DNA-BASED NANOSCALE INTEGRATION: International Symposium on DNA-Based Nanoscale Integration
Fabrication of DNA Mediated Devices: Alignment of single DNA and the 1‐D pattern of DNA self‐assembly859(2006); http://dx.doi.org/10.1063/1.2360581View Description Hide Description
In this study, we investigated the DNA anchoring technique on gold substrates and the DNA stretching method by molecular combing. The stretched DNA molecules were visualized by the fluorescent microscope. The stretched DNA was also evidenced by the silver reduction along DNA backbones with hydroquinone in both alkaline and acidic conditions. The scanning electron microscope (SEM) shows that the unstretched DNA molecules result in random silver coils, whereas the stretched DNA molecules give the straight silver wires of more than 10 μm long. The molecular combing technique was successfully demonstrated in bridging single DNA molecule over the gold microelectrodes, which is observed by the fluorescent microscope. The DNA anchoring on the gold surface was enhanced by the aminoethanethiol modification and by oligonucleotide hybridization. The aminoethanethiol modification of the electrode surface was analyzed by a Physical Electronics PHI 7200 ToF‐SIMS Spectrometer and a reflectron ToF analyzer. A more sophisticated DNA 1‐D structure was also achieved by the DNA self‐assembly and visualized by transmission electron microscope (TEM) with the negative staining. These achievements suggest a useful approach of converting biological macromolecules to potential applications in micro electronic industry.
859(2006); http://dx.doi.org/10.1063/1.2360582View Description Hide Description
DNA represents a highly promising molecule for the construction of a wide variety of materials and devices utilizing molecular units. Integration into today’s microsystems technology provides access to these interesting but usually solution‐based (and thereby difficult to control) constructs. A variety of techniques to realize this combination have been developed. Of special interest are techniques that are open for massive parallelization in order to provide sufficient numbers of test structures, but also to allow for a potential scale‐up on the way to future applications. We describe and review here a selection of promising technical developments in this direction, addressing the integration problem.
Rolling Circle Amplification For Spatially Directed Synthesis Of A Solid Phase Anchored Single‐Stranded DNA Molecule859(2006); http://dx.doi.org/10.1063/1.2360583View Description Hide Description
In this article the usefulness of the enzyme phi29 DNA polymerase and the principle of rolling circle amplification (RCA) for creating single‐stranded DNA (ssDNA) nanostructures is described. Currently we are working on the spatial orientation of a growing ssDNA molecule during its RCA‐based synthesis by the application of a hydrodynamic force. Starting at an immobilized primer at single molecule level, the aim is to construct a nanostructure of known location and orientation, providing multiple repeating binding sites that can be addressed via complementary base‐pairing. Proof‐of‐principle experiments demonstrate the potential of the enzymatic reaction. ssDNA molecules of more than 20 μm length were created at an immobilized primer and detected by means of fluorescence microscopy.
859(2006); http://dx.doi.org/10.1063/1.2360584View Description Hide Description
A new approach for the placement of biomolecules at Si surfaces is to utilize dislocation networks formed by direct wafer bonding. They provide the option for the interaction of biomolecules with these charged dislocation networks, resulting in patterned immobilization of the molecules. This would allow a combination of Si electronics with biological applications. Such parallel approaches open novel ways for the study of phenomena like DNA conductivity and the characterization of metalized DNA or DNA‐conjugated nanoparticles.
859(2006); http://dx.doi.org/10.1063/1.2360585View Description Hide Description
We present here a simple method to metallize DNA by Electroless Plating of palladium, a trusty metal for contacting SWNT devices. Indeed, DNA is a promising scaffolding candidate for molecular electronic bottom‐up self‐assembly approaches of SWNT devices. We report in this work the synthesis and characterization of individual Pd nanowires as thin as 30 nm showing ohmic behavior at room temperature.
859(2006); http://dx.doi.org/10.1063/1.2360586View Description Hide Description
Genes of interest can be selectively metallized via the incorporation of modified triphosphates. These triphosphates bear functions that can be further derivatised with aldehyde groups via the use of click chemistry. Treatment of the aldehyde‐labeled gene mixture with the Tollens reagent, followed by a development process results in the selective metallization of the gene of interest in the presence of natural DNA strands.
859(2006); http://dx.doi.org/10.1063/1.2360587View Description Hide Description
Specific metal deposition on metal nanoparticles plays an important role in molecular construction as well as for microscopic visualization and signal enhancement in various bioanalytical methods. To characterize this process we studied surface‐immobilized gold nanoparticle ensembles at single particle level by atomic force microscopy monitoring the very same particle arrangements after each enhancement step. Thereby, enhancement solutions of different composition are studied regarding their enhancement rate as measured by the growing height of the particles at single particle level. Other features of interest were the influence of the diameter of the seed particle on the growth process and the influence of exchange of enhancement solution. For the applied conditions (low nanoparticle surface concentration subjected to fresh enhancement solution 2 min each) we observed a linear growth regime, which was dependent on the particles’ seed diameter and differed considerably in enhancement rate, homogeneity, and specificity among the examined enhancement solutions. We extended these studies to an investigation of enzymatic metal deposition where an enzyme complex (horseradish peroxidase) catalyzes the growth of a metal layer.
859(2006); http://dx.doi.org/10.1063/1.2360588View Description Hide Description
A system has been developed for the quantitative determination of the dielectrophoretic response of DNA in solution. Local concentration of fluorescently labeled DNA has been measured by microscopical observation and subsequent evaluation of the acquired CCD images. The influence of frequency, amplitude and modulation of the applied field onto the dielectrophoretic collection of linearized pBlueScript dsDNA has been investigated between 10 kHz and 20 MHz.
Parallel Assisted Assembly of Multilayer DNA and Protein Nanoparticle Structures Using a CMOS Electronic Array859(2006); http://dx.doi.org/10.1063/1.2360589View Description Hide Description
A CMOS electronic microarray device was used to carry out the rapid parallel assembly of functionalized nanoparticles into multilayer structures. Electronic microarrays produce reconfigurable DC electric fields that allow DNA, proteins as well as charged molecules to be rapidly transported from the bulk solution and addressed to specifically activated sites on the array surface. Such a device was used to carry out the assisted self‐assembly DNA, biotin and streptavidin derivatized fluorescent nanoparticles into multilayer structures. Nanoparticle addressing could be carried out in about 15 seconds, and forty depositions of nanoparticles were completed in less than one hour. The final multilayered 3D nanostructures were verified by scanning electron microscopy.
859(2006); http://dx.doi.org/10.1063/1.2360590View Description Hide Description
The electrical conductivity of G‐wire DNA which is adsorbed to the surface of mica was examined with the assistance of silicon shadow masks. Four point probe masks were fabricated in silicon using photolithographic patterning and dry reactive ion etching. The silicon “stencils” were designed specifically for use in generating shadow deposited, metal contacts on top of G‐wire DNA samples adsorbed to the atomically flat surface of mica. Two types of metal contacts were used in these experiments; electron beam evaporated gold using a high vacuum system and argon sputtered gold using a low vacuum scanning electron microscopy sample coating apparatus. The metal electrode patterning was characterized through atomic force microscopy imaging. The conductivity of the G‐wire DNA samples was analyzed using a high impedance multimeter. The lower limit of resistance of the G‐wire DNA networks was determined to be in excess of 1 GΩ, indicating from these experiments that G‐wire DNA appears to be an insulator.
859(2006); http://dx.doi.org/10.1063/1.2360591View Description Hide Description
We have localized SWNTs on DNA templates across electrodes and measured the electrical properties of DNA‐templated SWNT assemblies. When a DNA‐templated SWNT was deposited on top of and bridging electrodes, the measured conductance was comparable to literature values. In contrast, SWNTs with end‐on contacts to the sides of electrodes had conductances hundreds of times lower than literature values, probably due to gaps between the SWNT ends and the electrodes. This work provides a novel approach for localizing SWNTs across contacts in a controlled manner, and our results may be useful in the fabrication of nanoelectronic devices with SWNTs as active components or electrical interconnects.
859(2006); http://dx.doi.org/10.1063/1.2360592View Description Hide Description
Various DNA‐based structures (single‐, double‐, triple‐stranded and quadruplex‐DNA) were characterized using non‐contact atomic‐force microscopy on two substrates: modified highly‐oriented pyrolitic graphite (HOPG) and mica. Deposition on mica, a conventional substrate used in studies of bio‐molecules, results in strong deformation of all above types of molecules while deposition on modified HOPG affects the morphology of DNA much less compared to mica. This is demonstrated by a larger measured height of the DNA molecules deposited on HOPG, as compared to mica, and an increased flexibility of the molecules, evidenced by a shorter molecular end‐to‐end distance on HOPG. The estimated heights of the triplex and the quadruplex DNA measured on HOPG are similar to the diameter of these molecules in liquid. We thus conclude that modified HOPG is a substrate more suitable than mica for AFM characterization of DNA morphology.