Nanoparticle-DNA conjugates bearing a specific number of short DNA strands by enzymatic manipulation of nanoparticle-bound DNA

Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.     

Detecting DNA methylation through changes in transverse proton relaxation

We present a facile, simple method to detect DNA methylation by measuring the transverse proton relaxation behaviour. Positively charged nanoparticles are arranged along the negatively charged backbone of DNA strands through electrostatic interactions. The arrangement of NPs along DNA strands aids to amplify and compare the transverse proton relaxation signal for un-cut versus cut DNA strands cleaved by sequence specific restriction enzymes. Results from this study suggest that the presence of methylation on DNA can be detected using superparamagnetic NPs using NMR.     

Cationic PLA nanoparticles for DNA delivery: comparison of three surface polycations for DNA binding, protection and transfection properties

Biodegradable cationic nanoparticles (cNP) made of poly(lactide) (PLA) have been shown to be promising carrier systems for in vivo DNA delivery and immunization. In previous work, we have described a versatile approach for the elaboration of cationic PLA cNP based on the use of pre-formed particles and subsequent adsorption of a model polycation, the poly(ethylenimine) (PEI). Here, we evaluated two more polycations, chitosan and poly(2-dimethyl-amino)ethyl methacrylate (pDMAEMA)) to determine the most suitable one for the development of PLA cNP as DNA carriers. Cationic PLA-PEI, PLA-chitosan and PLA-pDMAEMA nanoparticles were compared for interaction with plasmid DNA and, more importantly, with regards to the biological properties of bound DNA. pDMAEMA coating yielded the most positively charged nanoparticles with the highest DNA binding capacity (32 mg/g). Loaded with DNA, all three cNP were in the same size range ( approximately 500 nm) and had a negative zeta potential (-50 mV). PLA-chitosan was the only cNP that released DNA at pH 7; the two others required higher pH. Adsorption and release from cNP did not alter structural and functional integrity of plasmid DNA. Moreover, DNA coated onto cNP was partially protected from nuclease degradation, although this protection was less efficient for PLA-chitosan than others. The highest transfection efficiency in cell culture was obtained with PLA-pDMAEMA carriers. We have shown that at least three different cationic polymers (chitosan, PEI, pDMAEMA) can be used for the production of PLA-based particulate DNA carriers and most probably other cationic polymers can also be used in the same purpose. PLA-pDMAEMA cNP were the most promising system for DNA delivery in this in vitro study. Our future work will focus on the in vivo evaluation of these gene delivery systems.     

Sharp melting in DNA-linked nanostructure systems: thermodynamic models of DNA-linked polymers

Sharp melting that has been found for DNA-linked nanostructure systems such as DNA-linked gold nanoparticles enhances the resolution of DNA sequence detection enough to distinguish between a perfect match and single base pair mismatches. One intriguing explanation of the sharp melting involves the cooperative dehybridization of DNA strands between the nanostructures. However, in the DNA-linked gold nanoparticle system, strong optical absorption by the gold nanoparticles hinders the direct observation of cooperativity. Here, with a combination of theory and experiment, we investigate a DNA-linked polymer system in which we can show that the optical profile of the system at 260 nm is directly related to the individual DNA dehybridization profile, providing a clear distinction from other possible mechanisms. We find that cooperativity plays a crucial role in determining both the value of the melting temperature and the shape of the melting profile well away from the melting temperature. Our analysis suggests that the dehybridization properties of DNA strands in confined or dense structures differ from DNA in solution.     

Biochemically functionalized silica nanoparticles

In this report, we demonstrate the biochemical modification of silica based nanoparticles. Both pure and dye-doped silica nanoparticles were prepared, and their surfaces were modified with enzymes and biocompatible chemical reagents that allow them to function as biosensors and biomarkers. The nanoparticles produced in this work are uniform in size with a 1.6% relative standard deviation. They have a pure silica surface and can thus be modified easily with many biomolecules for added biochemical functionality. Specifically, we have modified the nanoparticle surfaces with enzyme molecules (glutamate dehydrogenase (GDH) and lactate dehydrogenase (LDH)) and a biocompatible reagent for cell membrane staining. Experimental results show that the silica nanoparticles are a good biocompatible solid support for enzyme immobilization. The immobilized enzyme molecules on the nanoparticle surface have shown excellent enzymatic activity in their respective enzymatic reactions. The nanoparticle surface biochemical functionalization demonstrates the feasibility of using nanoparticles for biosensing and biomarking applications.     

Ion-mediated interactions between charged and neutral nanoparticles

Monte-Carlo simulations are used to study the ion-mediated effective interaction between weakly charged and highly charged nanoparticles in an implicit solvent. Three models of nanoparticles are successively studied, from crude charged hard spheres to dipolar and non-spherical nanoparticles. The analysis of the effective potential revealed that in an electrolyte solution, even a neutral nanoparticle feels an important repulsive force in the presence of a charged nanoparticle, with a typical range similar to the Debye length. When the two nanoparticles carry charges of opposite sign, we have shown that this repulsion can reverse the effect of the direct attractive electrostatic potential at short distances. This also yields the change of sign of the effective potential as a function of the relative orientations of two anisotropic nanoparticles. Moreover, we found that the 3-body terms of the effective potentials can overcome the 2-body terms, which is not observed in the case of symmetrically charged nanoparticles.     

Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations

In this article, we investigate fluid-gel transformations of a DPPC lipid bilayer in the presence of nanoparticles, using coarse-grained molecular dynamics. Two types of nanoparticles are considered, specifically a 3 nm hydrophobic nanoparticle located in the core of the bilayer and a 6 nm charged nanoparticle located at the interface between the bilayer and water phase. Both negatively and positively charged nanoparticles at the bilayer interface are investigated. We demonstrate that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer. These effects are characterized using computer visualization of the gel phase in the presence of nanoparticles, radial distribution functions, and order parameters. The 3 nm hydrophobic nanoparticle immersed in the bilayer core and the positively charged nanoparticle at the bilayer surface have no effect on the temperature of the fluid-gel transformation, compared to the bulk case. Interestingly, a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.     

A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles

A highly sensitive and selective colorimetric lead biosensor based on DNAzyme-directed assembly of gold nanoparticles is reported. It consists of a DNAzyme and its substrate that can hybridize to a 5'-thio-modified DNA attached to gold nanoparticles. The hybridization brings gold nanoparticles together, resulting in a blue-colored nanoparticle assembly. In the presence of lead, the DNAzyme catalyzes specific hydrolytic cleavage, which prevents the formation of the nanoparticle assembly, resulting in red-colored individual nanoparticles. The detection level can be tuned to several orders of magnitude, from 100 nM to over 200 muM, through addition of an inactive variant of the DNAzyme. The concept developed here can be applied to the design of nucleic acid enzyme/nanoparticle sensors for analytes that are subject to in vitro selection, and thus can significantly expand the scope of nanomaterial applications and provide a novel approach to designing simple colorimetric biosensors.     

Colloidosomes from the controlled interaction of submicrometer triglyceride droplets and hydrophilic silica nanoparticles

The self-assembly of hydrophilic silica nanoparticles at the surface of charged submicrometer triglyceride droplets has been investigated with the aim to optimize the preparation of stable colloidosomes. The droplet charge, oil phase volume fraction, droplet/nanoparticle ratio, and salt concentration play important roles in controlling nanoparticle interactions and are reflected in the colloidosome zeta potential, size, stability, and interfacial structure (visualized by freeze-fracture SEM). Silica nanoparticle interactions with negatively charged droplets are weak, and partially covered droplets are identified. Positively charged droplets are strongly coated by silica nanoparticles and undergo charge reversal at specific droplet to nanoparticle ratios and electrolyte concentrations. Droplets at volume fractions (varphi) <10 (-4) undergo time-dependent limited coalescence until nanoparticle coverage is complete. For varphi in the range 10 (-4) to 2.5 x 10 (-4) and at certain critical droplet to nanoparticle ratios, droplets undergo neutralization or charge reversal coupled with aggregation and precipitation; this occurs in a time-independent manner. Specific conditions have been identified where stable 1-3 mum colloidosomes can be phase separated from heterocoagulates of droplets and nanoparticles.     

What controls the melting properties of DNA-linked gold nanoparticle assemblies?

We report a series of experiments and a theoretical model designed to systematically define and evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that contribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures. These variables include the size of the nanoparticles, the surface density of the oligonucleotides on the nanoparticles, the dielectric constant of the surrounding medium, target concentration, and the position of the nanoparticles with respect to one another within the aggregate. The experimental data may be understood in terms of a thermodynamic model that attributes the sharp melting to a cooperative mechanism that results from two key factors: the presence of multiple DNA linkers between each pair of nanoparticles and a decrease in the melting temperature as DNA strands melt due to a concomitant reduction in local salt concentration. The cooperative melting effect, originating from short-range duplex-to-duplex interactions, is independent of DNA base sequences studied and should be universal for any type of nanostructured probe that is heavily functionalized with oligonucleotides. Understanding the fundamental origins of the melting properties of DNA-linked nanoparticle aggregates (or monolayers) is of paramount importance because these properties directly impact one's ability to formulate high sensitivity and selectivity DNA detection systems and construct materials from these novel nanoparticle materials.     

Fabrication of ordered metallic and magnetic heterostructured DNA-Nanoparticle hybrids

Here we provide a method based on enzymatically catalyzed reactions to cleave and ligate DNA molecules coated with nanoparticles to fabricate multi-component structures. This is done by simultaneously digesting two solutions of nanoparticle coated DNA, one with iron oxide particles the other gold particles, which yields short DNA fragments with complementary single stranded overhangs. When added together and re-attached using ligase enzymes multi-component nanoparticle coated structures are formed providing a novel method to fabricate complicated nanoparticle arrangements from the bottom up. We evaluated the fabrication by characterizing the samples with gel electrophoresis and magnetic force microscopy (MFM). The electrophoresis provides proof that the coated DNA molecules were digested with restriction enzymes and ligated by the T4 ligase enzymes. MFM experiments allow us to visualize the multi-component strands and analyze the magnetic versus metallic segments.     

Corking nano test tubes by chemical self-assembly

There is tremendous current interest in using nanoparticles to deliver biomolecules and macromolecules (e.g., drugs and DNA) to specific sites in living systems. Release of the biomedical payload from the nanoparticle can be accomplished by chemical or enzymatic degradation of the nanoparticle or of the link between the payload and the nanoparticle. We are exploring an alternative payload-release strategy that builds on our work on template-synthesized nano test tubes. These are hollow nanotubes that are closed on one end and open on the other, and the dimensions can be controlled at will. If these nano test tubes could be filled with a payload and then the open end corked with a chemically labile cap, they might function as a universal delivery vehicle. We show here that silica nano test tubes can be covalently corked by chemical self-assembly of nanoparticles to the tubes. We also show that the nanoparticle corks remain attached to the mouths of the nano test tubes after liberation from the alumina template. For this proof-of-principle study, we used simple imine linkages to attach the corks to the test tubes. Schiff's bases are thermodynamically unstable in the presence of water; however, the multiple points of contact between the nano test tubes and nanoparticles allow the assembled structure to be metastable under our experimental conditions. Other chemical linkages-either more or less stable-may be more appropriate for other applications, and these are currently under development.     

Effective interactions in mixtures of silica microspheres and polystyrene nanoparticles

We investigate the effect of small concentrations of highly charged nanoparticles on the stability of uncharged colloidal microspheres using large-scale simulations. Employing pair potentials that accurately represent mixtures of silica microspheres and polystyrene nanoparticles as studied experimentally, we are able to demonstrate that nanoparticle-induced stabilization can arise from a relatively weak van der Waals attraction between the colloids and nanoparticles. This demonstrates that the nanoparticle haloing mechanism for colloidal stabilization is of considerable generality and potentially can be applied to large classes of systems. The range of optimal nanoparticle concentrations can be tuned by controlling the attraction between colloids and nanoparticles.     

Aptamer enzymatic cleavage protection assay for the gold nanoparticle-based colorimetric sensing of small molecules

A label-free, homogeneous aptamer-based sensor strategy was designed for the facile colorimetric detection of small target molecules. The format relied on the target-induced protection of DNA aptamer from the enzymatic digestion and its transduction into a detectable signal through the length-dependent adsorption of single-stranded DNA onto unmodified gold nanoparticles (AuNPs). The proof-of-principle of the approach was established by employing the anti-tyrosinamide aptamer as a model functional nucleic acid. In the absence of target, the aptamer was cleaved by the phosphodiesterase I enzymatic probe, leading to the release of mononucleotides and short DNA fragments. These governed effective electrostatic stabilization of AuNPs so that the nanoparticles remained dispersed and red-colored upon salt addition. Upon tyrosinamide binding, the enzymatic cleavage was impeded, resulting in the protection of the aptamer structure. As this long DNA molecule was unable to electrostatically stabilize AuNPs, the resulting colloidal solution turned blue after salt addition due to the formation of nanoparticle aggregates. The quantitative determination of the target can be achieved by monitoring the ratio of absorbance at 650 and 520 nm of the gold colloidal solution. A limit of detection of ∼5 μM and a linear range up to 100 μM were obtained. The sensing platform was further applied, through the same experimental protocol, to the adenosine detection by using its DNA aptamer as recognition tool. This strategy could extend the potentialities, in terms of both simplicity and general applicability, of the aptamer-based sensing approaches.     

DNA-polymer micelles as nanoparticles with recognition ability

The Watson-Crick binding of DNA single strands is a powerful tool for the assembly of nanostructures. Our objective is to develop polymer nanoparticles equipped with DNA strands for surface-patterning applications, taking advantage of the DNA technology, in particular, recognition and reversibility. A hybrid DNA copolymer is synthesized through the conjugation of a ssDNA (22-mer) with a poly(ethylene oxide)-poly(caprolactone) diblock copolymer (PEO-b-PCl). It is shown that, in water, the PEO-b-PCl-ssDNA(22) polymer forms micelles with a PCl hydrophobic core and a hydrophilic corona made of PEO and DNA. The micelles are thoroughly characterized using electron microscopy (TEM and cryoTEM) and small-angle neutron scattering. The binding of these DNA micelles to a surface through DNA recognition is monitored using a quartz crystal microbalance and imaged by atomic force microscopy. The micelles can be released from the surface by a competitive displacement event.     

Multilayers of oppositely charged SiO2 nanoparticles: effect of surface charge on multilayer assembly

The growth behavior of all-silica nanoparticle multilayer thin films assembled via layer-by-layer deposition of oppositely charged SiO2 nanoparticles was studied as a function of assembly conditions. Amine-functionalized SiO2 nanoparticles were assembled into multilayers through the use of three different sizes of negatively charged SiO2 nanoparticles. The assembly pH of the nanoparticle suspensions needed to achieve maximum growth for each system was found to be different. However, the surface charge /z/ of the negatively charged silica nanoparticles at the optimal assembly pH was approximately the same, indicating the importance of this parameter in determining the growth behavior of all-nanoparticle multilayers. When /z/ of the negatively charged nanoparticles lies between 0.6z(0) and 1.2z(0) (where z(0) is the pH-independent value of the zeta-potential of the positively charged nanoparticles used in this study), the multilayers show maximum growth for each system. The effect of particle size on the film structure was also investigated. Although nanoparticle size significantly influenced the average bilayer thickness of the multilayers, the porosity and refractive index of multilayers made from nanoparticles of different sizes varied by a small amount. For example, the porosity of the different multilayer systems ranged from 42 to 49%. This study further demonstrates that one-component all-nanoparticle multilayers can be assembled successfully by depositing nanoparticles of the same material but with opposite surface charge.     

Interaction forces between colloidal particles in a solution of like-charged, adsorbing nanoparticles

We have measured the force between a weakly charged micron-sized colloidal particle and flat substrate in the presence of highly charged nanoparticles of the same sign under solution conditions such that the nanoparticles physically adsorb to the colloidal particle and substrate. The objective was to investigate the net effect on the force profile between the microparticle and flat substrate arising from both nanoparticle adsorption and nanoparticles in solution. The experiments used colloidal probe atomic force microscopy (CP-AFM) to measure the force profile between a relatively large (5 μm) colloidal probe glass particle and a planar glass substrate in aqueous solutions at varying concentrations of spherical nanoparticles. At very low nanoparticle concentrations, the primary effect was an increase in the electrostatic repulsion between the surfaces due to adsorption of the more highly charged nanoparticles. As the nanoparticle concentration is increased, a depletion attraction formed, followed by longer-range structural forces at the highest nanoparticle concentrations studied. These results suggest that, depending on their concentration, such nanoparticles can either stabilize a dispersion of weakly-charged colloidal particles or induce flocculation. This behavior is qualitatively different from that in nonadsorbing systems, where the initial effect is the development of an attractive depletion force.     

Polycationic Pillar[5]arene Derivatives: Interaction with DNA and Biological Applications

Dendritic pillar[5]arene derivatives have been efficiently prepared by grafting dendrons with peripheral Boc‐protected amine subunits onto a preconstructed pillar[5]arene scaffold. Upon cleavage of the Boc‐protected groups, water‐soluble pillar[5]arene derivatives with 20 ( 13 ) and 40 ( 14 ) peripheral ammonium groups have been obtained. The capability of these compounds to form stable nanoparticles with plasmid DNA has been demonstrated by gel electrophoresis, transmission electron microscopy (TEM), and dynamic light scattering (DLS) investigations. Transfection efficiencies of the self‐assembled 13 /pCMV‐Luc and 14 /pCMV‐Luc polyplexes have been evaluated in vitro with HeLa cells. The transfection efficiencies found for both compounds are good, and pillar[5]arenes 13 and 14 show very low toxicity if any.     

Direct monitoring of DNA cleavages catalyzed by an ATP-dependent deoxyribonuclease on a 27 MHz quartz-crystal microbalance

Kinetic studies of enzymatic DNA cleavage reactions (the enzyme binding, hydrolysis along DNA strands, and then release of the enzyme from the completely hydrolyzed ssDNA) were carried out on a 27 MHz quartz-crystal microbalance.     

Silica nanoparticles at interfaces modulated by amphiphilic polymer and surfactant

The interfacial behavior of silica nanoparticles in the presence of an amphiphilic polymer poly( N-isopropylacrylamide) (PNIPAM) and an anionic surfactant sodium dodecyl sulfate (SDS) is studied using neutron reflectivity. While the nanoparticles do not show any attraction to hydrophilic and hydrophobic surfaces in pure water, presence of the amphiphilic polymer induces significant adsorption of the nanoparticles at the hydrophobic surface. This interfacial behavior is activated due to interaction of the nanoparticles with PNIPAM, the amphiphilic nature of which leads to strong adsorption at a hydrophobic surface but only weak interaction with a hydrophilic surface. The presence of SDS competes with nanoparticle-PNIPAM interaction and in turn modulates the interfacial properties of the nanoparticles. These adsorption results are discussed in relation to nanoparticle organization templated by dewetting of charged polymer solutions on a solid substrate. Our previous studies showed that nanoparticle assembly can be induced to form complex morphologies produced by dewetting of the polymer solutions, such as a polygonal network and long-chain structures. This approach, however, works on a hydrophilic substrate but not on a hydrophobic substrate. These observations can be explained in part by particle-substrate interactions revealed in the present study.