DNA-linked Nanoparticle Research Articles

Domain-Selective Enzymatic Cross-linking and Etching for Shape-Morphing DNA-Linked Nanoparticle Films.

The highly programmable and responsive molecular recognition properties of DNA provide unparalleled opportunities for fabricating dynamic nanostructures capable of structural transformation in response to various external stimuli. However, they typically operate in tightly controlled environments because certain conditions (ionic strength, pH, temperature, etc.) must be met for DNA duplex formation. In this study, we adopted site-specific enzymatic ligation and DNA-based layer-by-layer thin film fabrication to build shape-morphing DNA-linked nanoparticle films operational in a broad range of environments. The ligated films remained intact in unusual conditions such as pure water and high temperature causing dissociation of DNA duplexes and showed predictable and reversible shape morphing in response to various environmental changes and DNA exchange reactions. Furthermore, domain-selective ligation combined with photoinduced interlayer mixing allowed for the fabrication of unusual edge-sealed double-layered films through midlayer etching, which is difficult to realize by other methods.

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

Stimuli-Responsive DNA-Linked Nanoparticle Arrays as Programmable Surfaces

Self- and directed-assembly approaches have enabled precise control over the composition and geometry of 2D and 3D nanoparticle constructs. However, the resulting structures are typically static, providing only a single structural arrangement of the nanoparticle building blocks. In this work, the power of DNA-linked nanoparticle assembly is coupled to a grayscale patterning technique to create programmable surfaces for assembly and thermally activated reorganization of gold nanoparticle arrays. Direct grayscale patterning of DNA monolayers by electron-beam lithography (DNA-EBL) enables the production of surfaces with nanometer-scale control over the density of functional DNA. This enables tuning of the particle-surface interactions with single-nanoparticle resolution and without the need for a physical template as employed in most directed assembly methods. This technique is applied on suspended membrane structures to achieve high-resolution assembly of 2D nanoparticle arrays with highly mutable architectures. Gold nanorods assembled on grayscale-patterned surfaces exhibit temperature-dependent configurations and ordering behavior that result in tunable polarization-dependent optical properties. In addition, spherical gold particles assembled from a bimodal suspension produce arrays with temperature-dependent configurations of small and large particles. These results have important implications for the design and fabrication of reconfigurable nanoparticle arrays for application as structurally tunable optical metasurfaces.

Spermine induced reversible collapse of deoxyribonucleic acid-bridged nanoparticle-based assemblies

DNA-linked 2D and 3D nano-assemblies find use in a diverse set of applications, ranging from DNA-origami in drug delivery and medical imaging, to DNA-linked nanoparticle structures for use in plasmonics and (bio)sensing. However, once these structures have been fully assembled, few options are available to modulate structure geometry. Here, we investigated the use of the polycation spermine to induce DNA collapse in small oligonucleotide-linked (54 bp) gold nanoparticle structures by monitoring shifts in the localized surface plasmon resonance (LSPR) peak and by comparing the data with finite-difference time-domain (FDTD) simulations. Our data shows that low concentrations of spermine can be applied to induce large changes in DNA conformation, leading to a significant reduction in interparticle distance (from ∼25 to ∼3 nm) and enhanced plasmonic coupling. The DNA collapse is near-instantaneous and reversible, and its application at low and high DNA densities is demonstrated with surface plasmon resonance imaging (SPRi), showing the potential of spermine to dynamically modulate distances and geometry in DNA-based nano-assemblies.

Surface plasmon resonance biosensor for sensitive detection of microRNA and cancer cell using multiple signal amplification strategy

A sensitive and versatile surface plasmon resonance (SPR) biosensor was proposed for the detection of microRNA (miRNA) and cancer cell based on multiple signal amplification strategy. Thiol-modified hairpin probe, including a sequence complementary to the target miRNA, was first immobilized on the Au film. In the presence of target miRNA, the stem-loop structure of hairpin probe was unfolded, and then DNA-linked Au nanoparticles (AuNPs) were hybridized with the terminus of the unfolded hairpin probe. Subsequently, DNA-linked AuNPs initiated the formation of DNA supersandwich structure through the addition of two report DNA sequences. Owing to the electronic coupling between localized plasmon of the AuNPs and the surface plasmon wave, as well as the enhancement of the refractive index of the medium over the Au film induced by DNA supersandwich structure, the SPR response was significantly enhanced. Next, numerous positively charged silver nanoparticles (AgNPs) were absorbed onto the long-range DNA surpersandwich equably, resulting in a further increase of SPR response. Due to the enzyme-free multiple signal amplification strategy, as low as ca. 0.6 fM miRNA-21 could be detected. In addition, this biosensor showed high selectivity toward single-base mismatch. More importantly, this SPR biosensor was also used for cancer cell detection coupled with the cell-specific aptamer modified magnetic nanoparticles. Given that the biosensor avoided enzyme introduction, the limitation of the enzyme was overcome. The versatile biosensor has great potential for the broad applications in the field of clinical analysis.

Induced nanoparticle aggregation for short nucleic acid quantification by depletion isotachophoresis

A rapid (<20min) gel-membrane biochip platform for the detection and quantification of short nucleic acids is presented based on a sandwich assay with probe-functionalized gold nanoparticles and their separation into concentrated bands by depletion-generated gel isotachophoresis. The platform sequentially exploits the enrichment and depletion phenomena of an ion-selective cation-exchange membrane created under an applied electric field. Enrichment is used to concentrate the nanoparticles and targets at a localized position at the gel-membrane interface for rapid hybridization. The depletion generates an isotachophoretic zone without the need for different conductivity buffers, and is used to separate linked nanoparticles from isolated ones in the gel medium and then by field-enhanced aggregation of only the linked particles at the depletion front. The selective field-induced aggregation of the linked nanoparticles during the subsequent depletion step produces two lateral-flow like bands within 1cm for easy visualization and quantification as the aggregates have negligible electrophoretic mobility in the gel and the isolated nanoparticles are isotachophoretically packed against the migrating depletion front. The detection limit for 69-base single-stranded DNA targets is 10 pM (about 10 million copies for our sample volume) with high selectivity against nontargets and a three decade linear range for quantification. The selectivity and signal intensity are maintained in heterogeneous mixtures where the nontargets outnumber the targets 10,000 to 1. The selective field-induced aggregation of DNA-linked nanoparticles at the ion depletion front is attributed to their trailing position at the isotachophoretic front with a large field gradient.

Sharpening the Thermal Release of DNA from Nanoparticles: Towards a Sequential Release Strategy

Unlike the sharp melting behavior of DNA-linked nanoparticle aggregates, the melting of DNA strands from individual gold nanoparticles is broad despite the high surface density of bound DNA. Here, it is demonstrated how sharpened melting can be achieved in colloidal nanoparticle systems using branched DNA-doubler structures hybridized with complementary DNA-doublers bound to the gold nanoparticle. Moreover, sharpened transitions are observed when DNA-doublers are hybridized with linear DNA-modified gold nanoparticles. This result suggests that the DNA density on nanoparticles is intrinsically great enough to form cooperative structures with the DNA-doublers. Finally, by introducing abasic destabilizing groups, the melting temperature of these DNA-doublers decreases without decreasing the sharpness. Consequently, by varying the temperature, two DNA-doublers with different stabilities dissociate sequentially from the gold nanoparticle surface, without overlapping and within a narrow temperature window. Owing to the excellent thermal selectivities exhibited by this system, the implementation of DNA-doublers in sequential photothermal therapies and with other nanomedicine delivery agents that rely on DNA dissociation as the mechanism of selective release is anticipated.

Photoswitchable Oligonucleotide-Modified Gold Nanoparticles: Controlling Hybridization Stringency with Photon Dose

We describe a new class of stimulus-responsive DNA-functionalized gold nanoparticles that incorporate azobenzene-modified oligonucleotides. Beyond the classic directed assembly and sensing behaviors associated with oligonucleotide-modified nanoparticles, these particles also exhibit reversible photoswitching of their assembly behavior. Exposure to UV light induces a trans-cis isomerization of the azobenzene which destabilizes the DNA duplex, resulting in dissociation of the nanoparticle assemblies. The isomerization is reversible upon exposure to blue light, resulting in rehybridization and reassembly of the DNA-linked nanoparticle clusters. We show that perfectly complementary and partially mismatched strands exhibit clearly distinguishable photoinduced melting properties, and we demonstrate that photon dose can thus be used in place of temperature or ionic strength to control hybridization stringency with the ability to discriminate single-base mismatches.

A fishnet electrochemical Hg2+sensing strategy based on gold nanoparticle-bioconjugate and thymine–Hg2+–thymine coordination chemistry

A novel electrochemical biosensing strategy based on a three-dimensional fishnet of DNA-linked nanoparticle supramolecular structure triggered by the analyst for detection of Hg(2+) has been designed. The detection limit is 7.38 pM and the sensor's selectivity and facility have been significantly improved.

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)].

Sequence-Selective Recognition of Nucleic Acids under Extremely Low Salt Conditions Using Nanoparticle Probes

Extensive secondary structures in nucleic acid targets seriously impede the binding of complementary oligonucleotide probes. We report here a method to conduct the detection under extremely low salt conditions where the secondary structures are less stable and more accessible. A new type of nanoparticle probes prepared by functionalizing gold nanoparticles with nonionic morpholino oligos is employed. Because of the salt-independent hybridization of the probes with nucleic acid targets, nanoparticle assemblies can be formed in 2 mM Tris buffer solutions containing 0-5 mM NaCl, leading to the colorimetric target recognition. The sharp melting transitions of the target-probe hybrids allow discrimination of single-base imperfection, including substitution, deletion, and insertion. The method works effectively in detecting sequences that are likely to form secondary structure. In addition, the study provides direct evidence of the relationship between the aggregate structure and the melting behavior of the DNA-linked nanoparticles.

Programmable Assembly of DNA-Functionalized Liposomes by DNA

Bionanotechnology involves the use of biomolecules to control both the structure and property of nanomaterials. One of the most studied examples is DNA-directed assembly of inorganic nanoparticles such as gold nanoparticles (AuNPs). However, systematic studies on DNA-linked soft nanoparticles, such as liposomes, are still lacking. We herein report the programmable assembly and systematic characterization of DNA-linked liposomes as a function of liposome size, charge, fluidity, composition, DNA spacer, linker DNA sequence, and salt concentration for direct comparison to DNA-directed assembly of AuNPs. Similar to the assemblies of AuNPs, sharp melting transitions were observed for liposomes where the first derivative of the melting curve full width at half-maximum (fwhm) is equal to or less than 1 °C for all of the tested liposomes, allowing sequence specific DNA detection. We found that parameters such as liposome size, charge, and fluidity have little effect on the DNA melting temperature. Cryo-TEM studies showed that programmable assemblies can be obtained and that the majority of the liposomes maintained a spherical shape in the assembled state. While liposome and AuNP systems are similar in many aspects, there are also important differences that can be explained by their respective physical properties.

Stability of DNA-linked nanoparticle crystals I: Effect of linker sequence and length

The creation of three-dimensional, crystalline-ordered nanoparticle (NP) structures linked by DNA has proved experimentally challenging. Here we aim to systematically study parameters that influence the relative thermodynamic and kinetic stability of such crystals. To avoid experimental bottlenecks and directly control molecular-scale parameters, we carry out molecular dynamics simulations of a coarse-grained model in which short DNA strands (6 to 12 bp) are tethered to a NP core. We examine the influence of the number of bases per strand L, number of linking bases and the number of spacer bases s on the stability of crystal states. We also consider the effect of using a single linking NP type versus a binary linking system. We explicitly compute the free energy, entropy, and melting point TM for BCC and FCC lattices. We show that binary systems are preferable for generating BCC lattices, while a single NP type generates the most stable FCC crystals. We propose a simple model for short DNA strands that can account for TM of all our data. The model also indicates that the heat of fusion between crystal and amorphous phases grows linearly with , providing a route to maximize the relative crystal stability.

Theoretical Description of a DNA-Linked Nanoparticle Self-Assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA-tethered nanoparticles.

Using DNA to Link Gold Nanoparticles, Polymers and Molecules: a Theoretical Perspective.

This Perspective describes theoretical studies aimed at understanding the structural and thermal properties of materials in which DNA is used to link gold nanoparticles, or polymers or organic molecules. Particularly in the case of gold nanoparticles, the materials derived from this structural motif have proven to be important for biological sensing and other applications, however additional applications may arise as a result of recent advances in the preparation of crystalline materials based on DNA-linked particles. From a theory perspective these are challenging materials to describe due to the large number of atoms, and the polyelectrolyte character of DNA, however there has been important progress recently using all-atom and coarse-grained molecular dynamics, and with analytical theory. Among topics that we discuss are the structure and density of DNA when attached to gold particles, and the size and melting properties of DNA-linked nanoparticles in different environments.

Nanogap Array Fabrication Using Doubly Clamped Freestanding Silicon Nanowires and Angle Evaporations

We present a simple semiconductor process to fabricate nanogap arrays for application in molecular electronics and nano-bio electronics using a combination of freestanding silicon nanowires and angle evaporation. The gap distance is modulated using the height of the silicon dioxide, the width of the Si nanowires, and the evaporation angle. In addition, we fabricate and apply the nanogap arrays in single-electron transistors using DNA-linked Au nanoparticles for the detection of DNA hybridization.

Robust Detection of Plasmon Coupling in Core-Satellite Nanoassemblies Linked by DNA

Plasmon coupling is investigated in aqueous phase nanoassemblies composed of 13 nm gold “satellite” particles tethered by duplex DNA to a 50 nm gold “core” particle. The structures are comprised of a large core nanoparticle and small satellite particles such that formation of core-satellite assemblies can be detected through measurement of scattering spectra, even when an excess of unbound satellite particles are present. Rayleigh scattering spectra collected from bulk samples reveal enhanced scattering and/or red shifting of the plasmon resonance upon formation of assemblies, with the extent and character of the response determined by the number of base pairs in the duplex DNA tether. Distance-dependence of the coupling is investigated also through simulation using structural models based upon observed satellite coverage and prior measurements of interparticle separation in DNA-linked nanoparticle materials. Spectral differences between scattering from linked and unlinked assemblies are found to differ s...

Silver Nanoparticle−Oligonucleotide Conjugates Based on DNA with Triple Cyclic Disulfide Moieties

We report a new strategy for preparing silver nanoparticle-oligonucleotide conjugates that are based upon DNA with cyclic disulfide-anchoring groups. These particles are extremely stable and can withstand NaCl concentrations up to 1.0 M. When silver nanoparticles functionalized with complementary sequences are combined, they assemble to form DNA-linked nanoparticle networks. This assembly process is reversible with heating and is associated with a red shifting of the particle surface plasmon resonance and a concomitant color change from yellow to pale red. Analogous to the oligonucleotide-functionalized gold nanoparticles, these particles also exhibit highly cooperative binding properties with extremely sharp melting transitions. This work is an important step toward using silver nanoparticle-oligonucleotide conjugates for a variety of purposes, including molecular diagnostic labels, synthons in programmable materials synthesis approaches, and functional components for nanoelectronic and plasmonic devices.

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.

Recognition of DNA Sequence and Chain Length by Using DNA-Linked Nanoparticle

Recognition of DNA Sequence and Chain Length by Using DNA-Linked Nanoparticle