Site-selective immobilization of gold nanoparticles functionalized with DNA oligomers

Low-cost fabrication technologies for nanostructures: state-of-the-art and potential

In the last decade, some low-cost nanofabrication technologies used in several disciplines of nanotechnology have demonstrated promising results in terms of versatility and scalability for producing innovative nanostructures. While conventional nanofabrication technologies such as photolithography are and will be an important part of nanofabrication, some low-cost nanofabrication technologies have demonstrated outstanding capabilities for large-scale production, providing high throughputs with acceptable resolution and broad versatility. Some of these nanotechnological approaches are reviewed in this article, providing information about the fundamentals, limitations and potential future developments towards nanofabrication processes capable of producing a broad range of nanostructures. Furthermore, in many cases, these low-cost nanofabrication approaches can be combined with traditional nanofabrication technologies. This combination is considered a promising way of generating innovative nanostructures suitable for a broad range of applications such as in opto-electronics, nano-electronics, photonics, sensing, biotechnology or medicine.

A direct detection of Escherichia coli genomic DNA using gold nanoprobes

BACKGROUND

In situation like diagnosis of clinical and forensic samples there exists a need for highly sensitive, rapid and specific DNA detection methods. Though conventional DNA amplification using PCR can provide fast results, it is not widely practised in diagnostic laboratories partially because it requires skilled personnel and expensive equipment. To overcome these limitations nanoparticles have been explored as signalling probes for ultrasensitive DNA detection that can be used in field applications. Among the nanomaterials, gold nanoparticles (AuNPs) have been extensively used mainly because of its optical property and ability to get functionalized with a variety of biomolecules.

RESULTS

We report a protocol for the use of gold nanoparticles functionalized with single stranded oligonucleotide (AuNP- oligo probe) as visual detection probes for rapid and specific detection of Escherichia coli. The AuNP- oligo probe on hybridization with target DNA containing complementary sequences remains red whereas test samples without complementary DNA sequences to the probe turns purple due to acid induced aggregation of AuNP- oligo probes. The color change of the solution is observed visually by naked eye demonstrating direct and rapid detection of the pathogenic Escherichia coli from its genomic DNA without the need for PCR amplification. The limit of detection was ~54 ng for unamplified genomic DNA. The method requires less than 30 minutes to complete after genomic DNA extraction. However, by using unamplified enzymatic digested genomic DNA, the detection limit of 11.4 ng was attained. Results of UV-Vis spectroscopic measurement and AFM imaging further support the hypothesis of aggregation based visual discrimination. To elucidate its utility in medical diagnostic, the assay was validated on clinical strains of pathogenic Escherichia coli obtained from local hospitals and spiked urine samples. It was found to be 100% sensitive and proves to be highly specific without any cross reaction with non-Escherichia coli strains.

CONCLUSION

This work gives entry into a new class of DNA/gold nanoparticles hybrid materials which might have optical property that can be controlled for application in diagnostics. We note that it should be possible to extend this strategy easily for developing new types of DNA biosensor for point of care detection. The salient feature of this approach includes low-cost, robust reagents and simple colorimetric detection of pathogen.

Use of oligonucleotides carrying photolabile groups for the control of the deposition of nanoparticles in surfaces and nanoparticle association

An oligodeoxynucleotide hairpin containing a photolabile 2-nitrobenzyl group in the loop and terminated with a thiol function was prepared. The photocleavage of such a hairpin on gold yields a surface activated with a single stranded oligonucleotide which can be utilised to direct the assembly of nanoparticles conjugated with a complementary strand. Analysis of photocleaved surfaces gives nanoparticle coverage one order of magnitude higher than nonphotocleaved surfaces. This illustrates the ability of photocleavable hairpins to direct the assembly of nanomaterials on conducting materials. The conjugation of the photocleavable hairpin to a gold nanoparticle allows the observation of intermolecular interactions between hairpins linked in different nanoparticles, by comparing the thermal dissociations of a hairpin-nanoparticle conjugates at 260 nm and 520 nm. We have also shown that it is possible to permanently alter the physiochemical properties of DNA-nanoparticles by the introduction of a photocleavable group. Indeed for the first time it has been shown that by exposure to UV light the disassembly of nanoparticle aggregates can be induced.

ssDNA binding reveals the atomic structure of graphene

We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the π-π stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the π-π stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures.

DNA-mediated site-specific deposition of gold nanoparticles on silicon wafers

We report a method for the site-specific deposition of gold nanoparticles, as programmed by DNA sequences immobilized on the surface of silicon oxide-coated silicon wafers. After optimization of surface chemistries, selectivities of between 8:1 and 118:1 were achieved for the DNA-based sorting of populations of gold nanoparticle of 15 nm and 60 nm diameter from a common suspension via oligonucleotide duplex formation.

On the application potential of gold nanoparticles in nanoelectronics and biomedicine

Ligand-stabilized gold nanoparticles (AuNPs) are of high interest to research dedicated to future technologies such as nanoelectronics or biomedical applications. This research interest arises from the unique size-dependent properties such as surface plasmon resonance or Coulomb charging effects. It is shown here how the unique properties of individual AuNPs and AuNP assemblies can be used to create new functional materials for applications in a technical or biological environment. While the term technical environment focuses on the potential use of AuNPs as subunits in nanoelectronic devices, the term biological environment addresses issues of toxicity and novel concepts of controlling biomolecular reactions on the surface of AuNPs.

Peptide-coated silver nanoparticles: synthesis, surface chemistry, and pH-triggered, reversible assembly into particle assemblies

Simple tripeptides are scaffolds for the synthesis and further assembly of peptide/silver nanoparticle composites. Herein, we further explore peptide-controlled silver nanoparticle assembly processes. Silver nanoparticles with a pH-responsive peptide coating have been synthesized by using a one-step precipitation/coating route. The nature of the peptide/silver interaction and the effect of the peptide on the formation of the silver particles have been studied via UV/Vis, X-ray photoelectron, and surface-enhanced Raman spectroscopies as well as through electron microscopy, small angle X-ray scattering and powder X-ray diffraction with Rietveld refinement. The particles reversibly form aggregates of different sizes in aqueous solution. The state of aggregation can be controlled by the solution pH value. At low pH values, individual particles are present. At neutral pH values, small clusters form and at high pH values, large precipitates are observed.

"Chemical transformers" from nanoparticle ensembles operated with logic

The pH-responsive nanoparticles were coupled with information-processing enzyme-based systems to yield "smart" signal-responsive hybrid systems with built-in Boolean logic. The enzyme systems performed AND/OR logic operations, transducing biochemical input signals into reversible structural changes (signal-directed self-assembly) of the nanoparticle assemblies, thus resulting in the processing and amplification of the biochemical signals. The hybrid system mimics biological systems in effective processing of complex biochemical information, resulting in reversible changes of the self-assembled structures of the nanoparticles. The bioinspired approach to the nanostructured morphing materials could be used in future self-assembled molecular robotic systems.

Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters

The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-H...Au hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.

Colloidal lithography and current fabrication techniques producing in-plane nanotopography for biological applications

Substrate topography plays a vital role in cell and tissue structure and function in situ, where nanometric features, for example, the detail on single collagen fibrils, influence cell behaviour and resultant tissue formation. In vitro investigations demonstrate that nanotopography can be used to control cell reactions to a material surface, indicating its potential application in tissue engineering and implant fabrication. Developments in the catalyst, optical, medical and electronics industries have resulted in the production of nanopatterned surfaces using a variety of methods. The general protocols for nanomanufacturing require high resolution and low cost for fabricating devices. With respect to biological investigations, nanotopographies should occur across a large surface area (ensuring repeatability of experiments and patterning of implant surfaces), be reproducible (allowing for consistency in experiments), and preferably, accessible (limiting the requirement for specialist equipment). Colloidal lithography techniques fit these criteria, where nanoparticles can be utilized in combination with a functionalized substrate to produce in-plane nanotopographies. Subsequent lithographic processing of colloidal substrates utilizing, for example, reactive ion etching allows the production of modified colloidal-derived nanotopographies. In addition to two-dimensional in-plane nanofabrication, functionalized structures can be dip coated in colloidal sols, imparting nanotopographical cues to cells within a three-dimensional environment.

Light-induced in situ patterning of DNA-tagged biomolecules and nanoparticles

We present an in situ method for the selective manipulation of DNA-tagged nano-objects such as vesicles or gold colloids in aqueous solution, at neutral pH. The method makes use of the photosensitizer concept found in photodynamic therapy. Here, single-stranded DNA is immobilized onto a surface via the biotin/streptavidin linkage. If the streptavidin is fluorescently labeled, reactive species will be created during laser-induced photobleaching of the label. These reactive species can then completely or partly suppress the DNA hybridization and cause the removal of the streptavidin. The technique thereby enables a dynamic on-off control over surface density of immobilized DNA-tagged nano-objects. Furthermore, combining this in situ manipulation of DNA with prepatterning of single-stranded DNA in the micro and later in the nano range provides a means for the dynamic patterning required for applications in biosensing and nanotechnology.

Preparation, structural, and optical features of two-dimensional cross-linked DNA/gold-nanoparticle conjugates

The formation and the optical features of two-dimensional aggregates formed by DNA-directed immobilization and cross-linking of bifunctional DNA-gold nanoparticles at flat gold substrates are analyzed. The samples are structurally characterized by atomic force microscopy to evaluate the particle size, the particle densities, and the degree of aggregation. The optical characteristics determined by UV/visible measurements are correlated with the structural features observed.

Chip devices for miniaturized biotechnology

Chip devices were introduced in chemistry and molecular biology to improve the read-out of information from molecular systems by efficient analytical procedures and to organize automated experiments. Biochips and chip reactor systems are of interest for cellular processes, too, and can be regarded as components in interfaces for the information exchange between living nature and digital electronic systems. In this minireview, different types of chip reactors for biotechnological applications like nanotiterplates, chip thermocyclers and devices for segmented flow operations are discussed. Finally, an outlook is given on the application of chip reactor systems, which are promising tools for automated experiments with highly parallelized screening procedures, for artificial microcompartmentation, cell analogue systems, micro-ecological studies, investigations on modulated morphogenesis, and for a bioanalogue molecular nanotechnology.

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Charging process and Coulomb-force-directed printing of nanoparticles with sub-100-nm lateral resolution

This article reports on a new charging process and Coulomb-force-directed assembly of nanoparticles onto charged surface areas with sub-100-nm resolution. The charging is accomplished using a flexible nanostructured thin silicon electrode. Electrical nanocontacts have been created as small as 50 nm by placing the nanostructured electrode onto an electret surface. The nanocontacts have been used to inject charge into 50 nm sized areas. Nanoparticles were assembled onto the charge patterns, and a lateral resolution of 60 nm has been observed for the first time. A comparison of the nanoparticle patterns with the surface potential distribution recorded by Kelvin probe force microscopy (KFM) revealed a mismatch in the lateral resolution. One possible explanation is that nanoparticles may visualize charge patterns at a sub-60-nm length scale that is not well resolved using KFM.

Photocatalytic polypyrrole-TiO2-nanoparticles composite thin film generated at the air-water interface

Herein, we report a new method of generation of TiO(2) nanoparticles (NPs) incorporated thin films of polypyrrole (PPy) at the air-water interface. Aqueous TiO(2) NPs when treated with H(2)O(2) and left in a chamber of pyrrole vapor resulted in the formation of a film at the interface, in addition to bulk precipitate. Spectroscopic, X-ray diffraction, and electron microscopic measurements establish the formation of a thin film of PPy with the incorporation of TiO(2) NPs. The TiO(2)-containing PPy films when transferred onto glass substrates were able to photo catalyze the decomposition of aqueous organic dyes: methyl orange and methylene blue. Further, these films could also photo catalyze the oxidation of iodide to triiodide ions in aqueous potassium iodide solution. We find that the PPy-TiO(2) composite films catalyze the reactions in the presence of light more efficiently than a suspension of TiO(2) NPs.

Alternative nucleic acid analogues for programmable assembly: hybridization of LNA to PNA

Complementary locked nucleic acid (LNA) and peptide nucleic acid (PNA) hexamers bind to each other with significantly higher affinity than each binds to DNA, and with far greater affinity than DNA binds to complementary DNA. The hybridization is highly specific with a single mismatch causing decreases in T(m) values ranging from 12 (G/T) to 30 degrees C (A/A). Importantly, the hybridization of an LNA oligomer to a PNA oligomer is unaffected by the ionic strength of the buffer. These properties make the LNA/PNA pair an attractive candidate as a replacement for DNA in programmable assembly.

On the development of colloidal nanoparticles towards multifunctional structures and their possible use for biological applications

In this Review, we describe the synthesis of high-quality colloidal nanoparticles in organic solvents, the mechanisms by which they can be transferred into aqueous solution, and some of their applications in biology. In particular, we will place emphasis on the creation of multifunctional nanoparticles or nanoparticle assemblies.

Effect of macromolecular crowding on DNA:Au nanoparticle bioconjugate assembly

DNA:Au nanosphere bioconjugates have applications in biosensing and in the bottom-up assembly of materials. These bioconjugates can be selectively assembled into three-dimensional aggregates upon addition of complementary DNA oligonucleotides and can be dissociated by heating above a melting transition temperature at which the DNA duplexes are denatured. Herein we describe the impact of polymeric solutes on the thermal denaturation behavior of DNA:Au nanoparticle bioconjugate assemblies. Polymeric solutes can dramatically impact biochemical reactions via macromolecular crowding. Poly(ethylene glycol)s (PEGs) and dextrans of varying molecular weights were used as crowding reagents. While both PEG and dextran increased the stability of DNA:Au aggregates, melting transition temperatures in the presence of PEG were impacted more significantly. Polymer molecular weight was less important than polymer chemistry and weight percent in solution. For a high (15%) weight percent of PEG, aggregation was observed even in the absence of complementary oligonucleotides. These results underscore the importance of polymer chemistry in addition to physical volume exclusion in macromolecular crowding and point to the importance of understanding these effects when designing biorecognition-based nanoparticle assembly schemes in complex matrixes (i.e., any involving polymeric solutes).

Bifunctional DNA–gold nanoparticle conjugates as building blocks for the self-assembly of cross-linked particle layers

The DNA-directed self-assembly of surface-bound layers of gold nanoparticles offers a broad range of applications in biomedical analyses as well as in materials science. We here describe a new concept for the assembly of substrate-bound nanoparticle monolayers which employs bifunctional nanoparticles as building blocks, containing two independently addressable DNA oligomer sequences. One of the sequences was utilized for attaching the particle at the solid support, while the other sequence was used to establish cross-links between adjacently immobilized particles. AFM analyses proved the functionality of inter-particle cross-links leading to enhanced surface coverages and the formation of monolayered supramolecular aggregates attached to the substrate. We anticipate that further refinement of this approach will enable applications, for instance, the assembly of ordered layers useful as transducers in biosensing.

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.

Orthogonal assembly of nanoparticle building blocks on dip-pen nanolithographically generated templates of DNA

Nanoscale construction work with DNA: Dip-pen nanolithography (DPN) is used to generate nanostructures which can be subsequently functionalized with oligonucleotides a' and b' and used to assemble, in an orthogonal manner, gold nanoparticles (a, b in scheme) functionalized with sequences complementary to the DPN-generated structures.

DNA-gold conjugates for the detection of specific molecular interactions

DNA chips are an emerging technology for parallel detection of DNA molecules, with applications ranging from medicine to environmental monitoring. The typical set-up includes fluorescence labeling for detection of binding events on the chip surface. Here another labeling technique based on gold nanoparticles is presented. These labels are much more stable, and their optical signal is less influenced by the environment. The specificity of gold-labeled DNA probes and the ease of detection using optical reflection or transmission is demonstrated. In conclusion, gold-labeling is a promising candidate for more robust and reliable DNA-chip detection.

Semi-synthetic nucleic acid-protein conjugates: applications in life sciences and nanobiotechnology

Semi-synthetic conjugates of nucleic acids and proteins can be generated by either covalent coupling chemistry, or else by non-covalent biomolecular recognition systems, such as receptor-ligands of complementary nucleic acids. These nucleic acid-protein conjugates are versatile molecular tools which can be applied, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of laterally microstructured biochips containing functional biological groups, and the biomimetic 'bottom-up' synthesis of nanostructured supramolecular devices. This review summarizes the current state-of-the-art synthesis and characterization methods of artificial nucleic acid-protein conjugates, as well as applications and perspectives for future developments of such hybrid biomolecular components in life sciences and nanobiotechnology.

Bioorganic applications of semisynthetic DNA-protein conjugates

Semisynthetic DNA-protein conjugates are versatile molecular tools useful, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of highly functionalized laterally microstructured biochips, and the biomimetic "bottom-up" synthesis of nanostructured supramolecular devices. This concept paper summarizes the current state-of-the-art concerning the synthesis, characterization, and applications of such hybrid molecules, and also draws perspectives on future developments.