DNA-binding by functionalized gold nanoparticles: mechanism and structural requirements

Visualizing the 4D Impact of Gold Nanoparticles on DNA

The genotoxicity of AuNPs has sparked a scientific debate, with one perspective attributing it to direct DNA damage and another to oxidative damage through reactive oxygen species (ROS) activation. This controversy poses challenges for the widespread use of AuNPs in biomedical applications. To address this debate, we employed four-dimensional atomic force microscopy (4DAFM) to examine the ability of AuNPs to damage DNA in vitro in the absence of ROS. To further examine whether the size and chemical coupling of these AuNPs are properties that control their toxicity, we exposed individual DNA molecules to three different types of AuNPs: small (average diameter = 10 nm), large (average diameter = 22 nm), and large conjugated (average diameter = 39 nm) AuNPs. We found that all types of AuNPs caused rapid (within minutes) and direct damage to the DNA molecules without the involvement of ROS. This research holds significant promise for advancing nanomedicines in diverse areas like viral therapy (including COVID-19), cancer treatment, and biosensor development for detecting DNA damage or mutations by resolving the ongoing debate regarding the genotoxicity mechanism. Moreover, it actively contributes to the continuous endeavors aimed at fully harnessing the capabilities of AuNPs across diverse biomedical fields, promising transformative healthcare solutions.

Interfacing Nanomaterials with Biology through Ligand Engineering

Nanoparticles (NPs) have incredible potential in biology and biomedicine. Gold nanoparticles (AuNPs) have become a cornerstone of the nanomedicine revolution due to their ease of synthesis, inertness, and versatility. The widespread use of AuNPs can be traced to the development of accessible, bottom-up wet synthesis methods that emphasized the role of ligands in controlling the size, dispersity, and stability of colloids in solution. Decoration of AuNPs with organic ligands can be used to dictate the interactions of these nanomaterials with biosystems on multiple scales. The tunability of the AuNP ligand monolayer via covalent and noncovalent approaches allows the use of AuNPs in a broad range of biomedical fields.In this Account, we describe our use of AuNPs to answer a central question in the ligand engineering of colloidal nanoparticles: can we fabricate NPs that are nontoxic, modular, and functional in biological environments? We explored spherical AuNPs of different sizes and ligand structures, empirically exploring the AuNP-biomolecule interaction. We show here how the atom-by-atom control provided by organic synthesis can be used to create engineered ligands. Presenting these ligands on the surface of AuNPs creates multivalent constructs with unique and useful properties. Ligand design is a key feature of these AuNPs. We have developed ligands that have three distinct structural segments: 1) a hydrophobic alkanethiol interior that imparts stability; 2) a tetra(ethylene glycol) segment that creates a noninteracting tabula rasa surface; and 3) ligand headgroups that dictate how the AuNP interacts with the outside world. Our research into the design principles of ligands on AuNPs and their interactions with biological systems can be translated to other nanoparticle systems.This Account also summarizes the trajectory of ligand engineering in our laboratory and further afield. At the outset, experimental and theoretical fundamental studies were focused on the interactions between AuNPs and cellular components, such as proteins and lipid membranes. Understanding these behaviors provided the direction for investigating how ligands mediate the interface of AuNPs with mammalian and bacterial cells. In these experiments, it was particularly noteworthy that the ligand hydrophobicity and charge play a significant role in the uptake and toxicity of AuNPs. These revelations formed a basis for translating AuNPs to physiological environments. We present how we have integrated our synthetic abilities to construct AuNPs for biomedical applications, including delivery, bioorthogonal catalysis, antimicrobial and antitumor therapeutics, and biosensing.Overall, we hope that this Account will give the reader insight into how our research has evolved, changing AuNPs from synthetic curiosities into functional nanoplatforms for nanomedicine, all through the power of ligand design and synthesis.

Enhanced Single-Strand Breaks of a Nucleic Acid by Gold Nanoparticles under X-ray Irradiation

The hydroxyl radical concentration-dependent yield of single-strand breaks (SSBs), obtained through correction of scavenging and hindrance effects caused by gold nanoparticles (AuNPs), for fluorophore- and quencher-labeled DNA on AuNPs was 10 times that of free DNA based on fluorescence measurements of X-ray-irradiated DNA on AuNPs. By comparing the fluorescence data that revealed the number of SSBs with the results of mass spectrometry measurements that detected the total damage to DNA, we found that SSBs dominated DNA damage for DNA on AuNPs whereas non-SSB damage dominated for free DNA. The yield of RNA SSBs under X-ray irradiation was similar to that of DNA in the presence of AuNPs, whereas free RNA was more resistive to radiation than DNA. These results indicated the enhanced SSBs were likely catalyzed through the conversion from nucleobase damage to SSBs by AuNPs. The outcome of this work impacts materials and environmental science, sensing, nanotechnology, biology, and medicine.

Systematic and mechanistic analysis of AuNP-induced nanotoxicity for risk assessment of nanomedicine

For decades, nanoparticles (NPs) have been widely implemented in various biomedical fields due to their unique optical, thermal, and tunable properties. Particularly, gold nanoparticles (AuNPs) have opened new frontiers in sensing, targeted drug delivery, imaging, and photodynamic therapy, showing promising results for the treatment of various intractable diseases that affect quality of life and longevity. Despite the tremendous achievements of AuNPs-based approaches in biomedical applications, few AuNP-based nanomedicines have been evaluated in clinical trials, which is likely due to a shortage of understanding of the biological and pathological effects of AuNPs. The biological fate of AuNPs is tightly related to a variety of physicochemical parameters including size, shape, chemical structure of ligands, charge, and protein corona, and therefore evaluating the effects of these parameters on specific biological interactions is a major ongoing challenge. Therefore, this review focuses on ongoing nanotoxicology studies that aim to characterize the effect of various AuNP characteristics on AuNP-induced toxicity. Specifically, we focus on understanding how each parameter alters the specific biological interactions of AuNPs via mechanistic analysis of nano-bio interactions. We also discuss different cellular functions affected by AuNP treatment (e.g., cell motility, ROS generation, interaction with DNA, and immune response) to understand their potential human health risks. The information discussed herein could contribute to the safe usage of nanomedicine by providing a basis for appropriate risk assessment and for the development of nano-QSAR models.

Enzyme Activated Gold Nanoparticles for Versatile Site-Selective Bioconjugation

A new enzymatic method is reported for constructing protein- and DNA-AuNP conjugates. The strategy relies on the initial functionalization of AuNPs with phenols, followed by activation with the enzyme tyrosinase. Using an oxidative coupling reaction, the activated phenols are coupled to proteins bearing proline, thiol, or aniline functional groups. Activated phenol-AuNPs are also conjugated to a small molecule biotin and commercially available thiol-DNA. Advantages of this approach for AuNP bioconjugation include: (1) initial formation of highly stable AuNPs that can be selectively activated with an enzyme, (2) the ability to conjugate either proteins or DNA through a diverse set of functional handles, (3) site-specific immobilization, and (4) facile conjugation that is complete within 2 h at room temperature under aqueous conditions. The enzymatic oxidative coupling on AuNPs is applied to the construction of tobacco mosaic virus (TMV)-AuNP conjugates, and energy transfer between the AuNPs and fluorophores on TMV is demonstrated.

Polarimetric Measurements of Surface Chirality Based on Linear and Nonlinear Light Scattering

A molecule, molecular aggregate, or protein that cannot be superimposed on its mirror image presents chirality. Most living systems are organized by chiral building blocks, such as amino acids, peptides, and carbohydrates, and any change in their molecular structure (i.e., handedness or helicity) alters the biochemical and pharmacological functions of the molecules, many of which take place at surfaces. Therefore, studying surface chirogenesis at the nanoscale is fundamentally important and derives various applications. For example, since proteins contain highly ordered secondary structures, the intrinsic chirality can be served as a signature to measure the dynamics of protein adsorption and protein conformational changes at biological surfaces. Furthermore, a better understanding of chiral recognition and separation at bio-nanointerfaces is helpful to standardize chiral drugs and monitor the synthesis of adsorbents with high precision. Thus, exploring the changes in surface chirality with polarized excitations would provide structural and biochemical information of the adsorbed molecules, which has led to the development of label-free and noninvasive measurement tools based on linear and nonlinear optical effects. In this review, the principles and selected applications of linear and nonlinear optical methods for quantifying surface chirality are introduced and compared, aiming to conceptualize new ideas to address critical issues in surface biochemistry.

Photothermal-triggered system for oligonucleotides delivery from cationic gold nanorods surface: A molecular dynamic investigation

Bioconjugate gold-based nanostructures combining the plasmonic photothermal effect with photothermal-triggered DNA delivery are appealing materials for medical diagnostic and therapy for cell-based disease. In this study, we demonstrate the use of surface hybridization to prepare DNA-modified gold nanorods to be used as photo-delivery system for single stranded oligonucleotides. The as prepared DNA modified gold nanorods have strong absorption bands in the visible and near-infrared regions in which the absorbed light through photothermal effect, induces a surface temperature increasing up to the melting temperature with consequent DNA release. No evident DNA release was observed below the melting temperature. The experimental data were supported by molecular dynamic simulation investigation, showing the kinetics aspect of dsDNA de-hybridization at gold nanorods surface at temperature below (298 K) and above (333 K) the melting temperature of sequence investigated. We demonstrate that the cationic charges of surfactant, localized at nanorods surface, induce a remarkable de-hybridization of strands DNA, as confirmed by an increasing of hybridization enthalpy value of about 7 kcal/mol and by a faster de-hybridization process, respect the model of gold nanorods without positive charges. These data were corroborated by the increasing of the root mean square deviation value (about 4.4 Å, calculated at 333 K) indicating that the presence of cationic headgroup at gold surface induce separation of the double strand. This finding data paving the way for the development of nanostructured material for photothermal-triggered delivery systems of DNA for gene therapy application.

DNA-based low resistance palladium nano-spheres for effective hydrogen evolution reaction

Highly stable and less resistance Pd/DNA NSs are designed for HER in acidic medium and require a low overpotential (η10) of 79 mV. DNA plays multiple roles such as stabilizer, structure-directing agent and binder in the fabrication of electrodes.

Machine-Free Polymerase Chain Reaction with Triangular Gold and Silver Nanoparticles

Photothermal effects of metal nanoparticles (NPs) are used for various biotechnological applications. Although NPs have been used in a polymerase chain reaction (PCR), the effects of shape on the photothermal properties and its efficiency on PCR are less explored. The present study reports the synthesis of triangular gold and silver NPs, which can attain temperatures up to ∼90 °C upon irradiation with 808 nm laser. This photothermal property of synthesized nanoparticles was evaluated using various concentrations, irradiation time, and power to create a temperature profile required for variable-temperature PCR. This study reports a cost-effective, machine-free PCR using both gold and silver triangular NPs, with efficiency similar to that of a commercial PCR machine. Interestingly, addition of triangular NPs increases PCR efficiency in commercial PCR reactions. The higher PCR efficiencies are due to the direct binding and unfolding of double-stranded DNA as suggested by circular dichroism and UV spectroscopy. These findings suggest that triangular NPs can be used to develop cost-effective, robust machine-free PCR modules and can be used in various other photothermal applications.

Nanoparticle-delivered miriplatin ultrasmall dots suppress triple negative breast cancer lung metastasis by targeting circulating tumor cells

No effective therapy is yet available to treat triple negative breast cancer (TNBC), which has poor prognosis due to frequent metastasis. Cancer stem cells (CSCs) or CSC-like cells play crucial roles in cancer metastasis and are exceptionally tolerant with genetic lesions. The extent of DNA damages has an important impact on the fate of CSCs. Despite the importance of platinum [Pt(II)] agents in cancer therapy, accumulating reports showed the treatment failure of conventional Pt(II) drugs, which is likely due to their inadequate DNA damage effects. Miriplatin is a clinically approved drug only being locally-used for treating liver cancer. In this study, we developed a novel ultrasmall Pt(II) dot (uPtD) from miriplatin and encapsulated it into our recently-reported integrin α5(ITGA5) active targeting nanoparticles (uPtDs NPs) and tested their therapeutic efficacy against TNBC metastasis. It was found that uPtDs NPs displayed a superior DNA damage capability via enhanced-interactions with DNA and a significantly stronger effect in reducing CSC-like property of TNBC cells, compared to conventional cisplatin and miriplatin. Mechanistically, the severe DNA damages induced by uPtDs NPs activated the CHK_1/2-CDC25A-cyclin A/E pathway to induce cell cycle arrest. Moreover, uPtDs NPs could target the in vivo circulating tumor cells (CTCs) to suppress TNBC lung metastasis. Given the desired-safety profile of miriplatin, the uPtDs represent a promising therapeutic agent of the metal-based nanomedicines to reduce cancer metastasis. SIGNIFICANCE: The miriplatin ultrasmall dots developed from clinically-prescribed miriplatin may serve as a potent systemically-administered agent to target CTCs and reduce cancer metastasis.

Strategy for Finely Aligned Gold Nanorod Arrays Using Polymer Brushes as a Template

The development of a strategy for the assembly of nanoscale building blocks, in particular, anisotropic nanoparticles, into desired structures is important for the construction of functional materials and devices. However, control over the orientation of rod-shaped nanoparticles on a substrate for integration into solid-state devices remains challenging. Here, we report a strategy for the fabrication of finely aligned gold nanorod (GNR) arrays using polymer (DNA) brushes as a nanoscale template. The gold nanorods modified with cationic surface ligands were electrostatically adsorbed onto the DNA brush substrates under various conditions. The orientational behavior of the GNRs was examined by spectral analyses and transmission electron microtomography (TEMT). As a result, we found several important factors, such as moderate interaction between GNRs and polymers and polymer densities on the substrate, related to the vertical alignment of GNRs on the substrates. We also developed a purification method to remove the undesired adsorption of GNRs onto the arrays. Finally, we have succeeded in the fabrication of extensive vertical GNR arrays of high quality via the easy bottom-up process.

Assisted delivery of anti-tumour platinum drugs using DNA-coiling gold nanoparticles bearing lumophores and intercalators: towards a new generation of multimodal nanocarriers with enhanced action

New gold and lipoic based nanocarriers for the delivery of platinum(ii) and platinum(iv) drugs are developed, which allow enhanced loading of the drug on the surface of the nanocarriers and release in a pH-dependent fashion, with superior release at lower pHs which are associated with many tumours. The conjugate nanoparticles and their conjugates enter cells rapidly (within 3 hours). They tend to cluster in vesicles and are also observed by light and electron microscopies in the cytoplasm, endoplasmic reticulum and nucleus. We further incorporate aminoanthraquinone units that are both fluorophores and DNA intercalators. This results in nanocarriers that after drug release will remain surface decorated with DNA-binders challenging the conventional design of the nanocarrier as an inert component. The outcome is nanocarriers that themselves have distinctive, remarkable and unusual DNA binding properties being able to bind and wrap DNA (despite their anionic charge) and provide enhanced cytotoxic activity beyond that conferred by the platinum agents they release. DNA coiling is usually associated with polycations which can disrupt cell membranes; anionic nanoparticles that can cause novel and dramatic effects on DNA may have fascinating potential for new approaches to in-cell nucleic acid recognition. Our findings have implications for the understanding and interpretation of the biological activities of nanoparticles used to deliver other DNA-binding drugs including clinical drug doxorubicin and its formulations.

Evaluating DNA Derived and Hydrothermally Aided Cobalt Selenide Catalysts for Electrocatalytic Water Oxidation

Electrocatalysts with engaging oxygen evolution reaction (OER) activity with lesser overpotentials are highly desired to have increased cell efficiency. In this work, cobalt selenide catalysts were prepared utilizing both wet-chemical route (CoSe and CoSe-DNA) and hydrothermal route (Co_0.85Se-hyd). In wet-chemical route, cobalt selenide is prepared with DNA (CoSe-DNA) and without DNA (CoSe). The morphological results in the wet-chemical route had given a clear picture that, with the assistance of DNA, cobalt selenide had formed as nanochains with particle size below 5 nm, while it agglomerated in the absence of DNA. The morphology was nano networks in the hydrothermally assisted synthesis. These catalysts were analyzed for OER activity in 1 M KOH. The overpotentials required at a current density of 10 mA cm^-2 were 352, 382, and 383 mV for Co_0.85Se-hyd, CoSe, and CoSe-DNA catalysts, respectively. The Tafel slope value was lowest for Co_0.85Se-hyd (65 mV/dec) compared to CoSe-DNA (71 mV/dec) and CoSe (80 mV/dec). The chronoamperometry test was studied for 24 h at a potential of 394 mV for Co_0.85Se-hyd and was found to be stable with a smaller decrease in activity. From the OER study, it is clear that Co_0.85Se was found to be superior to others. This kind of related study can be useful to design the catalyst with increased efficiency by varying the method of preparation.

Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces

Ligand-functionalized inorganic nanoparticles, also known as monolayer-protected nanoparticles, offer great potential as vehicles for in vivo delivery of drugs, genes, and other therapeutics. These nanoparticles offer highly customizable chemistries independent of the size, shape, and functionality imparted by the inorganic core. Their success as drug delivery agents depends on their interaction with three major classes of biomolecules: nucleic acids, proteins, and membranes. Here, the authors discuss recent advances and open questions in the field of nanoparticle ligand design for nanomedicine, with a focus on atomic-scale interactions with biomolecules. While the importance of charge and hydrophobicity of ligands for biocompatibility and cell internalization has been demonstrated, ligand length, flexibility, branchedness, and other properties also influence the properties of nanoparticles. However, a comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Understanding and improving aggregated gold nanoparticle/dsDNA interactions by molecular spectroscopy and deconvolution methods

It is well known that single-stranded DNA (ssDNA) is easily able to adsorb on citrate-capped, non-functionalized gold nanoparticles (AuNPs). However, the affinity of double-stranded DNA (dsDNA) for them is much more limited. The present work demonstrates that long dsDNA suffers from a bending conformational change when anionic nanoparticles are present in solution. A striking decrease in the persistence length of the double helix in the absence of salt is observed through dynamic light scattering (DLS), viscometric, and atomic force microscopy (AFM) methods. Long dsDNA is therefore shown to be able to interact with anionic gold nanoparticles. To date, only ssDNA detection has been described by making use of interparticle cross-linking aggregation mechanisms; however, the data shown in this work allow for the development of new methods for detecting dsDNA in solution by using aggregated AuNPs as a starting point. The aggregation state is induced by the controlled addition of an inert electrolyte. A deconvolution procedure of the experimental plasmon shows how individual bands corresponding to aggregated nanoclusters diminish as the DNA concentration increases in the presence of 0.075 M NaCl.

Decorating a single giant DNA with gold nanoparticles

We decorated a single giant DNA (1.66 × 10⁵ base pairs) with gold nanoparticles through the simple procedure of mild warming, without denaturation of the DNA molecule. Single-molecule observation with fluorescence microscopy revealed that individual decorated DNA molecules stay in the bulk solution by avoiding aggregation and precipitation, and exhibit translational and conformational fluctuation, i.e., Brownian motion. An analysis of the intra-chain fluctuation of single DNA molecules revealed that the apparent spring constant and damping coefficient of a DNA chain increased by ca. 13- and 5-fold, respectively, upon decoration with gold nanoparticles. Observation by transmission electron microscopy revealed that gold nanoparticles were stably attached to the DNA skeleton. UV-visible measurements revealed the absence of any detectable change in surface plasmon resonance, suggesting that the gold nanoparticles assemble without the formation of a densely packed aggregate. CD measurements showed that the secondary structure of decorated DNA is still essentially the B-form.

We decorated a single giant DNA (1.66 × 10⁵ base pairs) with gold nanoparticles through the simple procedure of mild warming, without denaturation of the DNA molecule.

Hydrophobic and Hydrophilic Au and Ag Nanoparticles. Breakthroughs and Perspectives

This review provides a broad look on the recent investigations on the synthesis, characterization and physico-chemical properties of noble metal nanoparticles, mainly gold and silver nanoparticles, stabilized with ligands of different chemical nature. A comprehensive review of the available literature in this field may be far too large and only some selected representative examples will be reported here, together with some recent achievements from our group, that will be discussed in more detail. Many efforts in finding synthetic routes have been performed so far to achieve metal nanoparticles with well-defined size, morphology and stability in different environments, to match the large variety of applications that can be foreseen for these materials. In particular, the synthesis and stabilization of gold and silver nanoparticles together with their properties in different emerging fields of nanomedicine, optics and sensors are reviewed and briefly commented.

MiRNA extraction from cell-free biofluid using protein corona formed around carboxyl magnetic nanoparticles

MicroRNA (miRNA) in urine has been considered as a potential biomarker for early-stage diagnosis of multiple diseases like urinary system cancer, kidney injury and diabetes, owing to their many demonstrated advantages including long-term stability and noninvasiveness. However, the traditional enrichment and extraction processes of miRNAs from urine are cumbersome and tedious due to the low concentration and multiple carriers of miRNAs. Herein, we present a novel method to collect low concentrations of miRNAs from dilute solutions such as urine and cell culture medium. 10-nm core sized magnetic nanoparticles with carboxylic acid coating can adsorb low-concentration proteins, and form protein corona which makes them easy to aggregate and precipitate for subsequent isolation. In urine and cell culture medium, these nanoparticles can aggregate with proteins, including miRNAs-associated protein Argonaute 2 and microvesicle-related proteins, to form precipitates, so that miRNAs can be easily extracted from pellets by small amount of lysis buffer for subsequent analysis such as real-time PCR. Our method provides a facile way to enrich miRNAs from biofluids without the need of ultracentrifugation and immunoprecipitations, bringing remarkable convenience to miRNAs-based biomarker research.

Selective detection of Mg2+ ions via enhanced fluorescence emission using Au-DNA nanocomposites

The biophysical properties of DNA-modified Au nanoparticles (AuNPs) have attracted a great deal of research interest for various applications in biosensing. AuNPs have strong binding capability to the phosphate and sugar groups in DNA, rendering unique physicochemical properties for detection of metal ions. The formation of Au-DNA nanocomposites is evident from the observed changes in the optical absorption, plasmon band, zeta potential, DLS particle size distribution, as well as TEM and AFM surface morphology analysis. Circular dichroism studies also revealed that DNA-functionalized AuNP binding caused a conformational change in the DNA structure. Due to the size and shape dependent plasmonic interactions of AuNPs (33-78 nm) with DNA, the resultant Au-DNA nanocomposites (NCs) exhibit superior fluorescence emission due to chemical binding with Ca²⁺, Fe²⁺ and Mg²⁺ ions. A significant increase in fluorescence emission (λ_ex = 260 nm) of Au-DNA NCs was observed after selectively binding with Mg²⁺ ions (20-800 ppm) in an aqueous solution where a minimum of 100 ppm Mg²⁺ ions was detected based on the linearity of concentration versus fluorescence intensity curve (λ_em = 400 nm). The effectiveness of Au-DNA nanocomposites was further verified by comparing the known concentration (50-120 ppm) of Mg²⁺ ions in synthetic tap water and a real life sample of Gelusil (300-360 ppm Mg²⁺), a widely used antacid medicine. Therefore, this method could be a sensitive tool for the estimation of water hardness after careful preparation of a suitably designed Au-DNA nanostructure.

Unraveling the Interaction of Silver Nanoparticles with Mammalian and Bacterial DNA

The focus of this study was to understand and unravel the interaction of silver nanoparticles (AgNPs) with different types of Deoxyribonucleic acid (DNA), mammalian and bacterial, having different base pair compositions. Binding of spherical silver nanoparticles (AgNPs) to Calf thymus (CT) DNA, Escherichia coli (EC) DNA and Micrococcus lysodeikticus (ML) DNA has been studied to gain insights into their mode of interaction and specificity. Interaction of AgNPs with synthetic DNA has also been carried out. On the basis of absorption, thermal melting, isothermal calorimetry and viscosity studies, we could establish the mode of binding and specificity of the synthesized silver nanoparticles with mammalian and bacterial DNA. Thermal melting (Tm) studies indicated a decrease in the Tm of all the DNAs, confirming the destabilization of DNA stacks on interaction with AgNPs. Comparative interaction studies with single stranded (ss) and double stranded (ds) DNAs further confirmed the specificity of the particles toward ds DNA. On the basis of the results we could confirm that the synthesized AgNPs could be used for selective detection of DNA through their DNA binding mechanism. In addition, the AgNPs-DNA complexes exhibited distinct differences in the SERS spectra making it an interesting SERS platform for identifying ds DNA. The optical and physical properties of AgNPs help in differentiating the DNAs of different base pair compositions through their binding affinity and specificity.

Modified gold nanoparticles for intracellular delivery of anti-liver cancer siRNA

To overcome the rapid enzymatic degradation and low transfection efficiency of siRNA, the delivery carriers for siRNA is a therapeutic demand to increase its stability. Gold nanoparticles (AuNPs) modified by branched polyethyleneimine (bPEI) were developed as an efficient and safe intracellular delivery carriers for siRNA. The current study implied that siRNA designed against an oncogene c-Myc could be delivered by a modified AuNPs complex without significant cytotoxicity. The comparative semi-quantitative and quantitative real time PCR were used to measure the c-Myc gene expression after transfection with naked siRNA and siRNA/bPEI/AuNPs, but AuNPs interfered with PCR. However, the c-Myc protein translation was successfully detected in the transfected HuH7 cells with naked siRNA and siRNA/bPEI/AuNPs and it was found to be inhibited by siRNA/bPEI/AuNPs more than naked siRNA. The results validate the successful silencing of c-Myc gene. Accordingly, it may confirm the promising and effective delivery of siRNA by bPEI/AuNPs. The complex enhances the cellular uptake of siRNA without significant cytotoxicity and confirms that bPEI modified AuNPs could be used as a good candidate for safe cellular delivery of siRNA.

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

Spectroscopic investigation of interaction between bovine gamma globulin and gold nanoparticles

The interaction of Citrate-capped gold nanoparticles (AuNPs) with Bovine gamma globulin (BGG) was studied using Fourier transform infrared (FTIR), UV-Visible and Fluorescence spectroscopy. FTIR has confirmed the conjugation of AuNPs and BGG. Fluorescence quenching of tryptophan has confirmed the strong interaction between BGG and AuNPs. UV-Visible and Fluorescence spectroscopy have investigated the extent of interaction by determining the binding constants. Binding constants evaluated from UV-Visible and Fluorescence data are in good agreement with each other. An independent class of binding site on BGG for AuNPs has been predicted, where AuNPs interact with a highly solvent accessible tryptophan residue.

Gold nanoparticle interference study during the isolation, quantification, purity and integrity analysis of RNA

Investigations have been conducted regarding the interference of nanoparticles (NPs) with different toxicological assay systems, but there is a lack of validation when conducting routine tests for nucleic acid isolation, quantification, integrity, and purity analyses. The interference of citrate-capped gold nanoparticles (AuNPs) was investigated herein. The AuNPs were added to either BEAS-2B bronchial human cells for 24 h, the isolated pure RNA, or added during the isolation procedure, and the resultant interaction was assessed. Total RNA that was isolated from untreated BEAS-2B cells was spiked with various concentrations (v/v%) of AuNPs and quantified. A decrease in the absorbance spectrum (220–340 nm) was observed in a concentration-dependent manner. The 260 and 280 nm absorbance ratios that traditionally infer RNA purity were also altered. Electrophoresis was performed to determine RNA integrity, but could not differentiate between AuNP-exposed samples. However, the spiked post-isolation samples did produce differences in spectra (190–220 nm), where shifts were observed at a shorter wavelength. These shifts could be due to alterations to chromophores found in nucleic acids. The co-isolation samples, spiked with 100 µL AuNP during the isolation procedure, displayed a peak shift to a longer wavelength and were similar to the results obtained from a 24 h AuNP treatment, under non-cytotoxic test conditions. Moreover, hyperspectral imaging using CytoViva dark field microscopy did not detect AuNP spectral signatures in the RNA isolated from treated cells. However, despite the lack of AuNPs in the final RNA product, structural changes in RNA could still be observed between 190–220 nm. Consequently, full spectral analyses should replace the traditional ratios based on readings at 230, 260, and 280 nm. These are critical points of analyses, validation, and optimization for RNA-based techniques used to assess AuNPs effects.

High-speed, high-purity separation of gold nanoparticle-DNA origami constructs using centrifugation

DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions have yields of <100%, requiring the development of methods to purify the desired product. We study the performance of centrifugation as a separation approach by combining optical and hydrodynamic measurements and computations. We demonstrate that bench-top microcentrifugation is a simple and efficient method of separating the reaction products, readily achieving purities of >90%. The gold nanoparticles play a number of critical roles in our system, functioning not only as integral components of the purified products, but also as hydrodynamic separators and optical indicators of the reaction products during the purification process. We find that separation resolution is ultimately limited by the polydispersity in the mass of the gold nanoparticles and by structural distortions of DNA origami induced by the gold nanoparticles. Our study establishes a methodology for determining the design rules for nanomanufacturing DNA origami-nanoparticle constructs.

Gold nanoparticles for nucleic acid delivery

Gold nanoparticles provide an attractive and applicable scaffold for delivery of nucleic acids. In this review, we focus on the use of covalent and noncovalent gold nanoparticle conjugates for applications in gene delivery and RNA-interference technologies. We also discuss challenges in nucleic acid delivery, including endosomal entrapment/escape and active delivery/presentation of nucleic acids in the cell.

Impact of gold nanoparticles on zebrafish exposed to a spiked sediment

Increasing use of metallic nanomaterials is likely to result in release of these particles into aquatic environments; nevertheless it is unclear whether these materials present a hazard to aquatic organisms. The impact of contaminated sediment containing 14-nm gold nanoparticles (AuNPs) was investigated in the zebrafish Danio rerio exposed for 20 days to two concentrations, 16 and 55 µg/g dry weight. AuNPs were released from the sediment to the water column, and during this period the mean concentrations of AuNP in the filtered water fraction were 0.25 ± 0.05 and 0.8 ± 0.1 µg/L, respectively. A similar experiment with ionic gold contamination was simultaneously performed to obtain a positive control. AuNP exposure triggered various effects in fish tissues including modifications of genome composition, shown using a random amplified polymorphic DNA-PCR genotoxicity test. Expression of genes involved in oxidative stress, mitochondrial metabolism, detoxification and DNA repair were also modulated in response to AuNP contamination. Gold altered neurotransmission, since brain acetylcholine esterase activity increased for both tested doses of AuNP but not for ionic gold. Gold accumulation in fish tissues demonstrated the lower bioavailability of AuNP compared to ionic Au, and underlined the higher toxic potential of the nanoparticle form.

Noncovalent interactions of tiopronin-protected gold nanoparticles with DNA: two methods to quantify free energy of binding

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the "true" free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

Weakly charged cationic nanoparticles induce DNA bending and strand separation

Weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The charged ligands bind to the phosphate backbone of DNA and the uncharged ligands penetrate the helix and disrupt base pairing. Mobility shifts in electrophoresis, molecular dynamics, and UV-vis spectrophotometry give clues to the details of the interactions.

Cell alignment using patterned biocompatible gold nanoparticle templates

Biocompatible structures are produced for cellular patterning. The biocompatible surfaces are generated to provide protein nonfouling patterns, offering direct communication to the cells for controlling cell adhesion and proliferation. These biofunctional surfaces provide a platform for aligning the cells in the direction of patterns, indicating potential application in the field of tissue engineering.

Beauty is skin deep: a surface monolayer perspective on nanoparticle interactions with cells and bio-macromolecules

Surface recognition of biosystems is a critical component in the development of novel biosensors and delivery vehicles, and for the therapeutic regulation of biological processes. Monolayer-protected nanoparticles present a highly versatile scaffold for selective interaction with bio-macromolecules and cells. Through the engineering of the monolayer surface, nanoparticles can be tailored for surface recognition of biomolecules and cells. This review highlights recent progress in nanoparticle-bio-macromolecule/cellular interactions, emphasizing the effect of the surface monolayer structure on the interactions with proteins, DNA, and cell surfaces. The extension of these tailored interactions to hybrid nanomaterials, biosensing platforms, and delivery vehicles is also discussed.

Impact of dietary gold nanoparticles in zebrafish at very low contamination pressure: the role of size, concentration and exposure time

The impact of a daily ration of food containing gold nanoparticles (AuNPs) of two sizes (12 and 50 nm) was investigated in the zebrafish Danio rerio at very low doses (from 36-106 ng gold/fish/day). AuNP exposure resulted in various dysfunctions at the sub cellular scale, and AuNP concentration in food, AuNP size and exposure duration modulated the observed adverse effects. Indeed, we showed alteration of genome composition using a RAPD-PCR genotoxicity test as the number of hybridization sites of the RAPD probes was significantly modified after AuNP exposure. Moreover, the expression of genes involved in DNA repair, detoxification processes, apoptosis, mitochondrial metabolism and oxidative stress was also modulated in response to AuNP contamination. Mitochondrial dysfunctions appeared in brain and muscle for both tested doses (40 and 100 ng gold/fish/day), but gold accumulation in fish tissues could only be observed in the case of the highest exposure dose.

A kinetic study of the interaction of DNA with gold nanoparticles: mechanistic aspects of the interaction

A kinetic study of the interaction of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine with double stranded DNA was carried out in water and in salt (NaCl) solutions. The kinetic curves are biexponential and reveal the presence of three kinetic steps. The dependence of the reciprocal fast and slow relaxation time, on the DNA concentration, is a curve and tends to a plateau at high DNA concentrations. The simplest mechanism consistent with the kinetic results involves a simple three-step series mechanism reaction scheme. The first step corresponds to a very fast step that is related to a diffusion controlled formation of an external precursor complex (DNA, AuNPs); the second step involves the formation of a (DNA/AuNPs)(I) complex, as a result of the binding affinity between hydrophilic groups of the tiopronin and the DNA grooves. Finally, the third step has been interpreted as a consequence of a conformational change of the (DNA/AuNPs)(I) complex formed in the second step, to a more compacted form (DNA/AuNPs)(II). The values of the rate constants of each step decrease as NaCl concentration increases. The results have been discussed in terms of solvation of the species and changes in the viscosity of the solution.

A review of the in vivo and in vitro toxicity of silver and gold particulates: particle attributes and biological mechanisms responsible for the observed toxicity

This review is concerned with evaluating the toxicity associated with human exposure to silver and gold nanoparticles (NPs), due to the relative abundance of toxicity data available for these particles, when compared to other metal particulates. This has allowed knowledge on the current understanding of the field to be gained, and has demonstrated where gaps in knowledge are. It is anticipated that evaluating the hazards associated with silver and gold particles will ultimately enable risk assessments to be completed, by combining this information with knowledge on the level of human exposure. The quantity of available hazard information for metals is greatest for silver particulates, due to its widespread inclusion within a number of diverse products (including clothes and wound dressings), which primarily arises from its antibacterial behaviour. Gold has been used on numerous occasions to assess the biodistribution and cellular uptake of NPs following exposure. Inflammatory, oxidative, genotoxic, and cytotoxic consequences are associated with silver particulate exposure, and are inherently linked. The primary site of gold and silver particulate accumulation has been consistently demonstrated to be the liver, and it is therefore relevant that a number of in vitro investigations have focused on this potential target organ. However, in general there is a lack of in vivo and in vitro toxicity information that allows correlations between the findings to be made. Instead a focus on the tissue distribution of particles following exposure is evident within the available literature, which can be useful in directing appropriate in vitro experimentation by revealing potential target sites of toxicity. The experimental design has the potential to impact on the toxicological observations, and in particular the use of excessively high particle concentrations has been observed. As witnessed for other particle types, gold and silver particle sizes are influential in dictating the observed toxicity, with smaller particles exhibiting a greater response than their larger counterparts, and this is likely to be driven by differences in particle surface area, when administered at an equal-mass dose. A major obstacle, at present, is deciphering whether the responses related to silver nanoparticulate exposure derive from their small size, or particle dissolution contributes to the observed toxicity. Alternatively, a combination of both may be responsible, as the release of ions would be expected to be greater for smaller particles.