DNA-BASED MOLECULAR CONSTRUCTION: International Workshop on DNA-Based Molecular Construction
640(2002); http://dx.doi.org/10.1063/1.1520073View Description Hide Description
A method for the automated solid‐phase synthesis of DNA on a semiconductor chip with the potential for photolithography to fabricate hybrid electronic‐DNA devices was developed. The on‐chip oligonucleotide synthetic quality was comparable to standard CPG supports as confirmed by HPLC and gel electrophoresis. Enzymatic manipulation of the immobilised ssDNA was possible by radiolabelling with T4 polynucleotide kinase. Spatial control, afforded by photolithography, was visualised by phosphorimaging radiolabelled dsDNA. The charge transfer properties of DNA were investigated by the association of Ru[(NH3)6]3+ with the phosphate backbone and by intercalation with redox active methylene blue. Additionally ferrocene modified nucleosides were incorporated into oligonucleotides to act as electronic mediators for charge transfer. Initial investigations into the effect of the redox group on the nucleobase indicated their potential for use as bioelectronic building blocks for incorporation into silicon based molecular systems.
640(2002); http://dx.doi.org/10.1063/1.1520074View Description Hide Description
Nanoparticle‐labeling was recently introduced for probing immobilized DNA by scanning force microscopy or optical detection. The optical detection has the potential of high parallelization in combination with miniaturization, thereby enabling a high sample throughput. However, a quantification of the optical signal and a correlation of this signal with the surface density of bound nanoparticles are needed. We will demonstrate the application of the silver enhancement procedure for a signal amplification to extend the dynamic range of the method. The specificity of the enhanced nanoparticle‐labeling will be shown, and the influence of the surface density of immobilized molecules on the signal is studied. The results confirm that the proposed detection scheme is suitable for an application in molecular nanotechnology for the characterization of DNA‐modified surfaces.
640(2002); http://dx.doi.org/10.1063/1.1520075View Description Hide Description
The availability of a number of methods to controllably adsorb DNA on solid surfaces is useful to researchers working in different fields, such as structural biology, biophysical chemistry, diagnostics, sensorics, and nanotechnology. In this paper, we review some of the methods that have been devised in the last years to solve this problem. Thanks to the Scanning Force Microscope, we have recently been able to study the dynamics of DNA molecules adsorbed on mica. From the statistical analysis of the shapes of properly designed DNA molecules, we have also discovered an unexpected base‐sequence specificity in the adsorption of intrinsically curved DNA molecules on mica.
640(2002); http://dx.doi.org/10.1063/1.1520076View Description Hide Description
A method for molecular manipulation of DNA has been developed. The method uses microfabricated electrode system to create high‐intensity high‐frequency field in DNA solution, by which each DNA molecule is stretched to a straight shape, aligned with one end immobilized onto the electrode edge. Once stretched and immobilized, one has an access to, and can apply operations to any desired location on the strand. It has been shown that aimed portion of the stretched DNA can be dissected and picked up. Immobilization in some case cause steric hindrance and hamper the interaction of enzymes with the DNA. To prevent such hindrance, a microdevice has been developed which enables the anchoring of stretched DNA with its molecular termini, leaving middle part free. Using the device, enzymatic molecular surgery of DNA is demonstrated by pressing a DNA‐cutting‐enzyme coated microparticle against the stretched DNA. Real‐time observation of DNA enzymes moving along DNA strand is also made using the device.
640(2002); http://dx.doi.org/10.1063/1.1520077View Description Hide Description
To facilitate the directed positioning of molecules on a surface the use of nucleic acids is proposed. For nanostructuring with DNA the deposition of each molecule has to be directed. Two steps are necessary: First, the DNA has to be stretched and second the lengthy molecule has to be fixed at each end in a specific manner. For stretching DNA of several micrometer length AC fields are applied, for anchoring the ends in a specific manner the oligo‐tag method is applied using different immobilization techniques.
640(2002); http://dx.doi.org/10.1063/1.1520078View Description Hide Description
DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with π‐electron bases for electron transport, the address at 0.4 nm intervals, and the self‐assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide‐gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo‐doping. It has found that Poly(dG)⋅Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.
640(2002); http://dx.doi.org/10.1063/1.1520079View Description Hide Description
The unique potential of molecular nanotechnology is based on the fabrication of materials and devices starting from molecular units. Comparable to and based on the synthetic approach in supramolecular chemistry or molecular biology, an extended toolbox of molecular units as well as tailored reactions is provided by these fields. On the other hand, the progress in synthesis of molecular structures is not directly transferable into technical applications, what is mainly due to a missing integration of the synthetic products into technological interfaces and environments. Self‐organization as used by nature to create complex organisms appears to be a solution to this dilemma. We propose a scheme for the realization of a single electron‐tunneling (SET) device based on this principle, and demonstrate the realization of various steps toward this aim, especially a technique for immobilizing exactly one DNA molecule in a microelectrode setup based on self‐assembly.
640(2002); http://dx.doi.org/10.1063/1.1520080View Description Hide Description
Depositing silver, palladium or a silver‐gold metal mixture onto surface immobilized DNA has made conductive nanowires in the 50–100 nm diameter range, a significant improvement over conventional optical lithography. Platinum has also been deposited onto DNA to form nanoscale metallic structure arrangements on surfaces. We have developed a method of elongating DNA for facile analysis on silicon or mica substrates. Silver and copper metal have both been deposited on these aligned surface DNA fragments to make nanorod structures that are ∼2 nm in diameter, more than an order of magnitude smaller than earlier work.
640(2002); http://dx.doi.org/10.1063/1.1520081View Description Hide Description
G‐wires are DNA superstructures based on the intermolecular interactions of four Guanine bases. They allow the fabrication of structures reaching the micrometer scale using only short DNA oligonucleotides, what makes them potentially interesting for molecular nanotechnology. We investigated the assembly of G‐wires by SFM, using different sequences described in the literature. The assembled structures were adsorbed on mica and imaged by SFM. The influence of time and temperature of the growth was investigated, and the topology of the assemblies was studied.
640(2002); http://dx.doi.org/10.1063/1.1520082View Description Hide Description
The self‐assembly process of G‐wire DNA was investigated through scanning probe microscopy. Growth kinetics studies indicated the self‐assembly process is diffusion limited and provides Poisson‐like distribution of G‐wire lengths upon reaching equilibrium. This evidence suggests that self‐assembly is driven by thermodynamic processes. The average lengths of these molecules are around 100 nm long after 24 hours of growth. However, longer G‐wire DNA molecules (many micrometers) are found both in flexible and crystalline forms. The latter structures are extremely interesting candidates for molecular nanowires.