf thymus deoxyribonucleic acid (CT DNA) and its significance was analyzed using ultraviolet (UV)–visible light, fluorescence, circular dichroism (CD), zeta potential, viscometry, electrochemical, and polymerase chain reaction methods. Fluorescence quenching analysis revealed that the fluorescence of ZnS NPs was quenched using CT DNA through a static quenching mechanism. The negative values of thermodynamic parameters (ΔG, ΔH, and ΔS) showed that the binding process was spontaneous, exothermic, and van der Waals or hydrogen bonding plays an important role in the interaction of ZnS NPs with CT DNA. Thermal melting (T_m) studies indicated a decrease in the T_m of CT DNA, suggesting the destabilization of CT DNA upon interaction with ZnS NPs. In addition, the results obtained from competitive binding, zeta potential, CD, and viscometry measurements showed that the interaction of ZnS NPs with CT DNA is through groove binding. Electrochemical analysis further confirmed the observed results from various spectroscopic and other related studies, in which decrease in the redox peak current along with changes in peak potential (CV) and increase in the electrical resistance (EIS) indicated the interaction between ZnS NPs and CT DNA. Furthermore, PCR analysis using DNA polymerase revealed the potential of ZnS NPs to inhibit DNA replication in vitro. ZnS NP–CT DNA interaction studies can be explored to define new horizons in biomedical applications of ZnS NPs.     

DNAzyme-functionalized Pt nanoparticles/carbon nanotubes for amplified sandwich electrochemical DNA analysis

A novel DNAzyme-functionalized Pt nanoparticles/carbon nanotubes (DNAzyme/Pt NPs/CNTs) bioconjugate was fabricated as trace tag for ultrasensitive sandwich DNA detection. The Pt NPs/CNTs were prepared via layer-by-layer (LBL) assembly of the Pt NPs and polyelectrolyte on the carboxylated CNTs, followed by the functionalization with the DNAzyme and reporter probe DNA through the platinum-sulfur bonding. The subsequent sandwich-type DNA specific reaction would confine numerous DNAzyme/Pt NPs/CNTs bioconjugate onto the gold electrode surface for amplifying the signal. In the presence of 3,3',5,5' tetramethylbenzidine (TMB) which could be oxidized by the DNAzyme, electrochemical signals could be generated by chronoamperometry via the interrogation of reduction electrochemical signal of oxidized TMB. The constructed DNA sensor exhibited a wide linear response to target DNA ranging from 1.0fM to 10pM with the detection limit down to 0.6fM and exhibited excellent selectivity against even a single base mismatch. In addition, this novel DNA sensor showed fairly good reproducibility, stability, and reusability.     

Green synthesis and physiochemical characterization of nickel oxide nanoparticles: Interaction studies with Calf thymus DNA

One of the most promising applications of nanomaterials is that of nanobiosensors, using biomolecules such as nucleic acids as receptors. This study aimed to synthesize nickel oxide nanoparticles (NiO NPs) by an environmentally friendly green synthesis, using the extract of the herb Coriandrum sativum (coriander). The synthesized NPs were characterized using UV–Visible spectroscopy, Fourier transform infrared spectroscopy, X‐ray diffraction, X‐ray photon spectroscopy, field emission scanning electron microscopy coupled with energy dispersive spectroscopy, dynamic light scattering, zeta potential and transmission electron microscopy. All results confirmed the synthesis of pure, spherical, positively charged NiO NPs of around 95 nm in diameter with prominent hydroxyl groups attached to the surface. Furthermore, interaction studies of synthesized NiO NPs with calf thymus DNA (CT DNA) were performed using UV–Visible spectroscopy, UV–thermal melting, circular dichroism, and fluorescence spectroscopy. CT DNA served as a substitute for nucleic acid biosensors. All experimental studies indicated that the NiO NPs bound electrostatically with CT DNA. These studies may facilitate exploring the potential of NiO NP–nucleic acid conjugated materials to be used as nanobiosensors for various applications, especially in pharmacological, epidemiological, and environmental diagnostic applications, and in detection.     

Amplification of intermethylated sites experimental design and results analysis with <Emphasis Type="Italic">AIMS in silico</Emphasis> computer software

Amplification of intermethylated sites (AIMS) is a powerful tool for differential methylation screening of genomes. Its applications have nevertheless been limited until recently for the absence of systemic approach to AIMS experimental design and of appropriate computer software for the analysis of AIMS results. We have developed AIMS in silico computer suggestion tool capable of predicting possible experimental outcomes, which assists in designing AIMS experiments depending on the research aims and available instrumentation, and in analyzing experimental results from the point of view of genomic locations of the DNA fragments under study. With AIMS in silico we have characterized qualitatively and quantitatively AIMS products obtainable under different conditions; to ease experimental design we demonstrate AIMS products hierarchical structure. We discuss examples of designing AIMS experiments and of results analysis as well as possible relative to AIMS alternative approaches to differential methylation screening. AIMS in silico computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer epigenomes studies as well as towards diagnostics in oncology, including early screening.     

Alginic Acid-Coated Chitosan Nanoparticles Loaded with Legumain DNA Vaccine: Effect against Breast Cancer in Mice

Legumain-based DNA vaccines have potential to protect against breast cancer. However, the lack of a safe and efficient oral delivery system restricts its clinical application. Here, we constructed alginic acid-coated chitosan nanoparticles (A.C.NPs) as an oral delivery carrier for a legumain DNA vaccine. First, we tested its characteristic in acidic environments in vitro. DNA agarose electrophoresis data show that A.C.NPs protected DNA better from degradation in acidic solution (pH 1.5) than did chitosan nanoparticles (C.NPs). Furthermore, size distribution analysis showed that A.C.NPs tended to aggregate and form micrometer scale complexes in pH<2.7, while dispersing into nanoparticles with an increase in pH. Mice were intragastrically administrated A.C.NPs carrying EGFP plasmids and EGFP expression was detected in the intestinal Peyer’s patches. Full-length legumain plasmids were loaded into different delivery carriers, including C.NPs, attenuated Salmonella typhimurium and A.C.NPs. A.C.NPs loaded with empty plasmids served as a control. Oral vaccination was performed in the murine orthotopic 4T1 breast cancer model. Our data indicate that tumor volume was significantly smaller in groups using A.C.NPs or attenuated Salmonella typhimurium as carriers. Furthermore, splenocytes co-cultured them with 4T1 cells pre-stimulated with CoCl₂, which influenced the translocation of legumain from cytoplasm to plasma membrane, showed a 4.7 and 2.3 folds increase in active cytotoxic T lymphocytes (CD3⁺/CD8⁺/CD25⁺) when treated with A.C.NPs carriers compared with PBS C.NPs. Our study suggests that C.NPs coated with alginic acid may be a safe and efficient tool for oral delivery of a DNA vaccine. Moreover, a legumain DNA vaccine delivered orally with A.C.NPs can effectively improve autoimmune response and protect against breast cancer in mice.     

生物信息学在基因芯片中的应用

生物信息学和基因芯片是生命科学研究领域中的两种新方法和新技术,生物信息学与基因芯片密切相关,生物信息学促进了基因芯片的研究与应用,而基因芯片则丰富了生物信息学的研究内容。本论文探讨生物信息学在基因芯片中的应用,将生物信息学方法运用到高密度基因芯片设计和芯片实验数据管理及分析。从信息学的角度提出基因芯片设计准则,提出寡核苷酸探针的优化设计方法,将该方法运用于再测序型芯片和基因表达型芯片的设计,在此基础上研制出高密度基因芯片设计软件系统和实验结果分析系统。     

Green synthesis of strontium nanoparticles self‐assembled in the presence of carboxymethyl cellulose: an in vivo imaging study

Carboxymethyl cellulose (CMC) is one of the main derivatives of cellulose and is used as a drug carrier for hydrophobic and hydrophilic drugs, imaging in vivo, and biological applications. Encapsulation is a technology in which target compounds are coated with wall compounds to form microcapsules. This study reports a new chemical processing wet method for precipitation and encapsulation of strontium nanoparticles (Sr NPs) within CMC structures using a sonochemical method. Preparation parameters such as microwave power and irradiation time as well as morphology and particle size of Sr NPs were also investigated. Products were characterized by X‐ray diffraction, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis and atomic force microscopy. In this study, CMC was used as a biological stabilizer in a retentive phase to encapsulate Sr NPs. For the first time, Sr NPs were synthesized using CMC in a cost‐effective, simple, fast, micellation‐assisted, ultrasound method. Sr NPs were encapsulated in green capping agent structures of either 1%, 2% or 3% weight to provide an efficient optical nanostructure with a high yield at wavelengths 200–700 nm for use in in vivo imaging studies.     

Vital roles of sustainable nano-fertilizers in improving plant quality and quantity-an updated review

Nanotechnology has received much attention because of its distinctive properties and many applications in various fields. Nanotechnology is a new approach to increase agricultural production with premium quality, environmental safety, biological support, and financial stability. Ecofriendly technology is becoming progressively important in modern agricultural applications as alternatives to traditional fertilizers and pesticides. Nanotechnology offers an alternative solution to overcome the disadvantages of conventional agriculture. Therefore, recent developments in using nanoparticles (NPs) in agriculture should be studied. This review presented a novel overview about the biosynthesis of NPs, using NPs as nano-fertilizers and nano-pesticides, the applications of NPs in agriculture, and their role in enhancing the function of biofactors. We also, show recent studies on NPs-plant interactions, the fate and safety of nanomaterials in plants, and NPs' function in alleviating the adverse effects of abiotic stress and heavy metal toxicity. Nano-fertilizers are essential to reduce the use of inorganic fertilizers and reduce their antagonistic effects on the environment. Nano-fertilizers are more reactive, can penetrate the epidermis allowing for gradual release, and targeted distribution, and thus reducing nutrients surplus, enhancing nutrient use efficiency. We also, concluded that NPs are crucial in alleviating abiotic stress and heavy metal toxicity. However, some studies reported the toxic effects of NPs on higher plants by induction of oxidative stress signals via depositing NPs on the cell surface and in organelles. The knowledge in our review article is critical in defining limitations and future perspectives of using nano-fertilizers as an alternative to conventional fertilizers.     

Functionalized positive nanoparticles reduce mucin swelling and dispersion

Multi-functionalized nanoparticles (NPs) have been extensively investigated for their potential in household and commercial products, and biomedical applications. Previous reports have confirmed the cellular nanotoxicity and adverse inflammatory effects on pulmonary systems induced by NPs. However, possible health hazards resulting from mucus rheological disturbances induced by NPs are underexplored. Accumulation of viscous, poorly dispersed, and less transportable mucus leading to improper mucus rheology and dysfunctional mucociliary clearance are typically found to associate with many respiratory diseases such as asthma, cystic fibrosis (CF), and COPD (Chronic Obstructive Pulmonary Disease). Whether functionalized NPs can alter mucus rheology and its operational mechanisms have not been resolved. Herein, we report that positively charged functionalized NPs can hinder mucin gel hydration and effectively induce mucin aggregation. The positively charged NPs can significantly reduce the rate of mucin matrix swelling by a maximum of 7.5 folds. These NPs significantly increase the size of aggregated mucin by approximately 30 times within 24 hrs. EGTA chelation of indigenous mucin crosslinkers (Ca(2+) ions) was unable to effectively disperse NP-induced aggregated mucins. Our results have demonstrated that positively charged functionalized NPs can impede mucin gel swelling by crosslinking the matrix. This report also highlights the unexpected health risk of NP-induced change in mucus rheological properties resulting in possible mucociliary transport impairment on epithelial mucosa and related health problems. In addition, our data can serve as a prospective guideline for designing nanocarriers for airway drug delivery applications.     

Monte Carlo simulation of gold nanoparticles for X-ray enhancement application

BackgroundGold nanoparticles (Au NPs) are regarded as potential agents that enhance the radiosensitivity of tumor cells for theranostic applications. To elucidate the biological mechanisms of radiation dose enhancement effects of Au NPs as well as DNA damage attributable to the inclusion of Au NPs, Monte Carlo (MC) simulations have been deployed in a number of studies.Scope of ReviewThis review paper concisely collates and reviews the information reported in the simulation research in terms of MC simulation of radiosensitization and dose enhancement effects caused by the inclusion of Au NPs in tumor cells, simulation mechanisms, benefits and limitations.Major conclusionsIn this review, we first explore the recent advances in MC simulation on Au NPs radiosensitization. The MC methods, physical dose enhancement and enhanced chemical and biological effects is discussed, followed by some results regarding the prediction of dose enhancement. We then review Multi-scale MC simulations of Au NP-induced DNA damages for X-ray irradiation. Moreover, we explain and look at Multi-scale MC simulations of Au NP-induced DNA damages for X-ray irradiation.General significanceUsing advanced chemical module-implemented MC simulations, there is a need to assess the radiation-induced chemical radicals that contribute to the dose-enhancing and biological effects of multiple Au NPs.     

Induction of oxidative stress, lysosome activation and autophagy by nanoparticles in human brain-derived endothelial cells

Different types of NPs (nanoparticles) are currently under development for diagnostic and therapeutic applications in the biomedical field, yet our knowledge about their possible effects and fate in living cells is still limited. In the present study, we examined the cellular response of human brain-derived endothelial cells to NPs of different size and structure: uncoated and oleic acid-coated iron oxide NPs (8-9 nm core), fluorescent 25 and 50 nm silica NPs, TiO2 NPs (21 nm mean core diameter) and PLGA [poly(lactic-co-glycolic acid)]-PEO [poly(ethylene oxide)] polymeric NPs (150 nm). We evaluated their uptake by the cells, and their localization, generation of oxidative stress and DNA-damaging effects in exposed cells. We show that NPs are internalized by human brain-derived endothelial cells; however, the extent of their intracellular uptake is dependent on the characteristics of the NPs. After their uptake by human brain-derived endothelial cells NPs are transported into the lysosomes of these cells, where they enhance the activation of lysosomal proteases. In brain-derived endothelial cells, NPs induce the production of an oxidative stress after exposure to iron oxide and TiO2 NPs, which is correlated with an increase in DNA strand breaks and defensive mechanisms that ultimately induce an autophagy process in the cells.     

Preparation, characterization and transfection efficiency of cationic PEGylated PLA nanoparticles as gene delivery systems

The cationic polylactic acid (PLA) nanoparticle has emerged as a promising non-viral vector for gene delivery because of its biocompatibility and biodegradability. However, they are not capable of prolonging gene transfer and high transfection efficiency. In order to achieve prolonged delivery of cationic PLA/DNA complexes and higher transfection efficiency, in this study, we used copolymer methoxypolyethyleneglycol-PLA (MePEG-PLA), PLA and chitosan (CS) to prepare MePEG-PLA-CS NPs and PLA-CS NPs by a diafiltration method and prepared NPs/DNA complexes through the complex coacervation of nanoparticles with the pDNA. The object of our work is to evaluate the characterization and transfection efficiency of MePEG-PLA-CS versus PLA-CS NPs. The MePEG-PLA-CS NPs have a zeta potential of 15.7 mV at pH 7.4 and size under 100 nm, while the zeta potential of PLA-CS NPs was only 4.5 mV at pH 7.4. Electrophoretic analysis suggested that both MePEG-PLA-CS NPs and PLA-CS NPs with positive charges could protect the DNA from nuclease degradation and cell viability assay showed MePEG-PLA-CS NPs exhibit a low cytotoxicity to normal human liver cells. The potential of PLA-CS NPs and MePEG-PLA-CS NPs as a non-viral gene delivery vector to transfer exogenous gene in vitro and in vivo were examined. The pDNA being carried by MePEG-PLA-CS NPs, PLA-CS NPs and lipofectamine could enter and express in COS7 cells. However, the transfection efficiency of MePEG-PLA-CS/DNA complexes was better than PLA-CS/DNA and lipofectamine/DNA complexes by inversion fluorescence microscope and flow cytometry. It was distinctively to find that the transfection activity of PEGylation of complexes was improved. The nanoparticles were also tested for their ability to transport across the gastrointestinal mucosa in vivo in mice. In vivo experiments showed obviously that MePEG-PLA-CS/DNA complexes mediated higher gene expression in stomach and intestine of BALB/C mice compared to PLA-CS/DNA and lipofectamine/DNA complexes. These results suggested that MePEG-PLA-CS NPs have favorable properties for non-viral gene delivery.     

Silencing gene expression by targeting chromosomal DNA with antigene peptide nucleic acids and duplex RNAs

The value of recognizing cellular RNA sequences by short interfering RNAs (siRNAs) in mammalian cells is widely appreciated, but what might be learned if it were also possible to recognize chromosomal DNA? Recognition of chromosomal DNA would have many applications, such as inhibiting gene expression, activating gene expression, introducing mutations, and probing chromosome structure and function. We have shown that antigene peptide nucleic acids (agPNAs) and antigene duplex RNAs (agRNAs) block gene expression and probe chromosomal DNA. Here we describe a protocol for designing antigene agents and introducing them into cells. This protocol can also be used to silence expression with PNAs or siRNAs that target mRNA. From preparation of oligomers to analysis of data, experiments with agPNAs and agRNAs require approximately 14 d and 9 d, respectively.     

Application of nanoparticles in cancer therapy with an emphasis on cell cycle

Owing to their unique characteristics, nanoparticles (NPs) could be incorporated into valuable therapeutic modalities for different diseases; however, there are many concerns about risk factors in human applications. NPs carry therapeutic chemicals that could improve the outcome of cancer therapies. Nowadays, NPs are being recognized as important and strategic agents in treatment of several disorders due to their unique properties in targeting malignant cells in tumor sites. Numerous investigations have shown that the majority of chemotherapeutic agents can be modified through entrapment in submicron colloidal systems. Still, there are problems and limitations in application of NPs in cancer therapy. The aim of the present study is to focus on potential NPs usage in cancer treatment with an emphasis on the cell cycle of malignant cells.     

Electrochemical aptamer-based sensors

The valuable properties of aptamers, such as specificity, sensitivity, stability, cost-effectiveness and design flexibility, have favoured their use as biorecognition elements in biosensor development. These synthetic affinity probes can be developed for almost any target molecule, covering a wide range of applications in fields such as clinical diagnosis and therapy, environmental monitoring and food control. The combination of aptamers with high-performance electrochemical transducers, with their inherent high sensitivities, fast response times and simple equipment, has already provided several electrochemical aptamer-based sensors. Moreover, the small size and versatility of aptamers allow efficient immobilisations in high-density monolayers, an important feature towards miniaturisation and integration of compact electrochemical devices. This review describes the state-of-the-art of electrochemical aptamer-based sensors, entering into the details of the different strategies and types of electrochemical transduction and also considering their advantages when applied to the analysis of complex matrices.     

Impacts of a Silver‐Coated Future

Silver is a compound that is well known for its adverse environmental effects. More recently, silver in the form of silver nanoparticles (Ag NPs) has begun to be produced in increasingly larger amounts for antibacterial purposes in, for instance, textiles, wound dressings, and cosmetics. Several authors have highlighted the potential environmental impact of these NPs. To contribute to a risk assessment of Ag NPs, we apply a suggested method named “particle flow analysis” to estimating current emissions from society to the environment. In addition, we set up explorative scenarios to account for potential technology diffusion of selected Ag NP applications. The results are uncertain and need to be refined, but they indicate that emissions from all applications included may increase significantly in the future. Ag NPs in textiles and electronic circuitry may increase more than in wound dressings due to the limited consumption of wound dressings. Due to the dissipative nature of Ag NPs in textiles, the results indicate that they may cause the highest emissions in the future, thus partly confirming the woes of both scientists and environmental organizations. Gaps in current knowledge are identified. In particular, the fate of Ag NPs during different waste‐handling processes is outlined as an area that requires more research.     

Deletion of the Hoc and Soc capsid proteins affects the surface and cellular uptake properties of bacteriophage T4 derived nanoparticles

Recently the use of engineered viral scaffolds in biotechnology and medical applications has been increasing dramatically. T4 phage capsid derived nanoparticles (NPs) have potential advantages as sensors and in biotechnology. These applications require that the physical properties and cellular uptake of these NPs be understood. In this study we used a T4 deletion mutant to investigate the effects of removing both the Hoc and Soc proteins from the capsid surface on T4 tailless NPs. The surface charge, zeta potential, size, and cellular uptake efficiencies for both the T4 NP and T4ΔHocΔSoc NP mutant were measured and compared using dynamic light scattering and flow cytometry and significant differences were detected.     

Inorganic nanoparticle-based contrast agents for molecular imaging

Inorganic nanoparticles (NPs) including semiconductor quantum dots (QDs), iron oxide NPs and gold NPs have been developed as contrast agents for diagnostics by molecular imaging. Compared with traditional contrast agents, NPs offer several advantages: their optical and magnetic properties can be tailored by engineering the composition, structure, size and shape; their surfaces can be modified with ligands to target specific biomarkers of disease; the contrast enhancement provided can be equivalent to millions of molecular counterparts; and they can be integrated with a combination of different functions for multimodal imaging. Here, we review recent advances in the development of contrast agents based on inorganic NPs for molecular imaging, and also touch on contrast enhancement, surface modification, tissue targeting, clearance and toxicity. As research efforts intensify, contrast agents based on inorganic NPs that are highly sensitive, target-specific and safe to use are expected to enter clinical applications in the near future.     

Compressive Sensing DNA Microarrays

Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.