Structures of DNA-linked nanoparticle aggregates

The room-temperature structure of DNA-linked gold nanoparticle aggregates is investigated using a combination of experiment and theory. The experiments involve extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30 base-pair DNA. The theoretical studies use calculated spectra for models of the aggregate structures to determine which structure matches the observations. These models include diffusion-limited cluster-cluster aggregation (DLCA), reaction-limited cluster-cluster aggregation (RLCA), and compact (nonfractal) cluster aggregation. The diameter of the nanoparticles used in the experiments is larger than has been considered previously, and this provides greater sensitivity of spectra to aggregate structure. We show that the best match between experiment and theory occurs for the RLCA fractal structures. This indicates that DNA hybridization takes place under irreversible conditions in the room-temperature aggregation. Some possible structural variations which might influence the result are considered, including the edge-to-edge distance between nanoparticles, variation in the diameter of the nanoparticles, underlying lattice structures of on-lattice compact clusters, and positional disorders in the lattice structures. We find that these variations do not change the conclusion that the room-temperature structure of the aggregates is fractal. We also examine the variation in extinction at 260 nm as temperature is increased, showing that the decrease in extinction at temperatures below the melting temperature is related to a morphological change from fractal toward compact structures.     

Phase transitions in DNA-linked nanoparticle assemblies: a decorated-lattice model

We use decorated-lattice models to explore the phase behavior of two types of DNA-linked colloidal mixtures: systems with identical nanoparticles functionalized with two different DNA strands (mixture Aab) and mixtures involving two types of particles each one functionalized with a different DNA strand (mixture Aa-Ab). The model allows us to derive the properties of the mixtures from the well-known behavior of underlying spin-n Ising models with temperature and activity dependent effective interactions. The predicted evolution of the dissolution profiles for the colloidal assemblies as a function of temperature and number of single DNA strands on a nanoparticle M is in qualitative agreement with that observed in real systems. According to our model, the temperature at which the assemblies dissolve can be expected to increase with increasing M only for concentrations of colloids below a certain threshold. For more concentrated solutions, the dissolution temperature is a decreasing function of M. Linker-mediated interactions between Aa and Ab particles in the Aa-Ab mixture render the phase separation involving disordered aggregates metastable with respect to a phase transition between a solvent-rich and an ordered phase. The stability of the DNA-linked assembly is enhanced by the ordering of the colloidal network and the ordered aggregates dissolve at higher temperatures. Our results may explain the contrasting evolution of the dissolution temperatures with increasing probe size in Aab and Aa-Ab mixtures as observed experimentally.     

Stability of DNA-linked nanoparticle crystals: effect of number of strands, core size, and rigidity of strand attachment

Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)].     

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.     

Hybridization of oligonucleotide-modified silver and gold nanoparticles in aqueous dispersions and on gold films

Functionalization of silver and gold nanoparticles by 12mer-thiolated homo-oligonucleotides, SA and ST (containing only adenine or thymine, respectively), and their hybridization and dehybridization in aqueous dispersions have been described. In addition, ST and SA were self-assembled onto gold films and hybridized with their complementary pairs, unlabeled or labeled by gold and silver nanoparticles. The base pairing between DNA strands and the types of oligonucleotides (adenine or thymine) attached to the nanoparticles was detected by Polarization Modulated Fourier Transform Infrared Reflection Absorption Spectroscopy (PM-FTIRRAS).     

Molecular dynamics studies of ion distributions for DNA duplexes and DNA clusters: salt effects and connection to DNA melting

We present extensive molecular dynamics simulations of the ion distributions for DNA duplexes and DNA clusters using the Amber force field with implicit water. The distribution of ions and the electrostatic energy of ions around an isolated DNA duplex and clusters of DNA duplexes in different salt (NaCl) concentrations over the range 0.2-1.0 mol/L are determined on the basis of the simulation results. Using the electrostatic energy profile, we determine a local net charge fraction phi, which is found to increase with increasing of salt concentration. For DNA clusters containing two DNA duplexes (DNA pair) or four DNA duplexes, phi increases as the distance between the duplexes decreases. Combining this result with experimental results for the dependence of the DNA melting temperature on bulk salt concentration, we conclude that for a pair of DNA duplexes the melting temperature increases by 5-10 K for interaxis separations of 25-40 A. For a cluster of four DNA duplexes, an even larger melting temperature increase should occur. We argue that this melting temperature increase in dense DNA clusters is responsible for the cooperative melting mechanism in DNA-linked nanoparticle aggregates and DNA-linked polymer aggregates.     

Non-base pairing DNA provides a new dimension for controlling aptamer-linked nanoparticles and sensors

DNA aptamers have been recently applied as simple and fast colorimetric sensors for a wide range of molecules. A unique feature of these systems is the presence of non-base pairing oligonucleotides in both DNA aptamers and spacers on DNA-functionalized nanoparticles. We report here a systematic investigation on an adenosine aptamer-linked gold nanoparticle system. When the aptamer overhang and the spacer were aligned on the same side, adenosine-responsive disassembly was inhibited. This inhibition effect increased with the length of the spacer, and fully inhibited activity was observed with the spacer containing more than three nucleotides. In contrast to a linear relationship between the spacer length and melting temperature in double-stranded DNA systems without overhangs, the aptamer system displayed a nonlinear relationship, with the melting temperature decreasing exponentially with spacer length. Control experiments suggested that this inhibition effect was due to thermodynamic factors rather than kinetic traps. A comparison with aptamer beacon systems indicated that nanoparticles may play an important role in this inhibition effect, and no specific interactions between the aptamer overhang and spacer were detected. The identity of nucleotides in the spacer did not affect the conclusions. Furthermore, the rate of disassembly or color change was slower at lower temperature or higher ionic strength, but was little affected by pH from 5.2 to 9.2. Therefore, non-base pairing DNA provided another dimension for controlling DNA-linked nanoparticles in addition to pH, temperature, or ionic strength, and this knowledge has resulted in the most optimal construct for sensing applications.     

Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies

Using a simple mean-field model, we analyze the surface and bulk dissolution properties of DNA-linked nanoparticle assemblies. We find that the dissolution temperature and the sharpness of the dissolution profiles increase with the grafting density of the single-stranded DNA "probes" on the surface of colloids. The surface grafting density is controlled by the linker occupation number, in analogy with quantum particles obeying fractional statistics. The dissolution temperature increases logarithmically with the salt concentration. This is in agreement with the experimental findings [R. Jin, G. Wu, Z. Li, C. A. Mirkin, and G. C. Schatz, J. Am. Chem. Soc. 125, 1643 (2003)]. By exploiting the unique phase behavior of DNA-coated colloids, it should be possible to detect multiple "targets" in a single experiment by essentially mapping the DNA base-pair sequence onto the phase behavior of DNA-linked nanoparticle solution.     

Optically Triggered Melting of DNA on Individual Semiconducting Carbon Nanotubes

Optical excitation of nanostructures is known to induce local heating, a phenomenon that has been intensely exploited for drug release, gene delivery, cancer thermotherapy, and energy harvesting. However, the effect is typically small requiring collective heating of a large concentration or aggregates of particles. Herein, we show that optical excitation of individual semiconducting single‐walled carbon nanotubes triggers strongly localized heating adequate to melt non‐covalently attached double‐stranded oligonucleotides in solution. In contrast to conventional thermal dehybridization, this optically triggered DNA melting occurs at a solution temperature that is 22 °C lower than the DNA melting temperature. This unexpectedly large localized optical heating effect provides important new insights to design selective optical nanoheaters at the single particle level.     

A two-color-change, nanoparticle-based method for DNA detection

Herein, we describe the detailed synthesis of Ag/Au core-shell nanoparticles, the surface-functionalization of these particles with thiolated oligonucleotides, and their subsequent use as probes for DNA detection. The Ag/Au core-shell nanoparticles retain the optical properties of the silver core and are easily functionalized with thiolated oligonucleotides due to the presence of the gold shell. As such, the Ag/Au core-shell nanoparticles have optical properties different from their pure gold counterparts and provide another “color” option for target DNA-directed colorimetric detection. Size-matched Ag/Au core-shell and pure gold nanoparticles perform nearly identically in DNA detection and melting experiments, but with distinct optical signatures. Based on this observation, we report the development of a two-color-change method for the detection and simultaneous validation of single-nucleotide polymorphisms in a DNA target using Ag/Au core-shell and pure gold nanoparticle probes.     

Defects can increase the melting temperature of DNA-nanoparticle assemblies

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to developing reliable detection technology. We studied the effects of DNA base-pairing defects, such as mismatches and deletions, on the melting temperature of DNA-nanoparticle assemblies. We found that, contrary to the general assumption that defects lower the melting temperature of DNA, some defects increase the melting temperature of DNA-linked nanoparticle assemblies. The effects of mismatches and deletions were found to depend on the specific base pair, the sequence, and the location of the defects. Our results demonstrate that the surface-bound DNA exhibit hybridization behavior different from that of free DNA. Such findings indicate that a detailed understanding of DNA-nanoparticle assembly phase behavior is required for quantitative interpretation of DNA-nanoparticle aggregation.     

Rapid synthesis of stable and functional conjugates of DNA/gold nanoparticles mediated by Tween 80

Gold nanoparticles conjugated with DNA represent an attractive and alternative platform for broad applications in biosensors, medical diagnostic, and biological analysis. However, current methods to conjugate DNA to gold nanoparticles are time-consuming. In this study, we report a novel approach to rapidly conjugate DNA to gold nanoparticles (AuNPs) to form functional DNA/AuNPs in 2-3 h using Tween 80 as protective agent. With a fluorescence-based technique, we determine that the DNA density on the surface of AuNPs achieves about ～60 strands per particles, which is comparable to the loading density in the current methods. Moreover, the DNA/AuNPs synthesized by our approach exhibit an excellent stability as a function of temperature, pH, and freeze-thaw cycle, and the functionality of DNA/AuNPs conjugates is also verified. The work presented here has important implications to develop the fast and reproducible synthesis of stable DNA-functionalized gold nanoparticles.     

Cooperative melting in caged dimers of rigid small molecule-DNA hybrids

Rigid small-molecule DNA hybrids (rSMDHs) have been synthesized with three DNA strands attached to a rigid tris(phenylacetylene) core. When combined under dilute conditions, complementary rSMDHs form cage dimers that melt at >10 degrees C higher and much sharper than either unmodified DNA duplexes or rSMDH aggregates formed at higher concentrations. With a 2.97 average number of cooperative duplexes, these caged dimers constitute the first example of cooperative melting in well-defined DNA-small-molecule structures, demonstrating the important roles that local geometry and ion concentration play in the hybridization/dehybridization of DNA-based materials.     

Mechano-chemical stability of gold nanoparticles coated with alkanethiolate SAMs

Molecular dynamics simulations are used to probe the structure and stability of alkanethiolate self-assembled monolayers (SAMs) on gold nanoparticles. We observed that the surface of gold nanoparticles becomes highly corrugated by the adsorption of the SAMs. Furthermore, as the temperature is increased, the SAMs dissolve into the gold nanoparticle, creating a liquid mixture at temperatures much lower than the melting temperature of the gold nanoparticle. By analyzing the mechanical and chemical properties of gold nanoparticles at temperatures below the melting point of gold, with different SAM chain lengths and surface coverage properties, we determined that the system is metastable. The model and computational results that provide support for this hypothesis are presented.     

Electrochemical identification of artificial oligonucleotides related to bovine species. Potential for identification of species based on mismatches in the mitochondrial cytochrome C1 oxidase gene

Our studies show that electrochemical impedance spectroscopy (EIS) and scanning electrochemical microscopy (SECM) of films of ds-DNA on gold allow us to distinguish between mitochondrial DNA fragments of the cytochrome c(1) oxidase (mt-Cox1) of three related species of the subfamily 'Bovinae' (Bos taurus, Bison bison, and Bison bonasus). In EIS, a perfectly matched DNA gives rise to a considerably larger charge transfer resistance R(ct) compared to mismatched pairings. Differences in charge transfer resistance, ΔR(ct), before and after the addition of Zn(2+) ions provide an additional tool for identification. In addition, all ds-DNA films were studied by SECM and their kinetic parameters were determined. Perfectly matched ds-DNAs are readily distinguished from mismatched duplexes by their lower rate constants. Our system can be used multiple times by dehybridization and rehybridization of capture strands up to the 250 pmole level.     

A DNA–Azobenzene Nanopump Fueled by Upconversion Luminescence for Controllable Intracellular Drug Release

Stimulus‐responsive drug release possesses considerable significance in cancer therapy. This work reports an upconversion‐luminescence‐fueled DNA–azobenzene nanopump for rapid and efficient drug release. The nanopump is constructed by assembling the azobenzene‐functionalized DNA strands on upconversion nanoparticles (UCNPs). Doxorubicin (DOX) is loaded in the nanopump by intercalation in the DNA helix. Under NIR light, the UCNPs emit both UV and visible photons to fuel the continuous photoisomerization of azo, which acts as an impeller pump to trigger cyclic DNA hybridization and dehybridization for controllable DOX release. In a relatively short period, this system demonstrates 86.7 % DOX release. By assembling HIV‐1 TAT peptide and hyaluronic acid on the system, targeting of the cancer‐cell nucleus is achieved for perinuclear aggregation of DOX and enhanced anticancer therapy. This highly effective drug delivery nanopump could contribute to chemotherapy development.     

Ultrafast cooling of photoexcited electrons in gold nanoparticle-thiolated DNA conjugates involves the dissociation of the gold-thiol bond

Using UV-visible extinction spectroscopy and femtosecond pump-probe transient absorption spectroscopy, we have studied the effect of femtosecond laser heating on gold nanoparticles attached to DNA ligands via thiol groups. It is found that femtosecond pulse excitation of the DNA-modified nanoparticles at a wavelength of 400 nm leads to desorption of the thiolated DNA strands from the nanoparticle surface by the dissociation of the gold-sulfur bond. The laser-initiated gold-sulfur bond-breaking process is a new pathway for nonradiative relaxation of the optically excited electrons within the DNA-modified gold nanoparticles, as manifested by a faster decay rate of the excited electronic distribution at progressively higher laser pulse energies. The experimental results favor a bond dissociation mechanism involving the coupling between the photoexcited electrons of the nanoparticles and the gold-sulfur bond vibrations over one involving the conventional phonon-phonon thermal heating processes. The latter processes have been observed previously by our group to be effective in the selective photothermal destruction of cancer cells bound to anti-epidermal growth factor receptor-conjugated gold nanoparticles.     

Preferentially linear connection of gold nanoparticles in derivatization with phosphorothioate oligonucleotides

A gold nanosphere in water is considered to attain special stability in derivatization like an artificial atom when the octet rule is satisfied by forming four covalent bonds with two 5'-phosphorothioate-modified oligonucleotide molecules. Owing to this, the hybridization of two mutually complementary gold-bound oligonucleotides makes gold nanospheres preferentially connected linearly by duplexes to produce strands like linear artificial molecules. We have then fixated the linear strands of DNA-linked gold nanospheres by reducing Ag(+) ion clusters immobilized around duplexes to show the absorption spectrum of silver-coated artificial-molecular nanorods.     

Thermodynamics of DNA hybridization on gold nanoparticles

Dynamic light scattering is used as a sensitive probe of hybridization on DNA-functionalized colloidal gold nanoparticles. When a target DNA strand possesses an 8 base "dangling end", duplex formation on the surface of the nanoparticles leads to an increase in hydrodynamic radius. Duplex melting is manifested in a drop in hydrodynamic radius with increasing temperature, and the concentration dependence of the melting temperature provides a measure of the thermodynamics of binding. The hybridization thermodynamics are found to be significantly lower at higher hybridization densities than those previously reported for initial hybridization events. The pronounced deviation from Langmuir adsorption behavior is greater for longer duplexes, and it is, therefore, consistent with electrostatic repulsion between densely packed oligonucleotides. The results have implications for sensing and DNA-directed nanoparticle assembly.     

Size-dependent melting of silica-encapsulated gold nanoparticles

We report on the size dependence of the melting temperature of silica-encapsulated gold nanoparticles. The melting point was determined using differential thermal analysis (DTA) coupled to thermal gravimetric analysis (TGA) techniques. The small gold particles, with sizes ranging from 1.5 to 20 nm, were synthesized using radiolytic and chemical reduction procedures and then coated with porous silica shells to isolate the particles from one another. The resulting silica-encapsulated gold particles show clear melting endotherms in the DTA scan with no accompanying weight loss of the material in the TGA examination. The silica shell acts as a nanocrucible for the melting gold with little effect on the melting temperature itself, even though the analytical procedure destroys the particles once they melt. Phenomenological thermodynamic predictions of the size dependence of the melting point of gold agree with the experimental observation. Implications of these observations to the self-diffusion coefficient of gold in the nanoparticles are discussed, especially as they relate to the spontaneous alloying of core-shell bimetallic particles.