DNA-based Molecular Nanotechnology

Understanding the electronic properties of single- and double-stranded DNA

Understanding the charge transfer mechanism through deoxyribonucleic acid (DNA) molecules remains a challenge for numerous theoretical and experimental studies in order to be utilized in nanoelectronic devices. Various methods have attempted to investigate the conductivity of double-stranded (ds-) and single-stranded DNA (ssDNA) molecules. However, different electronic behaviors of these molecules are not clearly understood due to the complexity and lack of accuracy of the methods applied in these studies. In this work however, we demonstrated an electronic method to study the electrical behavior of synthetic ssDNA or dsDNA integrated within printed circuit board (PCB)-based metal (gold)-semiconductor (DNA) Schottky junctions. The results obtained in this work are in agreement with other studies reporting dsDNA as having higher conductivity than ssDNA as observed by us in the range of 4-6μA for the former and 2-3μA for the latter at an applied bias of 3V. Selected solid-state parameters such as turn-on voltage, series resistance, shunt resistance, ideality factor, and saturation current were also calculated for the specifically designed ss- and dsDNA sequences using the thermionic emission model. The results also showed that the highest conductance was observed for dsDNA with guanine and cytosine base pairs, while the lowest conductance was for ssDNA with adenine and thymine bases. We believe the results of this preliminary work involving the gold-DNA Schottky junction may allow the interrogation of DNA charge transfer mechanisms and contribute to better understanding its elusive electronic properties.

Phase Transitions in DNA/Surfactant Adsorption Layers

The adsorption layers of complexes between DNA and oppositely charged surfactants dodecyltrimethylammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB) at the solution/air interface were studied with surface tensiometry, dilational surface rheology, atomic force microscopy, Brewster angle microscopy, infrared absorption-reflection spectroscopy, and ellipsometry. Measurements of the kinetic dependencies of the surface properties gave a possibility to discover the time intervals corresponding to the coexistence of two-dimensional phases. One can assume that the observed phase transition is of the first order, unlike the formation of microaggregates in the adsorption layers of mixed solutions of synthetic polyelectrolytes and surfactants. The multitechniques approach together with the calculations of the adsorption kinetics allowed the elucidation of the structure of coexisting surface phases and the distinguishing of four main steps of adsorption layer formation at the surface of DNA/surfactant solutions.

Gold nanoparticles in biomedical applications: recent advances and perspectives

Gold nanoparticles (GNPs) with controlled geometrical, optical, and surface chemical properties are the subject of intensive studies and applications in biology and medicine. To date, the ever increasing diversity of published examples has included genomics and biosensorics, immunoassays and clinical chemistry, photothermolysis of cancer cells and tumors, targeted delivery of drugs and antigens, and optical bioimaging of cells and tissues with state-of-the-art nanophotonic detection systems. This critical review is focused on the application of GNP conjugates to biomedical diagnostics and analytics, photothermal and photodynamic therapies, and delivery of target molecules. Distinct from other published reviews, we present a summary of the immunological properties of GNPs. For each of the above topics, the basic principles, recent advances, and current challenges are discussed (508 references).

Molecular plasmonics: light meets molecules at the nanoscale

Certain metal nanoparticles exhibit the effect of localized surface plasmon resonance when interacting with light, based on collective oscillations of their conduction electrons. The interaction of this effect with molecules is of great interest for a variety of research disciplines, both in optics and in the life sciences. This paper attempts to describe and structure this emerging field of molecular plasmonics, situated between the molecular world and plasmonic effects in metal nanostructures, and demonstrates the potential of these developments for a variety of applications.

Magnetic particle-based hybrid platforms for bioanalytical sensors

Biomagnetic nano and microparticles platforms have attracted considerable interest in the field of biological sensors due to their interesting physico-chemical properties, high specific surface area, good mechanical stability and opportunities for generating magneto-switchable devices. This review discusses recent advances in the development and characterization of active biomagnetic nanoassemblies, their interaction with biological molecules and their use in bioanalytical sensors.

Optically controlled thermal management on the nanometer length scale

The manipulation of polymers and biological molecules or the control of chemical reactions on a nanometer scale by means of laser pulses shows great promise for applications in modern nanotechnology, biotechnology, molecular medicine or chemistry. A controllable, parallel, highly efficient and very local heat conversion of the incident laser light into metal nanoparticles without ablation or fragmentation provides the means for a tool like a 'nanoreactor', a 'nanowelder', a 'nanocrystallizer' or a 'nanodesorber'. In this paper we explain theoretically and show experimentally the interaction of laser radiation with gold nanoparticles on a polymethylmethacrylate (PMMA) layer (one-photon excitation) by means of different laser pulse lengths, wavelengths and pulse repetition rates. To the best of our knowledge this is the first report showing the possibility of highly local (in a 40 nm range) regulated heat insertion into the nanoparticle and its surroundings without ablation of the gold nanoparticles. In an earlier paper we showed that near-infrared femtosecond irradiation can cut labeled DNA sequences in metaphase chromosomes below the diffraction-limited spot size. Now, we use gold as well as silver-enhanced gold nanoparticles on DNA (also within chromosomes) as energy coupling objects for femtosecond laser irradiation with single-and two-photon excitation. We show the results of highly localized destruction effects on DNA that occur only nearby the nanoparticles.

Enzyme-directed positioning of nanoparticles on large DNA templates

A method to position nanoparticles onto DNA with high resolution using an enzyme-based approach is described. This provides a convenient route to assemble multiple nanoparticles (e.g., Au and CdSe) to specific positions with a high level of control and expandability to more complex assemblies. Atomic force microscopy is used to analyze the nanostructures, which have potential interest for biosensor, optical waveguide, molecular electronics, and energy transfer studies.

A parallel approach for subwavelength molecular surgery using gene-specific positioned metal nanoparticles as laser light antennas

An optical technique for the parallel manipulation of nanoscale structures with molecular resolution is presented. Bioconjugated metal nanoparticles are thereby positioned at the location of interest, such as, e.g., certain DNA sequences along metaphase chromosomes, prior to pulsed laser light irradiation of the whole sample. The nanoparticles are designed to absorb the introduced energy highly efficiently, in that way acting as nanoantenna. As result of the interaction, structural changes of the sample with subwavelength dimensions and nanoscale precision are observed at the location of the particles. The process leading to the nanolocalized destruction is caused by particle ablation as well as thermal damage of the surrounding material.

Introduction: array technology - an overview

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.

DNA-templated nickel nanostructures and protein assemblies

We report a straightforward method for the fabrication of DNA-templated nickel nanostructures on surfaces. These nickel nanomaterials have potential to be applied as nanowires, as templated catalyst lines, as nanoscale magnetic domains, or in directed protein localization. Indeed, we show here that histidine-tagged phosducin-like protein (His-PhLP) binds with high selectivity to both Ni2+-treated surface DNA and DNA-templated nickel metal to create linear protein assemblies on surfaces. The association of His-PhLP with DNA-templated nickel ions or metal is reversible under appropriate rinsing conditions. Nanoscale DNA-templated protein assemblies might be useful in the construction of high-density protein lines for proteomic analysis, for example. Importantly, these nanofabrication procedures are not limited to linear DNA and can be applied readily to other self-assembled DNA topologies.

Single-Molecule Studies on DNA and RNA

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.

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.

Large-scale purification of oligonucleotides by extraction and precipitation with butanole

Today the synthesis of oligonucleotides is a well-established process. Using automatic synthesizers even kilogram quantities can be produced in a few hours. However, the purification of the final product is still time-consuming and needs a complex apparatus. In this article, a simple and fast purification method for the large-scale syntheses of oligonucleotides is described. According to the method of Sawadago and van Dyke ([1991] Nucleic Acids Res 19:674-675) for small-scale oligonucleotide purification, oligonucleotides in mumol to mmol amounts were purified by liquid-liquid extraction using butanole as the extraction liquid. Choosing appropriate ratios of extraction liquid to oligonucleotide solution, simultaneous purification and precipitation could be achieved. It was found that the yield of the purified oligonucleotide was mainly affected by the temperature. Yield decreased with increasing temperature. The use of this improved extraction procedure allows the purification of gram to kilogram quantities of oligonucleotides in less than a day with simple equipment and high yield.

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.

DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires

DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of approximately 25 nm and have been observed with lengths up to 20 microm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods.