DNA-based applications in nanobiotechnology

Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review

DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.

A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches

In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.

Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives

DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.

Experimental and theoretical approaches to interactions between DNA and purine metabolism products

Deoxyribonucleic acid (DNA) is a significant target for small organic and inorganic drug molecules. Understanding the DNA interaction mechanism of these molecules is vital for new drug designs. In this work, interactions between xanthine (XT), theophylline (TP), and theobromine (TB) with calf-thymus double-strained DNA (dsDNA) were monitored via an experimental and theoretical approach. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used on the surface of the NiO/MWCNT/NNaM/PGE electrochemical platform in vitro. Kinetic parameters, including diffusion coefficients, surface concentrations, and standard heterogeneous rate constants, were measured in the absence and presence of DNA using scan rate studies. In the presence of DNA, kinetic parameters were observed to be reduced significantly. Thermodynamic parameters, such as DNA binding constants and standard free Gibbs energies, were calculated for each molecule using the CV and DPV techniques. Both techniques suggested a binding affinity order of XT > TB > TP. Theoretically, density functional theory was applied for geometry optimization, natural bond orbital analyses, and molecular orbital energies of XT, TP, and TB. Experimental and theoretical binding affinities confirm each other. The most energetically stable ligand-DNA complexes expressed that XT, TP, and TB interact with dsDNA via minor groove binding mode, using mostly hydrogen bonds.

Sugar based cationic magnetic core-shell silica nanoparticles for nucleic acid extraction

Nucleic acid (NA) extraction is an essential step in molecular testing for a wide range of applications. Conventional extraction protocols usually suffer from time consuming removal of non-nucleic acid impurities. In this study, a new magnetic nanoparticle (MNP) is presented to simplify the NA extraction. A core–shell design, comprising of a ferromagnetic core coated with mesoporous silica, forms the basis of the functional nanoparticle. Chemical functionalization of the silica coating includes a multistep synthesis, in which an activated nanoparticle is coupled with a triethylene glycol spaced glycosyl imidazole. The molecular design aims for charge interactions between the imidazolium-based positive nanoparticle surface and nucleic acids, with specific hydrogen bonding between the surface bonded carbohydrate and nucleic acid targets to ensure nucleic acid selectivity and avoid protein contamination. Two different carbohydrates, differing in molecular size, were selected to compare the efficiency in terms of NA extraction. A triethylene glycol spacer provides sufficient flexibility to remove particle surface constraints for the interaction. The Brunauer–Emmett–Teller (BET) analysis shows a significantly larger surface area for the disaccharide-based particles NpFeSiImMalt (∼181 m² g⁻¹) compared to the monosaccharide analogue NpFeSiImGlc (∼116 m² g⁻¹) at small particles sizes (range ∼ 15 nm) and sufficient magnetization (29 emu g⁻¹) for easy isolation by an external magnetic field. The particles enabled a high DNA particle loading ratio of 30–45 wt% (MNP/DNA ratio), reflecting an efficient extraction process. A high desorption rate (7 min) with more than 86% of unchanged DNA loading was recorded, indicating low damage to the target extract.

New design of cationic magnetic core–shell nanoparticles fabricated with a large hydrophilic group (carbohydrate molecules) enabled high adsorption of a nucleic acid, easy isolation and controlled the movement by applying an external magnetic field.

Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics

Protein-protein ligand is one of the most detection methods used in Nano biosensors. Based on the advantage of specific docking between two special 3D structures, they have become a potent candidate in bioanalysis and Nanodiagnostic tools. These tools lease users to do a simple, fast, cost-effective, sensitive, and specific detection of molecular biomarkers in real samples. Recent advantages of using protein-protein ligand Nano-biosensors application is remarkable due to its special docking that refers to each protein unique 3D conformation. However, it challenges different problems such as low rate of docking and hard process for fixation on the basic layer. These challenges make developers to optimize the structure and functions of proteins. The process has different Nano scale calculation that could be done with algorithms and solutions are available as bioinformatics tools. This article aimed to have a short overview of the abilities of bioinformatics tools for modeling and optimization of physiochemical features of proteins in Nano scale.

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Nano biosensors use different strategies which based on docking between two molecules to detect and identify different proteins.

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Molecular docking between transducer in Nano biosensors and proteins rely on physicochemical features of transducer, protein and docking strategy.

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Nano bioinformatics use bioinformatics tools and algorithms as a collective solution for developing functional structure in Nano scale.

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Nano bioinformatics use different bioinformatics tools to optimize physicochemical features of proteins as a new approach in Nano biosensors and drug discovery.

Development of rapid colorimetric assay for the detection of Influenza A and B viruses

The flu viruses are respiratory pathogens which, according to the World Health Organization (WHO), infect 5-10% of the world population resulting in 3-5 million cases of severe illness and 290,000 to 650,000 annual deaths. Early diagnosis and therapeutic intervention can ameliorate symptoms of infection and reduce mortality. The conventional diagnosis of viral infections, including flu viruses, has evolved over the years with diverse approaches, however, there are inherent short comings associated with these testing. There is an urgent need for rapid and low-cost diagnostic assays, due to the enormous annual burden of influenza diseases and its associated mortality. In this study, novel, low cost and easy to use colorimetric flu virus biosensor assay was developed. The sandwich assay format was utilized using antibodies immobilized onto cotton swabs, for the rapid detection of flu A and B viruses. These swabs serve as sample collection, analytes pre-concentration as well as sensing tool. The proof of concept was established for this assay in buffer and mucus samples. The limit of detection (LOD) of the colorimetric assay was 0.04 ng mL-1 for Flu A and Flu B respectively and with linear dynamic range between 0.04 ng ml-1 to 40 ng ml for both viruses in mucous samples. The assay can be performed at the patient's bed side by minimally skilled hospital personnel without the need for instrumentation. Cross-reactivity assays testing was done using Flu viruses specific activated swabs reacted with other common respiratory viral pathogens' antigen, in order to assess the specificity of the swabs.

PH-responsive strontium nanoparticles for targeted gene therapy against mammary carcinoma cells

Genetic intervention via the delivery of functional genes such as plasmid DNA (pDNA) and short-interfering RNA (siRNA) offers a great way to treat many single or multiple genetic defects effectively, including mammary carcinoma. Delivery of naked therapeutic genes or siRNAs is, however, short-lived due to biological clearance by scavenging nucleases and circulating monocytes. Low cellular internalization of negatively-charged nucleic acids further causes low transfection or silencing activity. Development of safe and effectual gene vectors is therefore undeniably crucial to the success of nucleic acid delivery. Inorganic nanoparticles have attracted considerable attention in the recent years due to their high loading capacity and encapsulation activity. Here we introduce strontium salt-based nanoparticles, namely, strontium sulfate, strontium sulfite and strontium fluoride as new inorganic nanocarriers. Generated strontium salt particles were found to be nanosized with high affinity towards negatively-charged pDNA and siRNA. Degradation of the particles was seen with a drop in pH, suggesting their capacity to respond to pH change and undergo dissolution at endosomal pH to release the genetic materials. While the particles are relatively nontoxic towards the cells, siRNA-loaded SrF₂ and SrSO₃ particles exerted superior transgene expression and knockdown activity of MAPK and AKT, leading to inhibition of their phosphorylation to a distinctive extent in both MCF-7 and 4T1 cells. Strontium salt nanoparticles have thus emerged as a promising tool for applications in cancer gene therapy.

RNA secondary structured logic gates for profiling the microRNA cancer biomarkers

Deregulation of microRNAs expression is symptomatic of cancer disease and occurs before the awareness of cancer signs. Early detection of cancer disease can improve or drop the disease entirely. DNA computing is an emerging field of detecting microRNAs based on toehold-mediated strand displacement reactions, which is a more efficient method than the commonly used method like real-time PCR. Accuracy and cost of diagnostic applications are essential criteria that are achieved by using the DNA logic gates based on the DNA computing method. In this study, the authors proposed the multi-input liver cancer biosensor with the RNA secondary structure motifs as the computational module and two approaches are suggested.

Printed-Circuit-Board-Based Two-Electrode System for Electronic Characterization of Proteins

Proteins have been increasingly suggested as suitable candidates for the fabrication of biological computers and other biomolecular-based electronic devices mainly due to their interesting structure-related intrinsic electrical properties. These natural biopolymers are environmentally friendly substitutes for conventional inorganic materials and find numerous applications in bioelectronics. Effective manipulation of protein biomolecules allows for accurate fabrication of nanoscaled device dimensions for miniaturized electronics. The prerequisite, however, demands an interrogation of its various electronic properties prior to understanding the complex charge transfer mechanisms in protein molecules, the knowledge of which will be crucial toward development of such nanodevices. One significantly preferred method in recent times involves the utilization of solid-state sensors where interactions of proteins could be investigated upon contact with metals such as gold. Therefore, in this work, proteins (hemoglobin and collagen) were integrated within a two-electrode system, and the resulting electronic profiles were investigated. Interestingly, structure-related electronic profiles representing semiconductive-like behaviors were observed. These characteristic electronic profiles arise from the metal (Au)-semiconductor (protein) junction, clearly demonstrating the formation of a Schottky junction. Further interpretation of the electronic behavior of proteins was done by the calculation of selected solid-state parameters. For example, the turn-on voltage of hemoglobin was measured to occur at a lower turn-on voltage, indicating the possible influence of the hem group present as a cofactor in each subunit of this tetrameric protein.

Recent advances in designing nanomaterial based biointerfaces for electrochemical biosensing cardiovascular biomarkers

Early diagnosis of cardiovascular disease (CVD) is critically important for successful treatment and recovery of patients. At present, detection of CVD at early stages of its progression becomes a major issue for world health. The nanoscale electrochemical biosensors exhibit diverse outstanding properties, rendering them extremely suitable for the determination of CVD biomarkers at very low concentrations in biological fluids. The unique advantages offered by electrochemical biosensors in terms of sensitivity and stability imparted by nanostructuring the electrode surface together with high affinity and selectivity of bioreceptors have led to the development of new electrochemical biosensing strategies that have introduced as interesting alternatives to conventional methodologies for clinical diagnostics of CVD. This review provides an updated overview of selected examples during the period 2005-2018 involving electrochemical biosensing approaches and signal amplification strategies based on nanomaterials, which have been applied for determination of CVD biomarkers. The studied CVD biomarkers include AXL receptor tyrosine kinase, apolipoproteins, cholesterol, C-reactive protein (CRP), D-dimer, fibrinogen (Fib), glucose, insulin, interleukins, lipoproteins, myoglobin, N-terminal pro-B-type natriuretic peptide (BNP), tumor necrosis factor alpha (TNF-α) and troponins (Tns) on electrochemical transduction format. Identification of new specific CVD biomarkers, multiplex bioassay for the simultaneous determination of biomarkers, emergence of microfluidic biosensors, real-time analysis of biomarkers and point of care validation with high sensitivity and selectivity are the major challenges for future research.

Nano-biosensor based on reduced graphene oxide and gold nanoparticles, for detection of phenylketonuria-associated DNA mutation

Phenylketonuria (PKU)-associated DNA mutation in newborn children can be harmful to his health and early detection is the best way to inhibit consequences. A novel electrochemical nano-biosensor was developed for PKU detection, based on signal amplification using nanomaterials, e.g. gold nanoparticles (AuNPs) decorated on the reduced graphene oxide sheet on the screen-printed carbon electrode. The fabrication steps were checked by field emission scanning electron microscope imaging as well as cyclic voltammetry analysis. The specific alkanethiol single-stranded DNA probes were attached by self-assembly methodology on the AuNPs surface and Oracet blue was used as an intercalating electrochemical label. The results showed the detection limit of 21.3 fM and the dynamic range of 80-1200 fM. Moreover, the selectivity results represented a great specificity of the nano-biosensor for its specific target DNA oligo versus other non-specific sequences. The real sample simulation was performed successfully with almost no difference than a synthetic buffer solution environment.

Advances in the design of nanomaterial-based electrochemical affinity and enzymatic biosensors for metabolic biomarkers: A review

This review (with 340 refs) focuses on methods for specific and sensitive detection of metabolites for diagnostic purposes, with particular emphasis on electrochemical nanomaterial-based sensors. It also covers novel candidate metabolites as potential biomarkers for diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis. Following an introduction into the field of metabolic biomarkers, a first major section classifies electrochemical biosensors according to the bioreceptor type (enzymatic, immuno, apta and peptide based sensors). A next section covers applications of nanomaterials in electrochemical biosensing (with subsections on the classification of nanomaterials, electrochemical approaches for signal generation and amplification using nanomaterials, and on nanomaterials as tags). A next large sections treats candidate metabolic biomarkers for diagnosis of diseases (in the context with metabolomics), with subsections on biomarkers for neurodegenerative diseases, autism spectrum disorder and hepatitis. The Conclusion addresses current challenges and future perspectives. Graphical abstract This review focuses on the recent developments in electrochemical biosensors based on the use of nanomaterials for the detection of metabolic biomarkers. It covers the critical metabolites for some diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis.

Fabrication of Nanostructures with Bottom-up Approach and Their Utility in Diagnostics, Therapeutics, and Others

Nanofabrication has been a critical area of research in the last two decades and has found wide-ranging application in improvising material properties, sensitive clinical diagnostics, and detection, improving the efficiency of electron transport processes within materials, generating high energy densities leading to pulse power, novel therapeutic mechanisms, environmental remediation and control. The continued improvements in the various fabrication technologies have led to realization of highly sensitive nanostructure-based devices. The fabrication of nanostructures is in principle carried out primarily using top-down or bottom-up approaches. This chapter summarizes the important bottom-up nanofabrication processes for realizing nanostructures and also highlights the recent research conducted in the domain of therapeutics and diagnostics.

Use of Carbon Nanotubes as a Solid Support To Establish Quantitative (Centrifugation) and Qualitative (Filtration) Immunoassays To Detect Gentamicin Contamination in Commercial Milk

Current methods to detect gentamicin (GEN), a broad-spectrum antibiotic that causes ototoxicity and nephrotoxicity when present in excess, have several limitations. Hence, we have developed two methods using multi-walled carbon nanotubes (MWCNTs) as a solid support to detect GEN. Hybridoma cells (2D12) producing high-sensitivity antibodies against GEN were established. The goat anti-mouse antibody was immobilized on MWCNTs directly or using bifunctional polyethylene glycol as a linker. On the basis of the physical characteristics of MWCNTs, a quantitative method involving centrifugation separation and a qualitative method involving filtration separation were established. Various experimental parameters were optimized for GEN detection, and recovery tests were performed. For the quantitative method, the limit of detection (LOD) was 0.048 ng/mL, whereas for the qualitative method, a LOD of 0.1 ng/mL was observed by the naked eye. The proposed immunoassays were applied to commercial milk samples. Thus, these methods show potential application for the detection of GEN.

Bismuth functionalized PVA film: field, plasmonic and pH effect on PVA originated broad photoluminescence

Bismuth (Bi) NPs have been synthesized by Laser Ablation Synthesis in Solution (LASiS) at different pH in different aqueous solutions [viz. H₂O (H), H₂O + NaOH (HN), and H₂O + HCl (HC)].

Aggregation of inorganic nanoparticles mediated by biomimetic oligomers

Assemblies of nanoparticles (NPs) have been broadly used for the construction of materials with unique spectroscopic and chiral properties for applications in various scientific disciplines such as sensing, bio-nanotechnology and medicine. Mediating the aggregation of NPs by synthetic biomimetic oligomers, namely, DNA, PNA, peptides and peptide mimics, rather than by small organic molecules has been shown to produce interesting supramolecular structures and enable the combination of the biocompatibility of the mediators and the spectroscopic properties of the NPs. Yet, the key to using this powerful approach for designing new functional materials is to understand the NPs aggregation patterns induced by biopolymers and biomimetic oligomers. Herein we describe the important developments in this field, from early studies to recent work with an emphasis on synthetic methods and tools for controlled assembly of metal NPs by biomimetic polymers and oligomers.

DNA-Based Nanobiosensors as an Emerging Platform for Detection of Disease

Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases) that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory.

The toxicity outcome of silica nanoparticles (Ludox®) is influenced by testing techniques and treatment modalities

We analyzed the influence of the kind of cytotoxicity test and its application modality in defining the level of hazard of the in vitro exposures to nanostructures. We assessed the cytotoxicity induced by two different Ludox® silica nanoparticles (NPs), AS30 and SM30, on three human cell lines, CCD-34Lu, A549, and HT-1080. Dynamic light scattering measurements showed particle agglomeration when NPs are diluted in culture medium supplemented with fetal calf serum. We examined the impact of such particle aggregation on the cytotoxicity by exposing the cells to NPs under different treatment modalities: short incubation (2 h) in serum-free medium or long incubation (24–72 h) in serum-containing medium. Under this last modality, NP suspensions tended to form aggregates and were toxic at concentrations five- to tenfold higher than in serum-free medium. The results of cell survival varied considerably when the long-term clonogenic assay was performed to validate the data of the short-term MTS assay. Indeed, the half maximum effective concentrations (EC₅₀) in all the three cell lines were four- to fivefold lower when calculated from the data of clonogenic assay than of MTS. Moreover, the mechanisms of NP toxicity were cell-type-specific, showing that CCD-34Lu are prone to the induction of plasma membrane damages and HT-1080 are prone to DNA double-strand break and apoptosis induction. Taken together, our results demonstrate that the choice of testing strategy and treatment conditions plays an important role in assessing the in vitro toxicity of NPs.

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Prospects of nanotechnology in clinical immunodiagnostics

Nanostructured materials are promising compounds that offer new opportunities as sensing platforms for the detection of biomolecules. Having micrometer-scale length and nanometer-scale diameters, nanomaterials can be manipulated with current nanofabrication methods, as well as self-assembly techniques, to fabricate nanoscale bio-sensing devices. Nanostructured materials possess extraordinary physical, mechanical, electrical, thermal and multifunctional properties. Such unique properties advocate their use as biomimetic membranes to immobilize and modify biomolecules on the surface of nanoparticles. Alignment, uniform dispersion, selective growth and diameter control are general parameters which play critical roles in the successful integration of nanostructures for the fabrication of bioelectronic sensing devices. In this review, we focus on different types and aspects of nanomaterials, including their synthesis, properties, conjugation with biomolecules and their application in the construction of immunosensing devices. Some key results from each cited article are summarized by relating the concept and mechanism behind each sensor, experimental conditions and the behavior of the sensor under different conditions, etc. The variety of nanomaterial-based bioelectronic devices exhibiting novel functions proves the unique properties of nanomaterials in such sensing devices, which will surely continue to expand in the future. Such nanomaterial based devices are expected to have a major impact in clinical immunodiagnostics, environmental monitoring, security surveillance and for ensuring food safety.